diff --git a/CHANGELOG b/CHANGELOG
index bf7d79fe8f2b54752a8d460224dd9459541fd53a..da700eca24229ad11c6919ec01e5213589252b26 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -5,6 +5,12 @@
 Changelog
 ================================================================================
 
+Release 3.3.1
+--------------------------------------------------------------------------------
+
+* Bugfix release: Updates OpenStructure dependency to 2.5.0 and fixes issues
+  with Singularity container.
+
 Release 3.3.0
 --------------------------------------------------------------------------------
 
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 32e8b9d5a0cd668e86a0be542dd92b6048382f82..fb943dfa45ed62a9f9058e5256b1c44a5229b10a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -25,7 +25,7 @@ include(PROMOD3)
 # versioning info
 set(PROMOD3_VERSION_MAJOR 3)
 set(PROMOD3_VERSION_MINOR 3)
-set(PROMOD3_VERSION_PATCH 0)
+set(PROMOD3_VERSION_PATCH 1)
 set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR})
 set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_STRING}.${PROMOD3_VERSION_PATCH})
 
@@ -103,7 +103,7 @@ if(NOT DISABLE_DOCUMENTATION)
   # this URL should always point to the latest version of OST
   set(OST_DOC_URL "https://www.openstructure.org/docs")
 endif()
-find_package(OPENSTRUCTURE 2.4.0 REQUIRED
+find_package(OPENSTRUCTURE 2.5.0 REQUIRED
              COMPONENTS io mol seq seq_alg mol_alg conop img mol_mm)
 
 if(CMAKE_COMPILER_IS_GNUCXX)
diff --git a/container/Dockerfile b/container/Dockerfile
index 247b5f20d931549e0b4424f51400ee13de7e424d..bab75e94add97ed6b33f6bc0441f7bb996edd59a 100644
--- a/container/Dockerfile
+++ b/container/Dockerfile
@@ -1,9 +1,9 @@
-ARG OPENSTRUCTURE_IMAGE_TAG="2.4.0-jammy"
+ARG OPENSTRUCTURE_IMAGE_TAG="2.5.0-jammy"
 FROM registry.scicore.unibas.ch/schwede/openstructure:${OPENSTRUCTURE_IMAGE_TAG}
 
 # ARGUMENTS
 ###########
-ARG PROMOD_VERSION="3.3.0"
+ARG PROMOD_VERSION="3.3.1"
 ARG SRC_FOLDER="/usr/local/src"
 
 
diff --git a/container/Singularity b/container/Singularity
index d66131adf2d38ebab6d27a323c8094cc5d01cb8f..b7cdd9c18899372ab521e848d9d39ffc3f80b3cb 100644
--- a/container/Singularity
+++ b/container/Singularity
@@ -1,5 +1,5 @@
 BootStrap: docker
-From: registry.scicore.unibas.ch/schwede/promod3:3.3.0-OST2.4.0-jammy
+From: registry.scicore.unibas.ch/schwede/promod3:3.3.1-OST2.5.0-jammy
 %post
 ##############################################################################
 # POST
@@ -13,26 +13,23 @@ ln -sf /bin/bash /bin/sh
 
 # INSTALL SYSTEM DEPS
 #####################
-apt-get update -y && apt-get install -y python3-pip
+apt-get update -y && apt-get install -y ipython3 jupyter python3-pip
+pip3 install ipywidgets==7.6.0
 pip3 install nglview \
-             ipython \
-             jupyter 
+             six
+
+# SET LOCALE
+############
+echo "LC_ALL=en_US.UTF-8" >> /etc/environment
+echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
+echo "LANG=en_US.UTF-8" > /etc/locale.conf
+locale-gen en_US.UTF-8
 
 # SETUP IPYTHON / JUPYTER
 #########################
-export IPYTHONDIR="/usr/local/share/ipython"
-export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
 export JUPYTER_PATH="/usr/local/share/jupyter"
-export JUPYTER_RUNTIME_DIR="/tmp/jupyter_runtime"
-mkdir -p /usr/local/share/ipython
 mkdir -p $JUPYTER_PATH
-mkdir -p $JUPYTER_RUNTIME_DIR
-mkdir -p $JUPYTER_CONFIG_DIR
 mkdir -p $JUPYTER_PATH/kernels/ost-kernel
-chmod a+rw -R /usr/local/share/ipython
-chmod a+rw -R $JUPYTER_PATH
-chmod a+rw -R $JUPYTER_CONFIG_DIR
-chmod a+rw -R $JUPYTER_RUNTIME_DIR
 cat > $JUPYTER_PATH/kernels/ost-kernel/kernel.json <<EOF
 {
   "display_name": "OST",
@@ -42,7 +39,7 @@ cat > $JUPYTER_PATH/kernels/ost-kernel/kernel.json <<EOF
     "-m", "ipykernel",
         "-f", "{connection_file}",
     "--InteractiveShellApp.exec_PYTHONSTARTUP=False",
-    "--InteractiveShellApp.exec_files=['/usr/local/lib64/python3.8/site-packages/ost/ost_startup.py']"
+    "--InteractiveShellApp.exec_files=/usr/local/lib64/python3.10/site-packages/ost/ost_startup.py"
   ],
   "env": {
   }
@@ -59,13 +56,7 @@ export TEMP="/tmp"
 export TEMPDIR="/tmp"
 export TMPDIR="/tmp"
 export TMP="/tmp"
-# As the Singularity mounts $HOME by default Jupyter and Ipython config files
-# are moved to separate directories. Proper environmental variables are also 
-# set
-export IPYTHONDIR="/usr/local/share/ipython"
-export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
 export JUPYTER_PATH="/usr/local/share/jupyter"
-export JUPYTER_RUNTIME_DIR="$TMPDIR/jupyter_runtime"
 
 
 %apprun ChemdictTool
@@ -200,7 +191,7 @@ and goes to CWD. Thus this sould work as expected out of the box.
 # NOTEBOOK ENV
 ##############################################################################
 export DNG_ROOT=$OST_ROOT
-export DNG_INITDIR=${DNG_ROOT}/lib64/python3.8/site-packages/ost
+export DNG_INITDIR=${DNG_ROOT}/lib64/python3.10/site-packages/ost
 
 
 %apprun IPython
@@ -260,9 +251,6 @@ load all necessary OST/ProMod3 components just like in the OST shell. We also en
 the nglview widget to interactively view molecular structures and trajectories.
 For more details on how to use nglview see http://nglviewer.org/nglview/latest/.
 
-As the Singularity mounts $HOME by default Jupyter and Ipython config files
-are moved to separate directories. Proper environmental variables are also set.
-
 To list of all available options:
 
     singularity run --app Notebook <IMAGE> --help
diff --git a/core/tests/test_setcompoundschemlib.py b/core/tests/test_setcompoundschemlib.py
index 1efe735b1ab4c27e8a0d2962907c60707ebae4ed..9e9ec48201a406eb140ccd5f5d6bc64b5a81d1a6 100644
--- a/core/tests/test_setcompoundschemlib.py
+++ b/core/tests/test_setcompoundschemlib.py
@@ -49,9 +49,10 @@ class SetCompoundsChemlibTests(unittest.TestCase):
         self.assertEqual(cmpd.formula, fake_gly[1])
 
     def testCompoundsLibLoadedOnImport(self):
-        # Check that importing promod3 loads the compounds library. First we
-        # test that we do not have a lib before importing, afterwards we import
-        # and check for Glycine. This test reads the systems/ installed lib
+        # Check that importing promod3 loads the compounds library. If we
+        # compiled OpenStructure with a valid compound library, it should
+        # already be loaded (as of OST 2.5.0) but if we import promod3, it
+        # should be there for sure. This test reads the systems/ installed lib
         # which means an external data dependency. Lets assume this is OK: if
         # we do not have a chemical components dictionary, we do not know amino
         # acids, so ProMod3 would not work... We also check for essential
@@ -61,10 +62,6 @@ class SetCompoundsChemlibTests(unittest.TestCase):
         # week, is that things may change and then our compounds list here will
         # have to be updated, too.
 
-        # before importing, we do not want to see a lib
-        clib = conop.GetDefaultLib()
-        self.assertIsNone(clib)
-
         # now there should be one
         import promod3# pylint: disable=unused-variable
         clib = conop.GetDefaultLib()
diff --git a/doc/conf.py.in b/doc/conf.py.in
index c01cff17230e43ad52465d37c2b28baea42714cd..c132f0eb3b03ddbb875e37b840497cacd498e417 100644
--- a/doc/conf.py.in
+++ b/doc/conf.py.in
@@ -286,7 +286,7 @@ rst_epilog = """
 .. |cmake| replace:: CMake
 .. |ost_l| replace:: OpenStructure
 .. |ost_s| replace:: OST
-.. |ost_version| replace:: 2.4.0
+.. |ost_version| replace:: 2.5.0
 .. |python| replace:: Python
 .. |sphinx| replace:: Sphinx
 .. _sphinx: http://sphinx-doc.org/
diff --git a/doc/html/_sources/changelog.rst.txt b/doc/html/_sources/changelog.rst.txt
index bf7d79fe8f2b54752a8d460224dd9459541fd53a..da700eca24229ad11c6919ec01e5213589252b26 100644
--- a/doc/html/_sources/changelog.rst.txt
+++ b/doc/html/_sources/changelog.rst.txt
@@ -5,6 +5,12 @@
 Changelog
 ================================================================================
 
+Release 3.3.1
+--------------------------------------------------------------------------------
+
+* Bugfix release: Updates OpenStructure dependency to 2.5.0 and fixes issues
+  with Singularity container.
+
 Release 3.3.0
 --------------------------------------------------------------------------------
 
diff --git a/doc/html/_sources/modelling/algorithms.rst.txt b/doc/html/_sources/modelling/algorithms.rst.txt
index c9db60f1f7f57dc8ac74e00d8db94b9cb018c4be..5545a9acfd90270e035ef0cbf2c45b6ffe5a1088 100644
--- a/doc/html/_sources/modelling/algorithms.rst.txt
+++ b/doc/html/_sources/modelling/algorithms.rst.txt
@@ -308,7 +308,7 @@ iteration.
 
 .. method:: FindMotifs(query, target_positions, hash_tresh=0.4, \
                        distance_thresh=1.0, refine_thresh=0.7, \
-                       flags=list())
+                       flags=list(), swap_thresh=False)
 
   Performs the detection and refinement stages of the geometric hashing 
   algorithm. 
@@ -322,6 +322,10 @@ iteration.
                         constructor. If you didn't provide anything there,
                         this can be ignored. Only the actual coordinates
                         matter in this case.
+  :param swap_thresh: *hash_thresh* and *refine_thresh* refer to fraction of
+                      covered positions in *query*. When setting this to
+                      True, they refer to the fraction of covered positions
+                      in *target_positions*.
 
   :returns:             All found matches
 
diff --git a/doc/html/_static/documentation_options.js b/doc/html/_static/documentation_options.js
index e42d212690329abb5fb8ac48021c049591f80733..4c289d9b2f01108607b8c0c3e562001137c59bde 100644
--- a/doc/html/_static/documentation_options.js
+++ b/doc/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '3.3.0',
+    VERSION: '3.3.1',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',
diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index e250c0387d6988e10e2be5816abbe0efd587ed46..9e41b3622e4984466e8c6a92a4039a38bc45f734 100644
--- a/doc/html/actions/index.html
+++ b/doc/html/actions/index.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>ProMod3 Actions &#8212; ProMod3 3.3.0 documentation</title>
+    <title>ProMod3 Actions &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Building ProMod3" href="../buildsystem.html" />
@@ -101,7 +102,7 @@ Example:</p>
 </li>
 </ul>
 <p>Structures can be provided in PDB (<code class="docutils literal notranslate"><span class="pre">-p</span></code>) or in any format readable by the
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.3.1)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.4.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is
 chosen by file ending. Recognized File Extensions: <code class="docutils literal notranslate"><span class="pre">.ent</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb</span></code>,
 <code class="docutils literal notranslate"><span class="pre">.ent.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif.gz</span></code>. At least one structure must be
 given and you cannot mix file formats. Multiple structures can be given and each
@@ -183,7 +184,7 @@ detects and models disulfid bonds and reconstructs all sidechains with the
 flexible rotamer model. The result is stored as <code class="file docutils literal notranslate"><span class="pre">out.pdb</span></code>.
 The output filename can be controlled with the <code class="docutils literal notranslate"><span class="pre">-o</span></code> flag.</p>
 <p>A structure can be provided in PDB (<code class="docutils literal notranslate"><span class="pre">-p</span></code>) or in any format readable by the
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.3.1)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.4.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is
 chosen by file ending. Recognized File Extensions: <code class="docutils literal notranslate"><span class="pre">.ent</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb</span></code>,
 <code class="docutils literal notranslate"><span class="pre">.ent.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif.gz</span></code>.</p>
 <p>Several flags control the modelling behaviour:</p>
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index c91acf1bae26aabd3aa6db5cd0a96a241f1178f1..c2fe078e002a4a1b68f57b3e68944fdd4dc8dc46 100644
--- a/doc/html/actions/index_dev.html
+++ b/doc/html/actions/index_dev.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>test_actions - Testing Actions &#8212; ProMod3 3.3.0 documentation</title>
+    <title>test_actions - Testing Actions &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="ProMod3’s Share Of CMake" href="../cmake/index.html" />
@@ -183,7 +184,7 @@ happens if a user throws dirty input data in.</p>
 </div>
 <div class="section" id="making-the-script-executable">
 <h3>Making the Script Executable<a class="headerlink" href="#making-the-script-executable" title="Permalink to this headline">¶</a></h3>
-<p>In ProMod3, unit tests are run via <a class="reference external" href="https://www.OpenStructure.org">OST</a>’s <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/base/testutils/#module-ost.testutils" title="(in OpenStructure v2.3.1)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.testutils</span></code></a> and Python’s
+<p>In ProMod3, unit tests are run via <a class="reference external" href="https://www.OpenStructure.org">OST</a>’s <a class="reference external" href="https://www.openstructure.org/docs/2.4/base/testutils/#module-ost.testutils" title="(in OpenStructure v2.4.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.testutils</span></code></a> and Python’s
 <a class="reference external" href="https://docs.python.org/3.7/library/unittest.html#unittest.TestCase" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">unittest.TestCase</span></code></a>. Those are called when the test module is executed
 as a script:</p>
 <div class="highlight-default notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>13
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index 78cfa9bc845f3fa97dee73903c2fa83f616a231d..d43a812e52dd74d5d9a7d18e3ce91fc7e7342621 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Building ProMod3 &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Building ProMod3 &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="ProMod3 and Containers" href="container/index.html" />
@@ -36,7 +37,7 @@
 <div class="section" id="dependencies">
 <h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>
 <p>ProMod3 is build on top of <a class="reference external" href="https://www.OpenStructure.org">OpenStructure</a> (OST), requiring at least version
-2.4.0. OST must be configured and compiled with <code class="docutils literal notranslate"><span class="pre">ENABLE_MM=1</span></code> to
+2.5.0. OST must be configured and compiled with <code class="docutils literal notranslate"><span class="pre">ENABLE_MM=1</span></code> to
 use <a class="reference external" href="https://github.com/openmm/openmm">OpenMM</a>. To create the build system, <a class="reference external" href="https://cmake.org/">CMake</a> is required. The same
 versions of <a class="reference external" href="https://www.python.org/">Python</a> and <a class="reference external" href="https://www.boost.org/">Boost</a> are needed as used in OST. For <a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a>
 we need at least version 3.3.0. To build the documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> is
@@ -45,7 +46,7 @@ release supporting Python 2.7 is 2.1.0 which also requires OST to be
 compiled with Python 2.7.</p>
 <p>The currently preferred versions are:</p>
 <ul class="simple">
-<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 2.4.0</li>
+<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 2.5.0</li>
 <li><a class="reference external" href="https://github.com/openmm/openmm">OpenMM</a> 7.1.1</li>
 <li><a class="reference external" href="https://cmake.org/">CMake</a> 3.12.1</li>
 <li><a class="reference external" href="https://www.python.org/">Python</a> 3.6.0</li>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 4f246044f6a6a310bcb9755979772f35199e9251..4edb3657140d2706111b7ea2c40b460e91d956b7 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Changelog &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Changelog &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="prev" title="References" href="references.html" />
@@ -32,6 +33,13 @@
             
   <div class="section" id="changelog">
 <h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="release-3-3-1">
+<h2>Release 3.3.1<a class="headerlink" href="#release-3-3-1" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li>Bugfix release: Updates OpenStructure dependency to 2.5.0 and fixes issues
+with Singularity container.</li>
+</ul>
+</div>
 <div class="section" id="release-3-3-0">
 <h2>Release 3.3.0<a class="headerlink" href="#release-3-3-0" title="Permalink to this headline">¶</a></h2>
 <ul class="simple">
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index 403551e94de69196008c9d1a10b20f9fff92efc3..445957fcca41c2b25cdb45f0fdb4292ae24bd4de 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>ProMod3’s Share Of CMake &#8212; ProMod3 3.3.0 documentation</title>
+    <title>ProMod3’s Share Of CMake &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Using Binary Files In ProMod3" href="../portableIO.html" />
diff --git a/doc/html/container/docker.html b/doc/html/container/docker.html
index 70b21e457a6b9ca919f128539fbf7faad29c393a..268489f69c5d92237cc5b76c595700c6f59adf97 100644
--- a/doc/html/container/docker.html
+++ b/doc/html/container/docker.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Docker &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Docker &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Singularity" href="singularity.html" />
@@ -75,7 +76,7 @@ pdbs/struct.pdb
 </div>
 <div class="section" id="the-compound-library">
 <span id="docker-compound-lib"></span><h2>The Compound Library<a class="headerlink" href="#the-compound-library" title="Permalink to this headline">¶</a></h2>
-<p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">CompoundLib</span></code></a> is generated.
+<p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">CompoundLib</span></code></a> is generated.
 Compound libraries contain information on chemical compounds, such as their
 connectivity, chemical class and one-letter-code. The compound library has
 several uses, but the most important one is to provide the connectivy
diff --git a/doc/html/container/index.html b/doc/html/container/index.html
index 11a0a45b2354ae1755686ac1a1a41870a35825a0..f37f181a37a3d1e06f1387433069cae35abd0f8a 100644
--- a/doc/html/container/index.html
+++ b/doc/html/container/index.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>ProMod3 and Containers &#8212; ProMod3 3.3.0 documentation</title>
+    <title>ProMod3 and Containers &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Docker" href="docker.html" />
diff --git a/doc/html/container/singularity.html b/doc/html/container/singularity.html
index 79d7f49b1e7d3062d09d3c7938c42060d6d74c0f..85b7c9b344afbeeade4d2091b41f090f565eb9ff 100644
--- a/doc/html/container/singularity.html
+++ b/doc/html/container/singularity.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Singularity &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Singularity &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="modelling - Protein Modelling" href="../modelling/index.html" />
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 1fdfbf12c0a454f631ecf3941e3ed35e522308d3..ef4e0f873baee4ab285bfd6b81f05b9daab63ee0 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Contributing &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Contributing &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="test_actions - Testing Actions" href="actions/index_dev.html" />
diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html
index 7a551e0371800bbc8d785ddae9b5273b80918942..cfff0da976ba58a7e8130acce8b2e20abd860001 100644
--- a/doc/html/core/geometry.html
+++ b/doc/html/core/geometry.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Geometry functions &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Geometry functions &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Runtime profiling" href="runtime_profiling.html" />
@@ -45,14 +46,14 @@
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>rule</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Gromacs rule</li>
 <li><strong>number</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Desired number of positions (max. 3)</li>
-<li><strong>anchors</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</li>
+<li><strong>anchors</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</li>
 </ul>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Constructed <em>number</em> positions.</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -68,16 +69,16 @@
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
 </ul>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Positions of O and OXT atoms.</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -94,9 +95,9 @@ dihedral (A-B-C-D).</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom A</li>
-<li><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom B</li>
-<li><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom C</li>
+<li><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom A</li>
+<li><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom B</li>
+<li><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom C</li>
 <li><strong>bond_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Bond length (C-D)</li>
 <li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (B-C-D)</li>
 <li><strong>dihedral</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Dihedral (A-B-C-D)</li>
@@ -106,7 +107,7 @@ dihedral (A-B-C-D).</p>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of atom D</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -123,16 +124,16 @@ C-alpha and C atoms.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
 </ul>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of C-beta atom</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -149,8 +150,8 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
-<li><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</li>
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
+<li><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</li>
 <li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</li>
 </ul>
 </td>
@@ -158,7 +159,7 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Transformation matrix</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat4</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat4</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -175,7 +176,7 @@ going through the origin.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
 <li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</li>
 </ul>
 </td>
@@ -183,7 +184,7 @@ going through the origin.</p>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Rotation matrix</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat3</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -200,7 +201,7 @@ going through the origin.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res</em> does not contain N, CA and C
 atoms.</td>
@@ -219,7 +220,7 @@ atoms.</td>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></td>
 </tr>
 </tbody>
 </table>
diff --git a/doc/html/core/graph_minimizer.html b/doc/html/core/graph_minimizer.html
index 6c1b852d7a1cc9d8fcfd2d69506801b6125e8e84..0a28f4c28aedb0d7d79df5bc78a8b315c5fcc168 100644
--- a/doc/html/core/graph_minimizer.html
+++ b/doc/html/core/graph_minimizer.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Graph Minimizer &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Graph Minimizer &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="SetCompoundsChemlib()" href="setcompoundschemlib.html" />
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index 02ce0b8a743df0d8fe0254150ab922cb55ddc4f1..3a603ac3d8a353319259d261e1cfe327438cb97d 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>helper - Shared Functionality For the Everything &#8212; ProMod3 3.3.0 documentation</title>
+    <title>helper - Shared Functionality For the Everything &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Geometry functions" href="geometry.html" />
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 0a8d27bc7bf0adf0a92aa6f9d71e444b145f25f7..237aa85f2e4a108fab43cf4a5fac8e3ca256ecab 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>core - ProMod3 Core Functionality &#8212; ProMod3 3.3.0 documentation</title>
+    <title>core - ProMod3 Core Functionality &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index 7547ac6444e2cf93673a1a526152480460c6fba9..1f7549b4cafa8492cbf1dd213059ef47e7b72cf4 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>pm3argparse - Parsing Command Lines &#8212; ProMod3 3.3.0 documentation</title>
+    <title>pm3argparse - Parsing Command Lines &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="helper - Shared Functionality For the Everything" href="helper.html" />
@@ -255,7 +256,7 @@ target sequences</li>
 </ul>
 <p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>:</p>
 <ul class="simple">
-<li><code class="xref py py-attr docutils literal notranslate"><span class="pre">profiles</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>, 
+<li><code class="xref py py-attr docutils literal notranslate"><span class="pre">profiles</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>, 
 ordered to match the target sequences.</li>
 </ul>
 <p>Exit codes related to profile input:</p>
diff --git a/doc/html/core/runtime_profiling.html b/doc/html/core/runtime_profiling.html
index f22d0b777e665bcae8314cddf1a88860ff34e699..627e3ff595077a71b695bd03ba869f19e77ab44a 100644
--- a/doc/html/core/runtime_profiling.html
+++ b/doc/html/core/runtime_profiling.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Runtime profiling &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Runtime profiling &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Graph Minimizer" href="graph_minimizer.html" />
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
index 1af7258a0b77d5cb2c5cdfa467db86337f4f8d31..369e60e56b82d72a224983561042c9553231fbcd 100644
--- a/doc/html/core/setcompoundschemlib.html
+++ b/doc/html/core/setcompoundschemlib.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>SetCompoundsChemlib() &#8212; ProMod3 3.3.0 documentation</title>
+    <title>SetCompoundsChemlib() &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Contributing" href="../user_contributions.html" />
diff --git a/doc/html/dev_setup.html b/doc/html/dev_setup.html
index 5a09c032e65f1f2b17e9d6a8e37176cabad99507..596af58a3aa25aa2c7fe0ccb39dcf8f8430978d6 100644
--- a/doc/html/dev_setup.html
+++ b/doc/html/dev_setup.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>ProMod3 Setup &#8212; ProMod3 3.3.0 documentation</title>
+    <title>ProMod3 Setup &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Contributing" href="contributing.html" />
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 91607a8019c11b7066bc5a07ccef624aa6e6bffe..b838c706184c9dfd262ceacd7bc3fed4d6aeec0f 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Documentation For Developers &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Documentation For Developers &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="ProMod3 Setup" href="dev_setup.html" />
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 5b605538c950d2db69e465bcd77b129727a40f3d..70abe79670087210a7cb258e2cadeebdebc4985b 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -7,7 +7,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Index &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Index &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -15,6 +15,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="#" />
     <link rel="search" title="Search" href="search.html" />
    
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
index e79788840098db2df078376db7ffd2831adbf510..a455d5e897e54d971fdc8d4a5a1d2d812b12c3f6 100644
--- a/doc/html/gettingstarted.html
+++ b/doc/html/gettingstarted.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Getting Started &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Getting Started &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="ProMod3 Actions" href="actions/index.html" />
@@ -87,7 +88,7 @@ is conserved</li>
 <li>Perform loop modelling to close all gaps (see <a class="reference internal" href="loop/index.html#module-promod3.loop" title="promod3.loop: Loop Handling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code></a> module)</li>
 <li>Reconstruct sidechains (using <a class="reference internal" href="sidechain/index.html#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code></a> module)</li>
 <li>Minimize energy of final model using molecular mechanics
-(using <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.3.1)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> from OST)</li>
+(using <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.4.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> from OST)</li>
 </ul>
 <p>Since a good amount of time is spent in OpenMM routines to minimize energy, we
 try to use the fast and multi-threaded “CPU” platform of OpenMM (should be
diff --git a/doc/html/index.html b/doc/html/index.html
index 94f13fec1f198235bb39ef5e18cb34ce67bbef7f..ebc11c4440487811a4ecf3de9ec53fbcb4b67911 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>ProMod3 &#8212; ProMod3 3.3.0 documentation</title>
+    <title>ProMod3 &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Documentation For Users" href="users.html" />
diff --git a/doc/html/license.html b/doc/html/license.html
index 04749084cd6ec9c8e570c832900220e9bf4f9e94..76c882cece963a333ef32cf56f0a5d504d8666a7 100644
--- a/doc/html/license.html
+++ b/doc/html/license.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>License &#8212; ProMod3 3.3.0 documentation</title>
+    <title>License &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="References" href="references.html" />
diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index 5affbe0d808be1eea3e7a49074249b8cca596901..50e1ea3a5beab8f8b74aefbf9e69c7e86fda63ef 100644
--- a/doc/html/loop/all_atom.html
+++ b/doc/html/loop/all_atom.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Handling All Atom Positions &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Handling All Atom Positions &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Generate ost.mol.mm systems" href="mm_system_creation.html" />
@@ -80,8 +81,8 @@ new loop is being added.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
 chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
 </tr>
 </tbody>
@@ -103,7 +104,7 @@ concatenated one after each other (indexing starts at 0)</li>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
 in <em>env_structure</em> are expected to be in the same
 order as the SEQRES items provided in constructor.</td>
 </tr>
@@ -133,7 +134,7 @@ means, that positions in the env. may be reset, newly set or cleared.</p>
 <li><strong>new_env_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnvPositions</span></code></a>) – Structural data to be set as environment.</li>
 <li><strong>new_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Structural data to be set as environment.</li>
 <li><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Backbone data to be set as environment.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</li>
 <li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</li>
 </ul>
 </td>
@@ -210,7 +211,7 @@ a loop to reset later with <a class="reference internal" href="#promod3.loop.All
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -344,7 +345,7 @@ and if found set the corresponding position, otherwise we unset it.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</li>
 </ul>
 </td>
 </tr>
@@ -390,7 +391,7 @@ out of bounds or if residues in the two containers are inconsistent
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Set position at that index.</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</li>
 </ul>
 </td>
 </tr>
@@ -440,7 +441,7 @@ out of bounds or if residues in the two containers are inconsistent
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position at given index.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom position index.</td>
 </tr>
@@ -544,7 +545,7 @@ if <em>atom_name</em> is not one of that residue’s heavy atoms.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of residue at index <em>res_index</em>.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</td>
 </tr>
@@ -659,7 +660,7 @@ out of bounds.</p>
 if required atom positions (CA-C-N-CA) are not set.
 Here, we use CA-C of residue <em>res_index</em> - 1 and N-CA of residue
 <em>res_index</em> (consistent with OST’s
-<code class="xref py py-meth docutils literal notranslate"><span class="pre">GetOmegaTorsion()</span></code>).</p>
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle.GetOmegaTorsion" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetOmegaTorsion()</span></code></a>).</p>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
@@ -823,9 +824,9 @@ atom (N, CA, C, O).</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">All residues packed in a single chain as an OST entity.
-Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</td>
+Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -845,8 +846,8 @@ function efficient, we require the backbone atoms (N, C, CA) to be set.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</li>
-<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</li>
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</li>
 </ul>
 </td>
 </tr>
@@ -939,7 +940,7 @@ integer in the range [0, <em>XXX_NUM_HYDROGENS</em>-1].</p>
 <dt id="promod3.loop.AminoAcidLookup">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AminoAcidLookup</code><a class="headerlink" href="#promod3.loop.AminoAcidLookup" title="Permalink to this definition">¶</a></dt>
 <dd><p>Collection of static methods to lookup properties of amino acid types
-(<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) and
+(<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) and
 hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a>).</p>
 <dl class="staticmethod">
 <dt id="promod3.loop.AminoAcidLookup.GetOLC">
@@ -952,7 +953,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
 </tr>
 </tbody>
 </table>
@@ -974,7 +975,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
 <li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumAtoms(aa)-1])</li>
 <li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</li>
 </ul>
@@ -1004,7 +1005,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
 <li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumHydrogens(aa)-1])</li>
 <li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</li>
 </ul>
@@ -1033,7 +1034,7 @@ atom.</p>
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
 <li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</li>
 </ul>
 </td>
@@ -1061,7 +1062,7 @@ and atom.</p>
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
 <li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</li>
 </ul>
 </td>
@@ -1085,7 +1086,7 @@ hydrogens of <em>aa</em>.</p>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
 </tr>
 </tbody>
 </table>
@@ -1117,7 +1118,7 @@ hydrogens of <em>aa</em>.</p>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
 </tr>
 </tbody>
 </table>
@@ -1150,7 +1151,7 @@ hydrogens of <em>aa</em>.</p>
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Amino acid type of the given heavy atom type</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a></p>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a></p>
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
@@ -1244,7 +1245,7 @@ when residue is peptide bound.</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. PRO)</td>
 </tr>
@@ -1268,7 +1269,7 @@ when residue is N terminal.</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. H3 for PRO)</td>
 </tr>
diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index adc18a285338a31c95c7f84aa7671b3a9efa8ec7..b2a0e71c9af3026a42465bfb1e428ebcf4f2935f 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Representing Loops &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Representing Loops &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Sampling Dihedral Angles" href="torsion_sampler.html" />
@@ -36,7 +37,7 @@
 <p>The most simple representation of structural information in ProMod3 is the
 <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>. It provides a way to store the backbone positions of
 residues. They provide structural manipulations, they can be manipulated and
-converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
+converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
 <span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">conop</span>
 <span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
@@ -86,7 +87,7 @@ residue has a CB position defined (i.e. even if it’s a glycine) and we only
 allow amino acid types belonging to the 20 default amino acids. Note that the
 omega torsion angle defined here for residue <em>i</em> is the dihedral between CA-C
 of residue <em>i</em> and N-CA of residue <em>i+1</em> (this is shifted by 1 residue
-compared to OST’s <code class="xref py py-meth docutils literal notranslate"><span class="pre">GetOmegaTorsion()</span></code>).</p>
+compared to OST’s <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle.GetOmegaTorsion" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetOmegaTorsion()</span></code></a>).</p>
 <dl class="method">
 <dt id="promod3.loop.BackboneList.BackboneList">
 <code class="descname">BackboneList</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.BackboneList" title="Permalink to this definition">¶</a></dt>
@@ -148,7 +149,7 @@ code which is not one of the 20 default amino acids or if
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
 which the backbone positions and one letter codes
 are extracted.</td>
 </tr>
@@ -172,7 +173,7 @@ required positions.</td>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</li>
-<li><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+<li><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
 which the backbone positions are extracted.</li>
 </ul>
 </td>
@@ -196,7 +197,7 @@ a residue not providing all necessary positions.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to a density map.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -206,7 +207,7 @@ a residue not providing all necessary positions.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>padding</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </li>
-<li><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – </li>
+<li><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – </li>
 <li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </li>
 <li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </li>
 </ul>
@@ -225,7 +226,7 @@ a residue not providing all necessary positions.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to an OST entity.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -242,8 +243,8 @@ be replaced, otherwise they will be added to the entity.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</li>
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</li>
 </ul>
 </td>
 </tr>
@@ -259,7 +260,7 @@ be replaced, otherwise they will be added to the entity.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a>) – </li>
+<li><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a>) – </li>
 <li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </li>
 <li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </li>
 </ul>
@@ -278,7 +279,7 @@ be replaced, otherwise they will be added to the entity.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"></td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.AlignedCuboid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.AlignedCuboid</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>all_atom</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </td>
 </tr>
@@ -382,7 +383,7 @@ actual fragment at specified <em>index</em></p>
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position of nitrogen / alpha carbon / beta carbon / carbon / oxygen
 atom for residue at given index.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</td>
 </tr>
@@ -407,7 +408,7 @@ atom for residue at given index.</td>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
 / oxygen atom to this.</li>
 </ul>
 </td>
@@ -459,7 +460,7 @@ atom for residue at given index.</td>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of the residue at given index.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</td>
 </tr>
@@ -476,7 +477,7 @@ atom for residue at given index.</td>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</li>
 </ul>
 </td>
 </tr>
@@ -502,12 +503,12 @@ and set the amino acid type according to the given one letter code.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
-<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
 <li><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
 </ul>
 </td>
@@ -577,12 +578,12 @@ to the given one letter code.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
-<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
 <li><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
 </ul>
 </td>
@@ -646,7 +647,7 @@ reconstructed if the residue handle is valid.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
 element of this backbone list)</td>
 </tr>
 </tbody>
@@ -663,7 +664,7 @@ element of this backbone list)</td>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
 </ul>
 </td>
 </tr>
@@ -683,7 +684,7 @@ element of this backbone list)</td>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start index.</li>
 <li><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – End index (one past last residue to transform).</li>
-<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
 </ul>
 </td>
 </tr>
@@ -699,7 +700,7 @@ element of this backbone list)</td>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>transform</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>transform</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</td>
 </tr>
 </tbody>
 </table>
@@ -719,12 +720,12 @@ residue <em>other_index</em> of <em>other</em> backbone list considering the
 positions of the N, CA and C atoms.</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</li>
 <li><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</li>
 <li><strong>other_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index in <em>other</em> backbone list.</li>
 </ul>
@@ -744,7 +745,7 @@ positions of the N, CA and C atoms.</p>
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Get minimum RMSD transformation of CA positions of this backbone
 list onto CA positions of <em>other</em> backbone list.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</td>
 </tr>
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index 540e0f8c4d81fe33abbcddbfbe19838418f93433..d031b39d5221fdb45a4ee1d1e8fc2161eab8df44 100644
--- a/doc/html/loop/index.html
+++ b/doc/html/loop/index.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>loop - Loop Handling &#8212; ProMod3 3.3.0 documentation</title>
+    <title>loop - Loop Handling &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Representing Loops" href="backbone.html" />
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index 51d3acd6a7d7f89955e4b4cdeec8cefbe4ea8376..a2d25fd6f34b570c9e97e65d9e7b1b1f6cc8647c 100644
--- a/doc/html/loop/load_loop_objects.html
+++ b/doc/html/loop/load_loop_objects.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Loading Precomputed Objects &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Loading Precomputed Objects &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="core - ProMod3 Core Functionality" href="../core/index.html" />
diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html
index 05816c62a4fd69fed419d722ae047bdb5719adcb..b1e50413487d64ba6adeddabb5329f3aecb9f064 100644
--- a/doc/html/loop/mm_system_creation.html
+++ b/doc/html/loop/mm_system_creation.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Generate ost.mol.mm systems &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Generate ost.mol.mm systems &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Loading Precomputed Objects" href="load_loop_objects.html" />
@@ -32,8 +33,8 @@
           <div class="body" role="main">
             
   <div class="section" id="generate-ost-mol-mm-systems">
-<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.3.1)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
-<p>To simplify the creation of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.3.1)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
+<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.4.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
+<p>To simplify the creation of <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.4.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
 proteins, we define a system creator for loops (<a class="reference internal" href="#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal notranslate"><span class="pre">MmSystemCreator</span></code></a>) and a
 specialized forcefield lookup for amino acids (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>).</p>
 <p>The example below showcases the creation and use of an MM system:</p>
@@ -278,7 +279,7 @@ acid types for <em>out_pos[res_indices[i]]</em> and <em>all_pos[res_indices[i]]<
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Simulation object setup by <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>. Use this to run
 MM simulations.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -425,7 +426,7 @@ FF specific data for amino acids in a protein. We distinguish amino acid types
 <dl class="class">
 <dt id="promod3.loop.ForcefieldLookup">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldLookup</code><a class="headerlink" href="#promod3.loop.ForcefieldLookup" title="Permalink to this definition">¶</a></dt>
-<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
+<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
 <ul class="simple">
 <li>get a consistent indexing of each atom of each residue in [<em>0, N-1</em>], where
 <em>N</em> = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a> (note that only OXT indexing depends on whether a
@@ -538,7 +539,7 @@ for details.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type for given <em>ff_aa</em></td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</td>
 </tr>
@@ -654,7 +655,7 @@ for details.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for LJ 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</td>
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
 </tr>
@@ -670,7 +671,7 @@ for details.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for electrostatic 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</td>
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
 </tr>
@@ -685,7 +686,7 @@ for details.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -709,7 +710,7 @@ for details.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -734,7 +735,7 @@ for details.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Sigma in nm for each atom
-(see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -759,7 +760,7 @@ for details.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Epsilon in kJ/mol for each atom
-(see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -905,7 +906,7 @@ for details.</p>
 <dt id="promod3.loop.ForcefieldAminoAcid">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldAminoAcid</code><a class="headerlink" href="#promod3.loop.ForcefieldAminoAcid" title="Permalink to this definition">¶</a></dt>
 <dd><p>Enumerates the amino acid types for forcefields. The first 20 values
-correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
+correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
 there are values for disulfid bridges (<em>FF_CYS2</em>), d-protonated histidine
 (<em>FF_HISD</em>, default for <em>ost.conop.HIS</em> is <em>FF_HISE</em>) and <em>FF_XXX</em> for unknown
 types. The full list of values is:</p>
@@ -922,7 +923,7 @@ types. The full list of values is:</p>
 <dd><p>Contains lists of bonds, angles, dihedrals, impropers and LJ pairs (exclusions
 are the combination of all bonds and 1,3 pairs of angles and are not stored
 separately). Each type of connectivity has it’s own class (see below) storing
-indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Topology</span></code></a>.
+indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Topology</span></code></a>.
 The indexing of atoms for internal connectivities is in [<em>0, N-1</em>], where <em>N</em>
 = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ForcefieldLookup.GetNumAtoms()</span></code></a>. For connectivities of pairs of
 residues, atoms of the first residue are in [<em>0, N1-1</em>] and atoms of the
@@ -1032,7 +1033,7 @@ False, False)</em>.</p>
 <dl class="class">
 <dt id="promod3.loop.ForcefieldBondInfo">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldBondInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
+<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
 <dl class="attribute">
 <dt id="promod3.loop.ForcefieldBondInfo.index_one">
 <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1094,7 +1095,7 @@ False, False)</em>.</p>
 <dl class="class">
 <dt id="promod3.loop.ForcefieldHarmonicAngleInfo">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
+<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
 <dl class="attribute">
 <dt id="promod3.loop.ForcefieldHarmonicAngleInfo.index_one">
 <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1171,7 +1172,7 @@ False, False)</em>.</p>
 <dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldUreyBradleyAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="Permalink to this definition">¶</a></dt>
 <dd><p>Define Urey-Bradley angle
-(see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
 <dl class="attribute">
 <dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one">
 <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1276,8 +1277,8 @@ False, False)</em>.</p>
 <dt id="promod3.loop.ForcefieldPeriodicDihedralInfo">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldPeriodicDihedralInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="Permalink to this definition">¶</a></dt>
 <dd><p>Define periodic dihedral or improper (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
 <dl class="attribute">
 <dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_one">
 <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1381,7 +1382,7 @@ False, False)</em>.</p>
 <dl class="class">
 <dt id="promod3.loop.ForcefieldHarmonicImproperInfo">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicImproperInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
+<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
 <dl class="attribute">
 <dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_one">
 <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1471,7 +1472,7 @@ False, False)</em>.</p>
 <dl class="class">
 <dt id="promod3.loop.ForcefieldLJPairInfo">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldLJPairInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
+<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
 <dl class="attribute">
 <dt id="promod3.loop.ForcefieldLJPairInfo.index_one">
 <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_one" title="Permalink to this definition">¶</a></dt>
diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
index f5413e9fd7c236b612a8b0182faa7369708076ec..e917888a0e6ee2c1fd02a4f295a1218bdd6a7524 100644
--- a/doc/html/loop/structure_db.html
+++ b/doc/html/loop/structure_db.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Structural Data &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Structural Data &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Handling All Atom Positions" href="all_atom.html" />
@@ -115,7 +116,7 @@ stuff to the structure db. (<a class="reference external" href="https://docs.pyt
 <dt id="promod3.loop.CoordInfo.shift">
 <code class="descname">shift</code><a class="headerlink" href="#promod3.loop.CoordInfo.shift" title="Permalink to this definition">¶</a></dt>
 <dd><p>Translation from original coordinates that has been applied before storing
-structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
+structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
 </dd></dl>
 
 </dd></dl>
@@ -257,7 +258,7 @@ database, you might want to consider two things:</p>
 <ol class="arabic simple">
 <li>Use a database of limited size to generate the actual profiles (something
 in between 5000 and 10000 nonredundant chains is enough)</li>
-<li>Use the <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
+<li>Use the <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
 running in parallel</li>
 </ol>
 <dl class="class">
@@ -392,11 +393,11 @@ in the according <a class="reference internal" href="#promod3.loop.CoordInfo" ti
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – identifier of the added structure (e.g. pdb id)</li>
 <li><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name of the chain in <em>ent</em> you want to add</li>
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a> /
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – The full entity that must contain a chain named
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a> /
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – The full entity that must contain a chain named
 as specified by <em>chain_name</em>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
 <em>chain_name</em>. The profile sequence must match <em>seqres</em>.</li>
 <li><strong>only_longest_stretch</strong> – Flag whether you want to add only the longest
 connected stretch of residues are all connected
@@ -532,9 +533,9 @@ full entry at <em>coord_idx</em></p>
 <li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the returned backbone list. If not
 set, the original sequence at specified location in the
 database is used.</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
 superposed onto.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
 superposed onto.</li>
 </ul>
 </td>
@@ -688,7 +689,7 @@ connected stretches of residues in the database.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Solvent accessibility for each residue of <em>fragment</em> or full entry
 at <em>coord_idx</em> in square A as calculated by
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Accessibility()</span></code></a> when adding the structure to
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Accessibility()</span></code></a> when adding the structure to
 the database.</p>
 </td>
 </tr>
@@ -727,7 +728,7 @@ full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
 model.</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
@@ -761,7 +762,7 @@ full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
 model.</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
@@ -802,7 +803,7 @@ containing that data.</li>
 probabilities as NULL model.</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>bb_list</em> and
@@ -824,7 +825,7 @@ frequencies in entry with <em>coord_idx</em></p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</li>
 <li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – StructureDB index of entry for which to set frequencies
 (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCoords()</span></code></a>-1])</li>
 </ul>
@@ -1127,8 +1128,8 @@ and <strong>c_stem</strong> and of the same length as the <strong>frag_size</str
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</li>
 <li><strong>frag_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues of the fragment</li>
 <li><strong>extra_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Whether to extend the search to include fragments from
 <em>extra_bins</em> additional bins surrounding the bin given by
@@ -1352,7 +1353,7 @@ linked to this object.</li>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
 </ul>
 </td>
 </tr>
@@ -1370,7 +1371,7 @@ linked to this object.</li>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
 </ul>
 </td>
 </tr>
diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index 0f280d3cb2606eb6b2556717c1f3451e6a2dc6de..04b213039aa44587e2d327407cb57c3d821d7acb 100644
--- a/doc/html/loop/torsion_sampler.html
+++ b/doc/html/loop/torsion_sampler.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Sampling Dihedral Angles &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Sampling Dihedral Angles &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Structural Data" href="structure_db.html" />
@@ -128,7 +129,7 @@ acids not matching any of the group definitions.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</td>
 </tr>
 </tbody>
 </table>
@@ -200,9 +201,9 @@ for details.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
 </ul>
 </td>
 </tr>
@@ -242,9 +243,9 @@ standard amino acid</td>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
 </ul>
 </td>
 </tr>
@@ -280,9 +281,9 @@ standard amino acid</td>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
 <li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>psi</em> angle</li>
 </ul>
 </td>
@@ -324,9 +325,9 @@ standard amino acid</td>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
 <li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>phi</em> angle</li>
 </ul>
 </td>
@@ -368,9 +369,9 @@ standard amino acid</td>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
 <li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</li>
 <li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</li>
 </ul>
@@ -414,9 +415,9 @@ standard amino acid</td>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
 <li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</li>
 <li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</li>
 </ul>
@@ -438,9 +439,9 @@ standard amino acid</td>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
 <li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</li>
 <li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</li>
 </ul>
diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html
index 20a4c6e471c12cc54588a0a1a01adab7b8d7f7a2..c4a6693b8cac004463b12f12fa57352eb9505fd5 100644
--- a/doc/html/modelling/algorithms.html
+++ b/doc/html/modelling/algorithms.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Modelling Algorithms &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Modelling Algorithms &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="sidechain - Sidechain Modelling" href="../sidechain/index.html" />
@@ -84,7 +85,7 @@ of the solutions</li>
 indices of the common subsets (rigid blocks) relative
 to the input <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a> objects
 and the second element being a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
 superpose the according positions in <strong>bb_list_one</strong>
 onto <strong>bb_list_two</strong></p>
 </td>
@@ -102,7 +103,7 @@ onto <strong>bb_list_two</strong></p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>
 objects from which the positions are extracted</li>
 <li><strong>seq_idx_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The idx of the first sequence from which the CA
 positions will be extracted</li>
@@ -123,9 +124,9 @@ of the solutions</li>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with the first element being a
 <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> defining the
 column indices of the common subsets (rigid blocks)
-relative to the input <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
+relative to the input <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
 and the second element being a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
 superpose the according positions from the first
 sequence onto the second sequence.</p>
 </td>
@@ -162,7 +163,7 @@ of the solutions</li>
 indices of the common subsets (rigid blocks) relative
 to the input <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code> objects
 and the second element being a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
 superpose the according positions in <strong>pos_one</strong>
 onto <strong>pos_two</strong></p>
 </td>
@@ -225,8 +226,8 @@ Weird things are happening otherwise.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</li>
-<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</li>
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</li>
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</li>
 <li><strong>psipred_pred</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – Psipred prediction for this chain.</li>
 <li><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length (num. residues) of fragments to be extracted.</li>
 <li><strong>fragments_per_position</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of fragments to be extracted at each
@@ -318,7 +319,7 @@ want to generate</li>
 <li><strong>avg_sampling_per_position</strong> – Number of Monte Carlo sampling steps
 the total number is: 
 len(<strong>sequence</strong>) * <strong>avg_sampling_per_position</strong></li>
-<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the 
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the 
 fragment search performance.</li>
 <li><strong>psipred_prediction</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – The psipred prediction for <strong>sequence</strong>. This
 increases the fragment search performance</li>
@@ -580,7 +581,7 @@ only coordinates matter.</li>
 
 <dl class="method">
 <dt id="promod3.modelling.FindMotifs">
-<code class="descclassname">promod3.modelling.</code><code class="descname">FindMotifs</code><span class="sig-paren">(</span><em>query</em>, <em>target_positions</em>, <em>hash_tresh=0.4</em>, <em>distance_thresh=1.0</em>, <em>refine_thresh=0.7</em>, <em>flags=list()</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FindMotifs" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">FindMotifs</code><span class="sig-paren">(</span><em>query</em>, <em>target_positions</em>, <em>hash_tresh=0.4</em>, <em>distance_thresh=1.0</em>, <em>refine_thresh=0.7</em>, <em>flags=list()</em>, <em>swap_thresh=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FindMotifs" title="Permalink to this definition">¶</a></dt>
 <dd><p>Performs the detection and refinement stages of the geometric hashing
 algorithm.</p>
 <table class="docutils field-list" frame="void" rules="none">
@@ -597,6 +598,10 @@ algorithm.</p>
 constructor. If you didn’t provide anything there,
 this can be ignored. Only the actual coordinates
 matter in this case.</li>
+<li><strong>swap_thresh</strong> – <em>hash_thresh</em> and <em>refine_thresh</em> refer to fraction of
+covered positions in <em>query</em>. When setting this to
+True, they refer to the fraction of covered positions
+in <em>target_positions</em>.</li>
 </ul>
 </td>
 </tr>
@@ -633,7 +638,7 @@ scripts and documentation are available in
 <dd><p>Searches <em>tpl_n</em> templates in <em>fs_server</em>/<em>pentamatch</em></p>
 <p>Step 1: Identifies <em>pentamatch_n</em> sequences in <em>pentamatch</em> with largest
 number of matching pentamers with respect to <em>trg_seq</em>.
-Step 2: Generate pairwise alignments with <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/alg/seqalg/#ost.seq.alg.LocalAlign" title="(in OpenStructure v2.3.1)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.seq.alg.LocalAlign()</span></code></a>
+Step 2: Generate pairwise alignments with <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/alg/seqalg/#ost.seq.alg.LocalAlign" title="(in OpenStructure v2.4.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.seq.alg.LocalAlign()</span></code></a>
 and only retain the ones with seqid &gt;= <em>seqid_thresh</em>.
 Step 3: Extract respective templates from <em>fs_server</em> and score them by
 the sum of plDDT of aligned residues divided by <em>trg_seq</em> length.
@@ -645,7 +650,7 @@ Step 4: Return top <em>tpl_n</em> (or less)</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>fs_server</strong> (<a class="reference internal" href="#promod3.modelling.FSStructureServer" title="promod3.modelling.FSStructureServer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FSStructureServer</span></code></a>) – Structure database - The AFDB</li>
 <li><strong>pentamatch</strong> (<a class="reference internal" href="#promod3.modelling.PentaMatch" title="promod3.modelling.PentaMatch"><code class="xref py py-class docutils literal notranslate"><span class="pre">PentaMatch</span></code></a>) – Pentamatch object specific for <em>fs_server</em></li>
-<li><strong>trg_seq</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>/<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Target sequence</li>
+<li><strong>trg_seq</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>/<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Target sequence</li>
 <li><strong>seqid_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Sequence Identity threshold [0-100] that alignment is
 considered further</li>
 <li><strong>tpl_n</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of templates that are finally returned based on
@@ -658,7 +663,7 @@ described scoring</li>
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of pairs with first element being the tpl score,
-the second element being a <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a> with
+the second element being a <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a> with
 first sequence being <em>trg_seq</em> and second sequence the hit found
 in <em>fs_server</em> with structure attached. If <em>fs_server</em> has been
 generated with the default procedure described in the docs,
@@ -684,7 +689,7 @@ idx refers to the raw idx of the template in <em>fs_server</em>.</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>fs_server</strong> (<a class="reference internal" href="#promod3.modelling.FSStructureServer" title="promod3.modelling.FSStructureServer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FSStructureServer</span></code></a>) – Structure database - The AFDB</li>
 <li><strong>pentamatch</strong> (<a class="reference internal" href="#promod3.modelling.PentaMatch" title="promod3.modelling.PentaMatch"><code class="xref py py-class docutils literal notranslate"><span class="pre">PentaMatch</span></code></a>) – Pentamatch object specific for <em>fs_server</em></li>
-<li><strong>trg_seq</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>/<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Target sequence</li>
+<li><strong>trg_seq</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>/<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Target sequence</li>
 <li><strong>transfer_bfactors</strong> – Simple heuristic to transfer bfactors (plDDT) to
 model. In case of an aligned residue, bfactor
 (i.e. plDDT) gets simply transferred.
diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html
index 367970a45918d669797c5add095557368852cf1c..231efce67e407fdfc2fd86ebb74f68f7608f9c00 100644
--- a/doc/html/modelling/gap_handling.html
+++ b/doc/html/modelling/gap_handling.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Handling Gaps &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Handling Gaps &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Handling Loop Candidates" href="loop_candidates.html" />
@@ -50,8 +51,8 @@ invalid residue handles to <cite>before</cite> or <cite>after</cite>.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a></li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a></li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a></li>
 <li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.seq" title="promod3.modelling.StructuralGap.seq"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seq</span></code></a></li>
 </ul>
 </td>
@@ -106,7 +107,7 @@ are valid and:</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Chain, the gap is belonging to</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -257,13 +258,13 @@ extend the gap past another gap.</p>
 <dl class="attribute">
 <dt id="promod3.modelling.StructuralGap.before">
 <code class="descname">before</code><a class="headerlink" href="#promod3.modelling.StructuralGap.before" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="promod3.modelling.StructuralGap.after">
 <code class="descname">after</code><a class="headerlink" href="#promod3.modelling.StructuralGap.after" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
 </dd></dl>
 
 <dl class="attribute">
@@ -308,7 +309,7 @@ False if no new extension possible.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.GapExtender.Extend" title="promod3.modelling.GapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
 </ul>
 </td>
 </tr>
@@ -349,7 +350,7 @@ valid termini.</td>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
 <li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <ul>
 <li>If -1, all possible non-terminal gaps are returned.</li>
 <li>If &gt;= 0, this restricts the max. gap-length
@@ -402,7 +403,7 @@ score = num_gap_extensions * <cite>extension_penalty</cite> + sum( <cite>penalti
 <li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</li>
 <li><strong>extension_penalty</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Penalty for length of gap.</li>
 <li><strong>penalties</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Penalty for each residue added to gap.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
 <li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <ul>
 <li>If -2, <a class="reference internal" href="#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a> is used instead of <a class="reference internal" href="#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a>
 (i.e. it stops at gaps and termini).</li>
diff --git a/doc/html/modelling/index.html b/doc/html/modelling/index.html
index 8329bb87acfa8d00d660ea8a1cafae5aaf4ad1fc..1dbcbd28e1679c4b77051ca4449bbc423b6ce96d 100644
--- a/doc/html/modelling/index.html
+++ b/doc/html/modelling/index.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>modelling - Protein Modelling &#8212; ProMod3 3.3.0 documentation</title>
+    <title>modelling - Protein Modelling &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Modelling Pipeline" href="pipeline.html" />
diff --git a/doc/html/modelling/loop_candidates.html b/doc/html/modelling/loop_candidates.html
index 98a3289adb73745b06583b32dcc2bb6c1866b3df..b0a14aff4c63471baf5b4a6c1341050652abb1f9 100644
--- a/doc/html/modelling/loop_candidates.html
+++ b/doc/html/modelling/loop_candidates.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Handling Loop Candidates &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Handling Loop Candidates &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Fitting Loops Into Gaps" href="loop_closing.html" />
@@ -122,8 +123,8 @@ a fragment database.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</li>
 <li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The sequence of residues to be added including the
 <em>n_stem</em> and <em>c_stem</em></li>
 <li><strong>frag_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – The fragment database</li>
@@ -234,9 +235,9 @@ not depending on a metropolis criterium.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
 should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
 should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li>
 <li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
 of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – A torsion sampler (used for all residues) or a list
@@ -278,9 +279,9 @@ candidate. This leads to an increase in number of loops.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
 should match</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
 should match</li>
 <li><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First pivot residue</li>
 <li><strong>pivot_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Second pivot residue</li>
@@ -354,7 +355,7 @@ anything is raised when calculating the scores.</p>
 <code class="descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>structure_db</em>, <em>prof</em>, <em>offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStructureProfileScores" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculates a score comparing the given profile <em>prof</em> starting at <em>offset</em>
 with the sequence / structure profile of each candidate as extracted from
-<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
+<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
 details, <em>prof.null_model</em> is used for weighting).</p>
 <p>Note that for profile scores a higher “score” is better! So take care when
 combining this to other scores, where it is commonly the other way around.</p>
@@ -370,7 +371,7 @@ with this DB).</p>
 <li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
 key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a></li>
 <li><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Structural database used in <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromDatabase()</span></code></a></li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</li>
 <li><strong>offset</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Loop starts at index <em>offset</em> in <em>prof</em>.</li>
 </ul>
 </td>
@@ -402,8 +403,8 @@ positions and the corresponding atoms in <em>c_stem</em>.</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
 key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a></li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</li>
 </ul>
 </td>
 </tr>
diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html
index 7cd4dcf9b6eb59022a7d70f9071066107d3f0fd9..6a4c5a923e8e0704cf045bc6fe9fd7b850daaa33 100644
--- a/doc/html/modelling/loop_closing.html
+++ b/doc/html/modelling/loop_closing.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Fitting Loops Into Gaps &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Fitting Loops Into Gaps &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Generating Loops De Novo" href="monte_carlo.html" />
@@ -73,11 +74,11 @@ to avoid moving into unfavourable regions of the backbone dihedrals.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the backbones to be closed</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
 If the residue before <em>n_stem</em> doesn’t exist, the
 torsion sampler will use a default residue (ALA) and
 and phi angle (-1.0472) to evaluate the first angle.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
 If the residue after <em>c_stem</em> doesn’t exist, the
 torsion sampler will use a default residue (ALA) and
 psi angle (-0.7854) to evaluate the last angle.</li>
@@ -114,8 +115,8 @@ This is faster but might lead to weird backbone dihedral pairs.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</li>
 <li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal number of iterations</li>
 <li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The algorithm stops as soon as the c_stem of the loop to
 be  closed has RMSD below the given <em>c_stem</em></li>
@@ -316,7 +317,7 @@ size or sequence as the initial one.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
 <li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
 </ul>
 </td>
@@ -338,7 +339,7 @@ size or sequence as the initial one.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
 <li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
 </ul>
 </td>
@@ -361,7 +362,7 @@ doesn’t do anything if specified residue is a glycine</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
 <li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
 </ul>
 </td>
@@ -383,7 +384,7 @@ doesn’t do anything if specified residue is a glycine</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
 <li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
 </ul>
 </td>
@@ -405,7 +406,7 @@ doesn’t do anything if specified residue is a glycine</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
 <li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
 </ul>
 </td>
diff --git a/doc/html/modelling/model_checking.html b/doc/html/modelling/model_checking.html
index d39b5fe78f18d2c81779a3672c75647d30420458..1aa89625db4cab9f530968c7f17a7fbae8967f56 100644
--- a/doc/html/modelling/model_checking.html
+++ b/doc/html/modelling/model_checking.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Model Checking &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Model Checking &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Handling Gaps" href="gap_handling.html" />
@@ -47,14 +48,14 @@ three of the atoms exist (center and radii are estimated then).</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of rings to perform ring checks. Each ring is a named
 tuple with:
-center (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>),
-plane (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/composite/#ost.geom.Plane" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Plane</span></code></a>),
+center (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>),
+plane (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/composite/#ost.geom.Plane" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Plane</span></code></a>),
 radius (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>),
-residue (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>).</td>
+residue (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>).</td>
 </tr>
 </tbody>
 </table>
@@ -70,11 +71,11 @@ residue (<a class="reference external" href="https://www.openstructure.org/docs/
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRings()</span></code></a>.</li>
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
 </ul>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of residues (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) which
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of residues (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) which
 have a punched ring.</p>
 </td>
 </tr>
@@ -93,7 +94,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRings()</span></code></a>.</li>
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
 </ul>
 </td>
 </tr>
@@ -118,7 +119,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>candidates</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code>) – Loop candidates meant to fill <em>gap</em> within <em>model</em>.
 Offending candidates are removed from this list.</li>
-<li><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</li>
+<li><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</li>
 <li><strong>gap</strong> (<a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>.) – Gap for which loop is to be filled.</li>
 <li><strong>orig_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – Mapping to old indexing of candidates. If given, it
 must have as many elements as <em>candidates</em>.</li>
@@ -161,15 +162,15 @@ within 0.065 (HIS), 0.075 (TRP), 0.057 (TYR), 0.060 (PHE).</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect non-planar rings.</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect non-planar rings.</li>
 <li><strong>max_dist_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – A residue that contains a ring is considered
 non-planar if the max distance of any ring-atom to
 the optimal ring plane is above this threshold.</li>
 </ul>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of residues (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>/
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueView</span></code></a>) which have a non-planar ring.</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of residues (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>/
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueView</span></code></a>) which have a non-planar ring.</p>
 </td>
 </tr>
 </tbody>
@@ -187,7 +188,7 @@ residue is considered non-planar.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect non-planar rings</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect non-planar rings</li>
 <li><strong>max_dist_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – A residue that contains a ring is considered
 non-planar if the max distance of any ring-atom to
 the optimal ring plane is above this threshold.</li>
@@ -251,7 +252,7 @@ with <code class="docutils literal notranslate"><span class="pre">MolProbity</sp
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a></p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.4/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
 executable is not found.</p>
 </td>
 </tr>
@@ -268,7 +269,7 @@ executable is not found.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</td>
 </tr>
 </tbody>
 </table>
diff --git a/doc/html/modelling/monte_carlo.html b/doc/html/modelling/monte_carlo.html
index e307c44dfc5ba42e349b2bac26a389f36de7ee99..6d1a98053f0329fd461aea8058aa1efc4d95577e 100644
--- a/doc/html/modelling/monte_carlo.html
+++ b/doc/html/modelling/monte_carlo.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Generating Loops De Novo &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Generating Loops De Novo &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Sidechain Reconstruction" href="sidechain_reconstruction.html" />
@@ -495,9 +496,9 @@ avoid moving into unfavourable phi/psi ranges.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
 should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
 should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li>
 <li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the conformation to be closed.</li>
 <li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
@@ -545,9 +546,9 @@ dihedral angles as it is the case for the <a class="reference internal" href="#p
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
 should adapt.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
 should adapt.</li>
 </ul>
 </td>
@@ -587,9 +588,9 @@ solutions. The KICCloser simply picks the first one.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
 adapt.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
 adapt.</li>
 <li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random generators.</li>
 </ul>
@@ -628,7 +629,7 @@ superposing the c_stem with the desired positions.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
 adapt.</td>
 </tr>
 </tbody>
@@ -666,7 +667,7 @@ superposing the n_stem with the desired positions.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
 adapt.</td>
 </tr>
 </tbody>
diff --git a/doc/html/modelling/pipeline.html b/doc/html/modelling/pipeline.html
index 5548082996d7a865a38f946ceb9ca0c9fdb77593..7eccbbe4c668b87581d2949f583aa907a9079fae 100644
--- a/doc/html/modelling/pipeline.html
+++ b/doc/html/modelling/pipeline.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Modelling Pipeline &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Modelling Pipeline &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Model Checking" href="model_checking.html" />
@@ -107,7 +108,7 @@ chain follows afterwards.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -133,13 +134,13 @@ Gaps of different chains are appended one after another.</p>
 <dl class="attribute">
 <dt id="promod3.modelling.ModellingHandle.seqres">
 <code class="descname">seqres</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.seqres" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceHandle</span></code></a> for each chain
+<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceHandle</span></code></a> for each chain
 of the target protein.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceList</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceList</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -148,7 +149,7 @@ of the target protein.</p>
 <dl class="attribute">
 <dt id="promod3.modelling.ModellingHandle.profiles">
 <code class="descname">profiles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.profiles" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
+<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
 the target protein (same order as in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a>). Please note, that this
 attribute won’t be set by simply calling <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>. You have
 to fill it manually or even better by the convenient function
@@ -157,7 +158,7 @@ to fill it manually or even better by the convenient function
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -344,7 +345,7 @@ alignment handle or an alignment handle list. Every list item is treated as a
 single chain in the final raw model.</p>
 <p>Each alignment handle must contain exactly two sequences and the second
 sequence is considered the template sequence, which must have a 
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a> attached.</p>
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a> attached.</p>
 <p>Before extracting the coordinates, the alignments are pre-processed 
 according to <em>aln_preprocessing</em>.</p>
 <p>This is a basic protein core modelling algorithm that copies backbone
@@ -374,7 +375,7 @@ as information about insertions and deletions in the gaps list.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
 list of alignment handles for raw model with multiple chains.</li>
 <li><strong>include_ligands</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True, if we wish to include ligands in the model. This
 searches for ligands in all OST handles of the views
@@ -387,7 +388,7 @@ in SMTL). All ligands are added to a new chain named
 (chains are consecutively named according to 
 characters in
 ‘ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz’). 
-If <em>aln</em> is of type <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>, 
+If <em>aln</em> is of type <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>, 
 <em>chain_names</em> is expected to be a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>.
 If <em>aln</em> is of type <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentList</span></code>,
 <em>chain_names</em> is expected to be a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of 
@@ -413,7 +414,7 @@ to False.</li>
 <li>the second sequence does not have an attached structure</li>
 <li>the residues of the template structure do not match with the
 alignment sequence (note that you can set an “offset” (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetSequenceOffset()</span></code></a>) for the
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetSequenceOffset()</span></code></a>) for the
 template sequence (but not for the target))</li>
 <li>the target sequence has a non-zero offset (cannot be honored as
 the resulting model will always start its residue numbering at 1)</li>
@@ -457,12 +458,12 @@ return an incomplete model.</p>
 <li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – The prepared template coordinates loaded with the input
 alignment.</li>
 <li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
-CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v2.3.1)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
-and <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v2.3.1)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
+CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v2.4.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
+and <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v2.4.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
 Both do a similarly good job without ligands (CHARMM
 slightly better), but you will want to be consistent
 with the optional force fields in <cite>extra_force_fields</cite>.</li>
-<li><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a 
+<li><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a 
 (ligand) residue cannot be parametrized with the
 default force field. The force fields are tried
 in the order as given and ligands without an
@@ -483,7 +484,7 @@ limited.</li>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Delivers the model as an OST entity.</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -658,7 +659,7 @@ environments get updated in <strong>target_mhandle</strong>.</p>
 <li><strong>target_chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – This is the chain where the info goes to</li>
 <li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First residue of the copied stretch</li>
 <li><strong>end_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Last residue of the copied stretch</li>
-<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
 they’re copied over</li>
 </ul>
 </td>
@@ -689,7 +690,7 @@ while ensuring consistency with the <a class="reference internal" href="#promod3
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the profiles attached afterwards</li>
-<li><strong>profiles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</li>
+<li><strong>profiles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</li>
 </ul>
 </td>
 </tr>
@@ -846,7 +847,7 @@ For the scondary-structure-penalty to work,
 the model-template must have the appropriate
 information before <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildRawModel()</span></code></a> is
 called (e.g. with 
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</li>
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</li>
 <li><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a> instead of
 of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>. Also works in combination
 with <cite>use_scoring_extender</cite>. This allows the gap
@@ -1216,7 +1217,7 @@ one is loaded if None.</li>
 <dt id="promod3.modelling.MinimizeModelEnergy">
 <code class="descclassname">promod3.modelling.</code><code class="descname">MinimizeModelEnergy</code><span class="sig-paren">(</span><em>mhandle</em>, <em>max_iterations=12</em>, <em>max_iter_sd=20</em>, <em>max_iter_lbfgs=10</em>, <em>use_amber_ff=False</em>, <em>extra_force_fields=[]</em>, <em>tolerance_sd=1.0</em>, <em>tolerance_lbfgs=1.0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MinimizeModelEnergy" title="Permalink to this definition">¶</a></dt>
 <dd><p>Minimize energy of final model using molecular mechanics.</p>
-<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.3.1)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
+<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.4.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
 It will iteratively (at most <em>max_iterations</em> times):</p>
 <ul class="simple">
 <li>run up to <em>max_iter_sd</em> minimization iter. of a steepest descend method</li>
@@ -1243,12 +1244,12 @@ minimization is aborted. This issue is logged and added as a major issue to
 <li><strong>max_iter_sd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations within SD method</li>
 <li><strong>max_iter_lbfgs</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations within LBFGS method</li>
 <li><strong>tolerance_sd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Tolerance parameter passed to ApplySD of 
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> object.</li>
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> object.</li>
 <li><strong>tolerance_lbfgs</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Tolerance parameter passed to ApplyLBFGS of 
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> object.</li>
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> object.</li>
 <li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
 CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>).</li>
-<li><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
+<li><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
 <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>).</li>
 </ul>
 </td>
@@ -1256,7 +1257,7 @@ CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFrom
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The model including all oxygens as used in the minimizer.</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -1345,8 +1346,8 @@ set to True, if the problem affects backbone atoms.</li>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a> /
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueView</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a> /
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueView</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -1420,17 +1421,17 @@ attribute yet, it is added.</p>
 <p>Columns that only contain gaps (‘-‘) are removed. If no such column can be 
 identified, the input alignment gets returned. A new alignment gets 
 constructed otherwise. The sequences of the new alignment retain name, offset
-and the potentially attached <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original
+and the potentially attached <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original
 sequences.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The processed alignment</td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -1472,16 +1473,16 @@ ATOMSEQ: ABCDEFGHI...
 <p>given a <em>min_terminal_anchor_size</em>&gt;2. If no shift can be performed, the 
 input alignment gets returned. A new alignment gets constructed otherwise. 
 The sequences of the new alignment retain name, offset and the potentially 
-attached <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original sequences.</p>
+attached <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original sequences.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The processed alignment</td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></td>
 </tr>
 </tbody>
 </table>
diff --git a/doc/html/modelling/sidechain_reconstruction.html b/doc/html/modelling/sidechain_reconstruction.html
index 53ea062ed1d80e4c55f8f08c33b6d87de26fd2bd..6f940d4f2b9683b7243a8227dba538cb3b34452b 100644
--- a/doc/html/modelling/sidechain_reconstruction.html
+++ b/doc/html/modelling/sidechain_reconstruction.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Sidechain Reconstruction &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Sidechain Reconstruction &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Modelling Algorithms" href="algorithms.html" />
@@ -36,7 +37,7 @@
 <p>Two methods are provided to fully reconstruct sidechains of residues:</p>
 <ul class="simple">
 <li>the <a class="reference internal" href="#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal notranslate"><span class="pre">ReconstructSidechains()</span></code></a> function handles a full OST
-<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></li>
+<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></li>
 <li>the <a class="reference internal" href="#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructor</span></code></a> is linked to an all atom environment
 and used to reconstruct sidechains of single loops</li>
 </ul>
@@ -91,7 +92,7 @@ and used to reconstruct sidechains of single loops</li>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
 reconstruction gets directly applied on the structure itself.</li>
 <li><strong>keep_sidechains</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether complete sidechains in <em>ent</em> (i.e. 
 containing all required atoms) should be kept rigid
@@ -203,7 +204,7 @@ environment before calling this!</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</li>
 <li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of loop.</li>
 <li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain the loop belongs to.</li>
 <li><strong>start_resnum_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Starts of loops.</li>
diff --git a/doc/html/portableIO.html b/doc/html/portableIO.html
index fb4c10e0697802ef1fe597a5c97a168c14d95452..a6c32dc2b2b514df92920276cd8f0e9edc9ecd08 100644
--- a/doc/html/portableIO.html
+++ b/doc/html/portableIO.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Using Binary Files In ProMod3 &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Using Binary Files In ProMod3 &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="License" href="license.html" />
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 400d92030f69ae9d638f76c183d330d2c8b79f40..6e2f5e7db7d0a12594e206a9cd1d2dc018c249b8 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Python Module Index &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Python Module Index &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
 
diff --git a/doc/html/references.html b/doc/html/references.html
index a7cf963db411916dad7bf40f62986f3848c5c595..94e58f063eebaaeb2a754e2111048478bb764a6d 100644
--- a/doc/html/references.html
+++ b/doc/html/references.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>References &#8212; ProMod3 3.3.0 documentation</title>
+    <title>References &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Changelog" href="changelog.html" />
diff --git a/doc/html/scoring/all_atom_scorers.html b/doc/html/scoring/all_atom_scorers.html
index de7b370f9fe6a9c4f54473f63f259f8aed3046f2..4259699ea7dace262ea01a8318a41b144683a411 100644
--- a/doc/html/scoring/all_atom_scorers.html
+++ b/doc/html/scoring/all_atom_scorers.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>All Atom Scorers &#8212; ProMod3 3.3.0 documentation</title>
+    <title>All Atom Scorers &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Other Scoring Functions" href="other_scoring_functions.html" />
diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html
index 1c6e7ef03738a3a47531008b353601f329acef43..aaceae9f48df6c85dab28e76395c6fbf32a44335 100644
--- a/doc/html/scoring/backbone_score_env.html
+++ b/doc/html/scoring/backbone_score_env.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Backbone Score Environment &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Backbone Score Environment &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Backbone Scorers" href="backbone_scorers.html" />
@@ -58,8 +59,8 @@ task.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
 chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
 </tr>
 </tbody>
@@ -96,7 +97,7 @@ structural data was already set, all the existing data gets cleared first.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
 in <em>env_structure</em> are expected to be in the same
 order as the SEQRES items provided in constructor.</td>
 </tr>
@@ -120,7 +121,7 @@ positions.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Structural data to be set as environment.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</li>
 <li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</li>
 </ul>
 </td>
@@ -269,7 +270,7 @@ providing lists of integers.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -376,7 +377,7 @@ The constraint functions are built after the principle of QMEANDisCo.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</li>
 <li><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunctionType</span></code></a>) – Whether you want to assess pairwise distances between CA
 or CB atoms</li>
 </ul>
@@ -391,7 +392,7 @@ or CB atoms</li>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
 SEQRES and the second sequence the actual structural
 info. The second sequence must have a view attached.</td>
 </tr>
diff --git a/doc/html/scoring/backbone_scorers.html b/doc/html/scoring/backbone_scorers.html
index 24f2cd2ef3a9ef6a800d41c8d459d3e848b4d5f9..4cfd63fa5509f898946b2503bf70f9e2d8a4a079 100644
--- a/doc/html/scoring/backbone_scorers.html
+++ b/doc/html/scoring/backbone_scorers.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Backbone Scorers &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Backbone Scorers &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="All Atom Scorers" href="all_atom_scorers.html" />
@@ -370,7 +371,7 @@ called for every type of amino acids and for every <em>count</em> &lt;= <em>max_
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</li>
 <li><strong>count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of surrounding CB positions for which to set energy.</li>
 <li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
 </ul>
@@ -504,8 +505,8 @@ SetEnergy(aa2, aa1, bin, energy).</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
-<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
 <li><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</li>
 <li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
 </ul>
@@ -684,8 +685,8 @@ SetEnergy(aa2, aa1, dist_bin, beta_bin, alpha_bin, energy).</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
-<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
 <li><strong>dist_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</li>
 <li><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the alpha angle.</li>
 <li><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the beta angle.</li>
diff --git a/doc/html/scoring/index.html b/doc/html/scoring/index.html
index 606b2b56daee011aeca20c3498c8990756b6e429..070c044134c9af6ee0786c3debe00527e6e54c7f 100644
--- a/doc/html/scoring/index.html
+++ b/doc/html/scoring/index.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>scoring - Loop Scoring &#8212; ProMod3 3.3.0 documentation</title>
+    <title>scoring - Loop Scoring &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Backbone Score Environment" href="backbone_score_env.html" />
diff --git a/doc/html/scoring/other_scoring_functions.html b/doc/html/scoring/other_scoring_functions.html
index 2648f13f707bce27881de467b4c6be0e48baffe9..f9440a12361bd8b8a36a03957e004fe76d7eb989 100644
--- a/doc/html/scoring/other_scoring_functions.html
+++ b/doc/html/scoring/other_scoring_functions.html
@@ -6,7 +6,7 @@
   <head>
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     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Other Scoring Functions &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Other Scoring Functions &#8212; ProMod3 3.3.1 documentation</title>
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     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="loop - Loop Handling" href="../loop/index.html" />
diff --git a/doc/html/search.html b/doc/html/search.html
index 0e575bda06a6effc3c18a7919b846566d7248223..19e3491e8fbfe5a323d608623eb91895542be903 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
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     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Search &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Search &#8212; ProMod3 3.3.1 documentation</title>
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diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 9c6db87e7c87d959cc9603e6561f22232d7fc947..dcab7f12ef364767ed2eee252bde6744f56332ee 100644
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egin:[1,8,21,22,28,34,40],behalf:20,behav:[1,51],behaviour:[0,13,39,40,49,50,51],behind:8,being:[3,5,8,10,21,26,28,31,34,35,44,51],believ:53,bell:8,belong:[3,4,16,21,22,26,29,31,34,35,36,39,40,41,45,49,50],belov:26,below:[0,8,20,21,25,26,28,31,32,36,37,39,41,44,49],below_thre:26,benefici:20,besid:[2,4,10,13,26],best:[4,31,35,44],best_candid:31,beta:[9,22,33,41],beta_bin:41,better:[25,31,34,35,39,41],between:[1,3,10,13,22,25,26,28,29,31,32,34,35,36,37,39,40,41,42,43,44,45,49,50,51],beyond:13,bfactor:28,biasini2013:[19,38],biasini:38,bienert:38,big:[25,37],bilinearli:51,bin:[1,8,16,18,26,27,28,39,41,51],bin_siz:[28,51],binari:[1,4,8,16,17,25,26,27,28,39,41,51],bind:[0,3,13,20,28],bins_per_dimens:27,bioinformat:38,biol:38,biolog:38,biologi:[19,38],biophi:38,biopolym:38,bit:[1,8,16,31,35],bitwis:26,blank:8,blob:28,block:[3,30,45,47],blosum62:[13,23,26,28,40],boilerpl:20,bond:[0,3,9,22,25,26,32,33,35,36,38,41,47,49,50,51,54],bond_force_const:25,bond_length:[9,25],bool:[1,8,10,11,13,14,21,22,25,26,28,29,31,32,33,34,35,36,37,39,41,44,49,50,51],boost:[2,8,37],boost_librari:4,boost_root:2,bootstrap:[6,7],bore:34,both:[3,21,26,29,35,44,47,51],bound:[21,25,28,31,49,50],boundari:28,br_vinaparticl:49,bracket:20,bradlei:25,branch:[4,8,17],branchnam:16,brew:4,bridg:[24,25,32,35,36],briefli:16,bring:8,broken:1,bromin:49,broyden:35,bsd:20,bug:[3,8,16],bugfix:3,build:[1,3,4,6,7,8,16,18,19,25,28,30,34,44,45,47,48,50,54],build_disulfid:36,builder:2,buildfromrawmodel:[30,35],buildrawmodel:[0,3,30,31,35],buildsidechain:35,buildup:[47,49],built:[4,5,25,26,40,45],bunch:[1,13,16],bundl:20,bytecod:1,c_coord:9,c_num:29,c_p_vinaparticl:[49,50],c_po:[9,22,41],c_stem:[9,23,26,29,31,32,34],c_stem_plddt:28,c_stem_psi:34,c_str:37,c_ter:[32,50],c_vinaparticl:[49,50],ca_coord:9,ca_pairwise_funct:40,ca_po:[9,22],ca_pos_on:[43,44],ca_pos_two:[43,44],ca_posit:[28,44],ca_rmsd:[23,26],cach:[2,26,28],calcul:[8,22,26,27,28,31,32,33,34,39,40,41,42,44,45,46,47,49,50],calculateallatomscor:31,calculatebackbonescor:31,calculatelinearcombin:[31,34,39,41],calculatescor:[39,41,42],calculatescoreprofil:[39,41],calculatesequenceprofilescor:31,calculatestemrmsd:31,calculatestructureprofilescor:31,call:[1,2,4,8,11,13,14,15,16,21,25,26,27,29,31,33,34,35,36,37,39,40,41,49,50,51],callabl:[13,16],calpha:35,calul:27,came:8,can:[0,1,2,3,4,5,7,8,9,10,11,13,14,15,16,18,19,21,22,23,25,26,27,28,29,30,31,32,34,35,36,37,39,40,41,42,44,45,46,47,48,50,51,52,53],cand:35,candid:[3,30,33,34,35,54],cannot:[0,8,13,20,25,26,27,28,29,35,37,39,41,48,49,50,51],canutescu2003:[32,38,49],canutescu2003b:[38,39,41,43,44],canutescu:38,cap:10,capabl:[24,30,34],captur:1,carbon:[9,22,43,49,50],carbonyl:[49,50],care:[0,8,10,31,32,35,37,41],carlo:[0,3,10,28,31,34,35,46],carmsd:[22,23,26],carri:[8,11,20],cast:[28,37],categori:4,caus:[16,20,33],caution:21,caviti:26,cb_in_sidechain:50,cb_pack:[28,35,41],cb_packing_scor:37,cb_pairwise_funct:40,cb_po:22,cb_pos_on:[43,44],cb_pos_two:[43,44],cb_posit:44,cbeta:[28,31,34,35,41,42],cbeta_scor:[37,42],cbetaenvlisten:8,cbetascor:[8,35,37,42],cbpackingscor:[8,35,37,42],ccd:[3,30,31,34],ccdcloser:34,cdef:35,center:[33,49],central:[22,27,41],centroid:31,certain:[1,2,4,8,10,16,26,27,28,29,35,37,39,40,41],certainli:1,ch1particl:49,ch2particl:49,ch3particl:49,ch_name:26,chain:[0,8,13,21,22,23,24,28,29,31,34,35,36,38,39,40,41],chain_idx:[8,21,31,34,35,36,39,40,41],chain_idx_list:36,chain_idx_on:40,chain_idx_two:40,chain_index:[26,34,39],chain_indic:40,chain_nam:[26,35],chainhandl:[21,22,29],chainid:0,chakravarti:38,chakravarty1999:[26,38],challeng:28,chanc:[8,10,35],chang:[1,3,4,5,7,8,10,16,20,21,27,28,29,32,34,35,36,39],change_frequ:[10,34],changelog:[8,19],chapter:[29,33],charact:[13,20,26,28,35],charg:[8,20,21,25,32,49,50],charmm:[21,25,35],check:[0,1,2,3,5,8,11,13,14,16,22,25,26,30,32,34,35,37,50,51,54],check_dupl:28,check_io:37,check_xml:8,checkbasetyp:37,checker:7,checkfinalmodel:35,checkmagicnumb:37,checkout:[8,16],checktypes:37,chem:38,chemdict_tool:5,chemdicttool:7,chemic:[5,15,21,35,39],chemistri:[35,38],chemlib:[5,7],chi1:51,chi2:51,chi3:51,chi4:51,chi:51,child:13,childclass:1,chimerax:3,chlorin:49,chmod:8,choos:[20,31,34],chose:5,chosen:[0,13,34,35],chunk:28,chunk_byt:28,chunk_dir:28,cif:[0,5,7,13],ciiipgatcpgdyan:35,circumv:50,cis:[22,49,51],cl_vinaparticl:49,claim:20,clash:[3,28,31,32,34,35,39,41,42,44,47],clash_scor:42,clash_thresh:35,clashscor:[31,33,34,35,42],classic:48,claus:20,clean:[2,8,16],cleanli:37,clear:[14,21,22,31,35,40],clearenviron:[21,40],cleargap:29,clearpo:21,clearresidu:21,clip:13,clone:[8,18],close:[16,18,22,26,28,31,32,34,35,36,44],close_at:28,closed_posit:34,closegap:35,closelargedelet:35,closer:[3,26,30,31],closerbas:34,closesmalldelet:[32,35],closest:[28,35],closur:[32,35,38],clustal:[0,13],cluster:[3,31,37,40],cluster_thresh:[28,40],clutter:[1,8,26],cmake:[3,8,14,15,17,18,20,54],cmake_support:[4,8,16,20],cmakecach:2,cmakelist:[1,2,4,8,16],coars:8,code:[0,1,2,3,4,5,6,7,8,11,13,14,15,16,17,18,19,20,21,22,26,27,33,35,47,49,53],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egin:[1,8,21,22,28,34,40],behalf:20,behav:[1,51],behaviour:[0,13,39,40,49,50,51],behind:8,being:[3,5,8,10,21,26,28,31,34,35,44,51],believ:53,bell:8,belong:[3,4,16,21,22,26,29,31,34,35,36,39,40,41,45,49,50],belov:26,below:[0,8,20,21,25,26,28,31,32,36,37,39,41,44,49],below_thre:26,benefici:20,besid:[2,4,10,13,26],best:[4,31,35,44],best_candid:31,beta:[9,22,33,41],beta_bin:41,better:[25,31,34,35,39,41],between:[1,3,10,13,22,25,26,28,29,31,32,34,35,36,37,39,40,41,42,43,44,45,49,50,51],beyond:13,bfactor:28,biasini2013:[19,38],biasini:38,bienert:38,big:[25,37],bilinearli:51,bin:[1,8,16,18,26,27,28,39,41,51],bin_siz:[28,51],binari:[1,4,8,16,17,25,26,27,28,39,41,51],bind:[0,3,13,20,28],bins_per_dimens:27,bioinformat:38,biol:38,biolog:38,biologi:[19,38],biophi:38,biopolym:38,bit:[1,8,16,31,35],bitwis:26,blank:8,blob:28,block:[3,30,45,47],blosum62:[13,23,26,28,40],boilerpl:20,bond:[0,3,9,22,25,26,32,33,35,36,38,41,47,49,50,51,54],bond_force_const:25,bond_length:[9,25],bool:[1,8,10,11,13,14,21,22,25,26,28,29,31,32,33,34,35,36,37,39,41,44,49,50,51],boost:[2,8,37],boost_librari:4,boost_root:2,bootstrap:[6,7],bore:34,both:[3,21,26,29,35,44,47,51],bound:[21,25,28,31,49,50],boundari:28,br_vinaparticl:49,bracket:20,bradlei:25,branch:[4,8,17],branchnam:16,brew:4,bridg:[24,25,32,35,36],briefli:16,bring:8,broken:1,bromin:49,broyden:35,bsd:20,bug:[3,8,16],bugfix:3,build:[1,3,4,6,7,8,16,18,19,25,28,30,34,44,45,47,48,50,54],build_disulfid:36,builder:2,buildfromrawmodel:[30,35],buildrawmodel:[0,3,30,31,35],buildsidechain:35,buildup:[47,49],built:[4,5,25,26,40,45],bunch:[1,13,16],bundl:20,bytecod:1,c_coord:9,c_num:29,c_p_vinaparticl:[49,50],c_po:[9,22,41],c_stem:[9,23,26,29,31,32,34],c_stem_plddt:28,c_stem_psi:34,c_str:37,c_ter:[32,50],c_vinaparticl:[49,50],ca_coord:9,ca_pairwise_funct:40,ca_po:[9,22],ca_pos_on:[43,44],ca_pos_two:[43,44],ca_posit:[28,44],ca_rmsd:[23,26],cach:[2,26,28],calcul:[8,22,26,27,28,31,32,33,34,39,40,41,42,44,45,46,47,49,50],calculateallatomscor:31,calculatebackbonescor:31,calculatelinearcombin:[31,34,39,41],calculatescor:[39,41,42],calculatescoreprofil:[39,41],calculatesequenceprofilescor:31,calculatestemrmsd:31,calculatestructureprofilescor:31,call:[1,2,4,8,11,13,14,15,16,21,25,26,27,29,31,33,34,35,36,37,39,40,41,49,50,51],callabl:[13,16],calpha:35,calul:27,came:8,can:[0,1,2,3,4,5,7,8,9,10,11,13,14,15,16,18,19,21,22,23,25,26,27,28,29,30,31,32,34,35,36,37,39,40,41,42,44,45,46,47,48,50,51,52,53],cand:35,candid:[3,30,33,34,35,54],cannot:[0,8,13,20,25,26,27,28,29,35,37,39,41,48,49,50,51],canutescu2003:[32,38,49],canutescu2003b:[38,39,41,43,44],canutescu:38,cap:10,capabl:[24,30,34],captur:1,carbon:[9,22,43,49,50],carbonyl:[49,50],care:[0,8,10,31,32,35,37,41],carlo:[0,3,10,28,31,34,35,46],carmsd:[22,23,26],carri:[8,11,20],cast:[28,37],categori:4,caus:[16,20,33],caution:21,caviti:26,cb_in_sidechain:50,cb_pack:[28,35,41],cb_packing_scor:37,cb_pairwise_funct:40,cb_po:22,cb_pos_on:[43,44],cb_pos_two:[43,44],cb_posit:44,cbeta:[28,31,34,35,41,42],cbeta_scor:[37,42],cbetaenvlisten:8,cbetascor:[8,35,37,42],cbpackingscor:[8,35,37,42],ccd:[3,30,31,34],ccdcloser:34,cdef:35,center:[33,49],central:[22,27,41],centroid:31,certain:[1,2,4,8,10,16,26,27,28,29,35,37,39,40,41],certainli:1,ch1particl:49,ch2particl:49,ch3particl:49,ch_name:26,chain:[0,8,13,21,22,23,24,28,29,31,34,35,36,38,39,40,41],chain_idx:[8,21,31,34,35,36,39,40,41],chain_idx_list:36,chain_idx_on:40,chain_idx_two:40,chain_index:[26,34,39],chain_indic:40,chain_nam:[26,35],chainhandl:[21,22,29],chainid:0,chakravarti:38,chakravarty1999:[26,38],challeng:28,chanc:[8,10,35],chang:[1,3,4,5,7,8,10,16,20,21,27,28,29,32,34,35,36,39],change_frequ:[10,34],changelog:[8,19],chapter:[29,33],charact:[13,20,26,28,35],charg:[8,20,21,25,32,49,50],charmm:[21,25,35],check:[0,1,2,3,5,8,11,13,14,16,22,25,26,30,32,34,35,37,50,51,54],check_dupl:28,check_io:37,check_xml:8,checkbasetyp:37,checker:7,checkfinalmodel:35,checkmagicnumb:37,checkout:[8,16],checktypes:37,chem:38,chemdict_tool:5,chemdicttool:7,chemic:[5,15,21,35,39],chemistri:[35,38],chemlib:[5,7],chi1:51,chi2:51,chi3:51,chi4:51,chi:51,child:13,childclass:1,chimerax:3,chlorin:49,chmod:8,choos:[20,31,34],chose:5,chosen:[0,13,34,35],chunk:28,chunk_byt:28,chunk_dir:28,cif:[0,5,7,13],ciiipgatcpgdyan:35,circumv:50,cis:[22,49,51],cl_vinaparticl:49,claim:20,clash:[3,28,31,32,34,35,39,41,42,44,47],clash_scor:42,clash_thresh:35,clashscor:[31,33,34,35,42],classic:48,claus:20,clean:[2,8,16],cleanli:37,clear:[14,21,22,31,35,40],clearenviron:[21,40],cleargap:29,clearpo:21,clearresidu:21,clip:13,clone:[8,18],close:[16,18,22,26,28,31,32,34,35,36,44],close_at:28,closed_posit:34,closegap:35,closelargedelet:35,closer:[3,26,30,31],closerbas:34,closesmalldelet:[32,35],closest:[28,35],closur:[32,35,38],clustal:[0,13],cluster:[3,31,37,40],cluster_thresh:[28,40],clutter:[1,8,26],cmake:[3,8,14,15,17,18,20,54],cmake_support:[4,8,16,20],cmakecach:2,cmakelist:[1,2,4,8,16],coars:8,code:[0,1,2,3,4,5,6,7,8,11,13,14,15,16,17,18,19,20,21,22,26,27,33,35,47,49,53],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Actions","<code class=\"docutils literal notranslate\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3\u2019s Share Of CMake","Docker","ProMod3 and Containers","Singularity","Contributing","Geometry functions","Graph Minimizer","<code class=\"docutils literal notranslate\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal notranslate\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal notranslate\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"docutils literal notranslate\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","ProMod3 Setup","Documentation For Developers","Getting Started","ProMod3","License","Handling All Atom Positions","Representing Loops","<code class=\"docutils literal notranslate\"><span class=\"pre\">loop</span></code> - Loop 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Constructor","Rotamer Library","Subrotamer Optimization","Contributing","Documentation For Users"],titleterms:{"class":[21,22,26,27,29,31,36,39,40,41],"default":35,"function":[4,9,11,12,29,36,40,43,49,50],For:[4,11,17,54],Into:32,The:[1,5,7,16,21,22,26,27,31,35,36,45,49,50,51],Using:[2,37],With:33,acid:[21,25,27],action:[0,1,4,5,8],actiontestcas:1,afdb:28,algorithm:28,align:35,all:[21,32,39],allatomclashscor:39,allatomenv:21,allatomenvposit:21,allatominteractionscor:39,allatomoverallscor:39,allatompackingscor:39,allatomposit:21,allatomscor:39,amino:[21,25,27],angl:27,api:1,app:7,argument:13,atom:[21,32,39],avail:7,backbon:[32,40,41,51],backbonelist:22,backboneoverallscor:41,backbonescor:41,backbonescoreenv:40,base:[26,39,41],baseclass:50,binari:37,block:[28,49],bond:44,branch:16,build:[0,2,5,35,49],can:49,candid:31,cbetascor:41,cbpackingscor:41,ccd:32,chain:26,changelog:3,check:33,clashscor:41,closer:34,cmake:[1,2,4,16],code:37,command:13,compound:[5,7],configur:51,construct:40,constructor:50,contain:6,contribut:[8,53],conveni:40,cooler:34,core:12,creat:[1,25],data:[26,37],databas:26,defin:[26,27],definit:4,depend:[2,51],detect:33,develop:17,dihedr:27,directori:16,distinguish:21,disulfid:44,docker:5,document:[4,8,17,19,54],entri:51,environ:40,evalu:44,everyth:11,exampl:[31,37],execut:[1,5],exisit:37,extend:29,featur:[8,26],fiddl:35,file:[11,37],find:26,finder:28,fit:32,forcefield:25,fragment:26,frame:45,from:43,gap:[29,32],gener:[25,34],geometr:26,geometri:9,get:[18,49],git:16,graph:[10,46],group:49,handl:[21,23,29,31,35],have:1,hbondscor:41,header:37,helper:11,hook:16,how:[8,49],imag:5,instal:2,integr:1,introduct:[4,11,13],issu:8,keep:31,kic:32,librari:[5,7,48,51],licens:[8,20],line:13,load:[24,48],lookup:25,loop:[22,23,25,31,32,34,42],loopcandid:31,mainten:4,make:[1,2],messag:11,minim:10,model:[0,18,28,30,31,33,35,47],modul:[4,8],mol:25,molprob:33,motif:28,must:1,non:[33,51],novo:[28,34],object:[24,34,45],optim:52,ost:25,other:43,output:1,own:[5,8],pairwis:40,pairwisescor:41,pars:13,parser:13,part:45,parti:8,particl:49,pipelin:[18,35],planar:33,pm3argpars:13,portabl:37,posit:21,precomput:24,profil:14,promod3:[0,2,4,5,6,8,12,16,18,19,37],protein:30,psipredpredict:26,punch:33,quick:8,raw:35,reconstruct:36,reducedscor:41,refer:38,registri:5,relax:32,releas:3,repres:[22,49],rigid:[28,45],ring:33,rotam:[46,48,49,50,51],rotamerconstructor:50,rotamerid:49,run:[1,2,5,18],runtim:14,sampl:27,sampler:[27,34],score:[31,40,42,43,49,50],scorer:[8,34,39,41],script:[1,5,8],scwrl3:[43,49],scwrl4:49,sequenc:26,setcompoundschemlib:15,setup:16,share:[4,8,11],sidechain:[0,36,47,49],sidechainreconstructiondata:36,sidechainreconstructor:36,singular:7,smallest:49,specif:50,ssagreementscor:41,stage:16,start:[8,18],step:35,structur:[16,26],subclass:1,subrotam:52,system:25,test:[1,4,8,11],test_act:1,third:8,torsion:27,torsionscor:41,track:31,triplet:27,type:51,unit:[1,4,8],user:54,vina:49,write:8,your:8}})
\ No newline at end of file
diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html
index 0ab78f1095cb968d4b9a1304c5051b111f246d80..0b1d32367613367ccd9963f462f0294ab46c8387 100644
--- a/doc/html/sidechain/disulfid.html
+++ b/doc/html/sidechain/disulfid.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Disulfid Bond Evaluation &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Disulfid Bond Evaluation &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Loading Rotamer Libraries" href="loading.html" />
@@ -66,10 +67,10 @@ rotamers to the result of the geometric expression.</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>rotamer_one</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – First rotamer</li>
 <li><strong>rotamer_two</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – Second rotamer</li>
-<li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</li>
-<li><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</li>
-<li><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</li>
-<li><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</li>
+<li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</li>
+<li><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</li>
+<li><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</li>
+<li><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</li>
 </ul>
 </td>
 </tr>
@@ -102,8 +103,8 @@ possible, the one with the optimal sum of scores gets estimated.</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>rotamer_groups</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
 <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>/<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a>) – Every group represents a cysteine</li>
-<li><strong>ca_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</li>
-<li><strong>cb_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</li>
+<li><strong>ca_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</li>
+<li><strong>cb_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</li>
 <li><strong>score_threshold</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The score two rotamers must have to be considered
 as a disulfid bond</li>
 <li><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to true and the input consists of flexible
diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html
index 0c4e69f76d9f06ced8b62d5b0b2c9c280f2a3f94..edea19a3247e3b722dcf1ad18c359b6b407ff0f3 100644
--- a/doc/html/sidechain/frame.html
+++ b/doc/html/sidechain/frame.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Frame - The Rigid Part &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Frame - The Rigid Part &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Rotamer Constructor" href="rotamer_constructor.html" />
diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html
index cc59c634e77b3fa91f1f7a6d51c173b2fde12acf..e2d8d5341bb8a2674ea6aa3c4c0193f1c9209f50 100644
--- a/doc/html/sidechain/graph.html
+++ b/doc/html/sidechain/graph.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Rotamer Graph &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Rotamer Graph &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Disulfid Bond Evaluation" href="disulfid.html" />
diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html
index 855b5a7cd5b033add84bdc7877e501e409fa439b..95b85c1a42d228363605f6ca5fadcc02e63e3df0 100644
--- a/doc/html/sidechain/index.html
+++ b/doc/html/sidechain/index.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>sidechain - Sidechain Modelling &#8212; ProMod3 3.3.0 documentation</title>
+    <title>sidechain - Sidechain Modelling &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Representing Sidechains - Rotamers &amp; Co." href="rotamer.html" />
diff --git a/doc/html/sidechain/loading.html b/doc/html/sidechain/loading.html
index a0efe0432eda3eaad35edccfd91602a29bdd5a63..331b5e35c793d00857c02ca38c91cbe82aa43753 100644
--- a/doc/html/sidechain/loading.html
+++ b/doc/html/sidechain/loading.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Loading Rotamer Libraries &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Loading Rotamer Libraries &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Subrotamer Optimization" href="subrotamer_optimizer.html" />
diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
index 3ae62751fe7a39fba0b3534fddd0e8f218f99341..4f5f95470c67447688426c01f224c85ac5785104 100644
--- a/doc/html/sidechain/rotamer.html
+++ b/doc/html/sidechain/rotamer.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Representing Sidechains - Rotamers &amp; Co. &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Representing Sidechains - Rotamers &amp; Co. &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Frame - The Rigid Part" href="frame.html" />
@@ -89,7 +90,7 @@ or as <code class="docutils literal notranslate"><span class="pre">promod3.sidec
 <div class="section" id="how-can-i-get-an-id">
 <h3>How can I get an ID?<a class="headerlink" href="#how-can-i-get-an-id" title="Permalink to this headline">¶</a></h3>
 <p>The RotamerID enum can directly be accessed from Python. Two convenient
-functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
+functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
 or from amino acid three letter codes.</p>
 <dl class="method">
 <dt id="promod3.sidechain.TLCToRotID">
@@ -114,12 +115,12 @@ exactly the naming convention defined above.</p>
 <dd><p>Directly translates <strong>aa</strong> into a RotamerID. Note, that it is not possible
 to generate special IDs this way
 (e.g. HSD, HSE or the special prolines/cysteins) since they’re simply not
-defined in <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+defined in <a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</td>
 </tr>
@@ -217,7 +218,7 @@ evaluated by the underlying scoring function.</td>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The position of the particle</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -275,7 +276,7 @@ function</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</li>
 <li><strong>particle_type</strong> (<a class="reference internal" href="#promod3.sidechain.SCWRL4ParticleType" title="promod3.sidechain.SCWRL4ParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">SCWRL4ParticleType</span></code></a>) – The type of the particle</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
 <li><strong>charge</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The charge of the particle, relevant for the hydrogen
 bond term</li>
 <li><strong>lone_pairs</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – Direction of all possible lone pairs of the particle,
@@ -284,7 +285,7 @@ particle is a potential hydrogen bond acceptor.
 An example would be the Serine OG atom, where you can
 represent the two lone pairs with vectors pointing
 from the OG position towards the lone pair centers.</li>
-<li><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle,
+<li><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle,
 relevant for the hydrogen bond term. If set, the
 particle is a potential hydrogen bond donor. An
 example would be the Serine HG hydrogen. The
@@ -316,7 +317,7 @@ function</p>
 <li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</li>
 <li><strong>radius</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The hard-sphere radius of the particle, relevant for the
 repulsion term.</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
 </ul>
 </td>
 </tr>
@@ -428,7 +429,7 @@ function</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</li>
 <li><strong>radius</strong> (<a class="reference internal" href="#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>) – The type of the particle</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
 </ul>
 </td>
 </tr>
@@ -506,7 +507,7 @@ in this process.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
 <li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
 <strong>res</strong></li>
 <li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of <strong>res</strong>. Nothing happens in case of the
@@ -782,7 +783,7 @@ No atoms are removed from <strong>res</strong> in this process.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
 <li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
 the sidechain</li>
 <li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
@@ -1182,7 +1183,7 @@ particles of the same residue.</li>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Rotamer index</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
 <li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
 the sidechain</li>
 <li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
@@ -1316,7 +1317,7 @@ particles of the same residue.</li>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Rotamer index</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
 <li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
 the sidechain</li>
 <li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html
index fc7229f75dd6e2860034418835fc85037e9fc22b..fe7e92accec4a51a4fb9bc4cfccfdb913df87a62 100644
--- a/doc/html/sidechain/rotamer_constructor.html
+++ b/doc/html/sidechain/rotamer_constructor.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Rotamer Constructor &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Rotamer Constructor &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Rotamer Library" href="rotamer_lib.html" />
@@ -68,7 +69,7 @@ an interface implemented by scoring function specific constructors
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</li>
 <li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the required backbone atoms</li>
 <li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
 extract the required backbone atoms</li>
@@ -123,7 +124,7 @@ don’t show up in a rotamer).</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
 <li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</li>
 <li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
 extract the backbone positions</li>
@@ -166,7 +167,7 @@ you observe in a rotamer).</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
 <li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</li>
 <li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
 extract the backbone positions</li>
@@ -254,7 +255,7 @@ any rotamers for ALA and GLY.</td>
 <dl class="method">
 <dt id="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue">
 <code class="descname">ConstructFrameResidue</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
 This can be useful to mark a region occupied by a ligand. Note, that
 there won’t be any parametrization of hbonds in this function. All heavy
 atoms of the residue will be represented as carbons and hydrogens are
@@ -264,7 +265,7 @@ skipped.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
 construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</li>
 <li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
 </ul>
@@ -280,7 +281,7 @@ construct a <a class="reference internal" href="frame.html#promod3.sidechain.Fra
 <dl class="method">
 <dt id="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic">
 <code class="descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em>, <em>comp_lib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
 a heuristic treatment of the atoms based on the passed compounds library.
 This is meant to be used as an alternative to <a class="reference internal" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue"><code class="xref py py-func docutils literal notranslate"><span class="pre">ConstructFrameResidue()</span></code></a>,
 which will be called by this function if the residue is not known by the given
@@ -298,10 +299,10 @@ as in the <code class="xref py py-class docutils literal notranslate"><span clas
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
 construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</li>
 <li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
-<li><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</li>
+<li><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</li>
 </ul>
 </td>
 </tr>
@@ -461,7 +462,7 @@ to be assigned</li>
 <dl class="method">
 <dt id="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic">
 <code class="descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em>res</em>, <em>res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
 a heuristic treatment of the atoms. It is important that the residue has
 proper bonds assigned, as they influence the atom typing procedure.
 Furthermore, you need hydrogens to automatically estimate the correct
@@ -479,7 +480,7 @@ If the atom has the bool properties “is_hbond_acceptor” AND
 in <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>. If the generic properties are not set,
 every oxygen is assumed to be an hbond acceptor. But only an hbond donor
 if its bound to a hydrogen (or deuterium). You can set the generic
-properties for an <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.AtomHandle</span></code></a> by calling
+properties for an <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.AtomHandle</span></code></a> by calling
 at.SetBoolProp(“is_hbond_donor”, False) and
 at.SetBoolProp(“is_hbond_acceptor”, True). An oxygen with those
 generic properties is assigned O_A_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</li>
@@ -503,7 +504,7 @@ corresponding <a class="reference internal" href="rotamer.html#promod3.sidechain
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
 <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></li>
 <li><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index that is set in <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></li>
 </ul>
@@ -525,7 +526,7 @@ as in the <a class="reference internal" href="#promod3.sidechain.VINARotamerCons
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
 <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a></td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a></td>
@@ -545,7 +546,7 @@ contains the atoms from <em>residue</em>.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
 <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a></td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a></td>
diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
index b2f7c4e36626f8ea03dbea899ead36b5eda4d1d4..b80adf5fcd6fc600a1a69f50ef35dca9e5b91c9c 100644
--- a/doc/html/sidechain/rotamer_lib.html
+++ b/doc/html/sidechain/rotamer_lib.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Rotamer Library &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Rotamer Library &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Rotamer Graph" href="graph.html" />
@@ -433,7 +434,7 @@ NaN.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></td>
 </tr>
@@ -457,7 +458,7 @@ are NaN.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</li>
 <li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – The identity of the returned <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></li>
 </ul>
 </td>
diff --git a/doc/html/sidechain/subrotamer_optimizer.html b/doc/html/sidechain/subrotamer_optimizer.html
index c1ae5456ea803a5af66a4d12bbfd122efe321a03..949fd907f452a5907e0f0998185ae9d8e5996a1a 100644
--- a/doc/html/sidechain/subrotamer_optimizer.html
+++ b/doc/html/sidechain/subrotamer_optimizer.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Subrotamer Optimization &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Subrotamer Optimization &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="scoring - Loop Scoring" href="../scoring/index.html" />
diff --git a/doc/html/user_contributions.html b/doc/html/user_contributions.html
index 109d865d4bafda395c30bb65af8b2f9c7a6bf7d5..49966f020f6e8e44efb4b2b91ada8de7565b709a 100644
--- a/doc/html/user_contributions.html
+++ b/doc/html/user_contributions.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Contributing &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Contributing &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Documentation For Developers" href="developers.html" />
diff --git a/doc/html/users.html b/doc/html/users.html
index 82c3ffa195f703025db6ebc0aa823dcc98d19534..bdc7e621c50e2c92c330c6c9c07997bc491343cb 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Documentation For Users &#8212; ProMod3 3.3.0 documentation</title>
+    <title>Documentation For Users &#8212; ProMod3 3.3.1 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -14,6 +14,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="_static/language_data.js"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Getting Started" href="gettingstarted.html" />
diff --git a/doc/tests/scripts/model.pdb b/doc/tests/scripts/model.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..b5ea368f1b2291f9882223d144bb28d67622e9a8
--- /dev/null
+++ b/doc/tests/scripts/model.pdb
@@ -0,0 +1,329 @@
+ATOM      1  N   THR A   1      17.058  14.169   3.566  1.00 13.79           N  
+ATOM      2  CA  THR A   1      16.973  12.869   4.357  1.00 10.80           C  
+ATOM      3  C   THR A   1      15.717  12.792   5.167  1.00  9.19           C  
+ATOM      4  O   THR A   1      15.267  13.818   5.673  1.00  9.85           O  
+ATOM      5  CB  THR A   1      18.173  12.733   5.294  1.00 13.02           C  
+ATOM      6  OG1 THR A   1      19.350  12.622   4.511  1.00 15.06           O  
+ATOM      7  CG2 THR A   1      18.155  11.517   6.244  1.00 14.23           C  
+ATOM      8  N   THR A   2      15.107  11.597   5.303  1.00  7.81           N  
+ATOM      9  CA  THR A   2      13.850  11.417   6.016  1.00  8.31           C  
+ATOM     10  C   THR A   2      14.082  10.710   7.328  1.00  5.80           C  
+ATOM     11  O   THR A   2      14.790   9.711   7.408  1.00  6.94           O  
+ATOM     12  CB  THR A   2      12.773  10.665   5.243  1.00 10.32           C  
+ATOM     13  OG1 THR A   2      13.155   9.360   4.828  1.00 12.81           O  
+ATOM     14  CG2 THR A   2      12.512  11.409   3.939  1.00 11.90           C  
+ATOM     15  N   CYS A   3      13.486  11.239   8.408  1.00  5.24           N  
+ATOM     16  CA  CYS A   3      13.663  10.729   9.754  1.00  5.39           C  
+ATOM     17  C   CYS A   3      12.279  10.484  10.319  1.00  4.45           C  
+ATOM     18  O   CYS A   3      11.411  11.343  10.183  1.00  6.54           O  
+ATOM     19  CB  CYS A   3      14.383  11.769  10.648  1.00  5.99           C  
+ATOM     20  SG  CYS A   3      15.922  12.435   9.949  1.00  0.00           S  
+ATOM     21  N   CYS A   4      11.999   9.322  10.938  1.00  3.90           N  
+ATOM     22  CA  CYS A   4      10.657   8.992  11.396  1.00  4.24           C  
+ATOM     23  C   CYS A   4      10.614   8.772  12.908  1.00  3.72           C  
+ATOM     24  O   CYS A   4      11.593   8.320  13.497  1.00  5.30           O  
+ATOM     25  CB  CYS A   4      10.102   7.733  10.692  1.00  4.41           C  
+ATOM     26  SG  CYS A   4       9.789   7.997   8.918  1.00  0.00           S  
+ATOM     27  N   PRO A   5       9.505   9.080  13.592  1.00  3.96           N  
+ATOM     28  CA  PRO A   5       9.448   9.070  15.054  1.00  4.25           C  
+ATOM     29  C   PRO A   5       9.251   7.675  15.608  1.00  4.96           C  
+ATOM     30  O   PRO A   5       9.386   7.479  16.814  1.00  7.44           O  
+ATOM     31  CB  PRO A   5       8.230   9.953  15.377  1.00  5.11           C  
+ATOM     32  CG  PRO A   5       7.326   9.804  14.155  1.00  5.24           C  
+ATOM     33  CD  PRO A   5       8.341   9.760  13.022  1.00  5.20           C  
+ATOM     34  N   SER A   6       8.879   6.698  14.769  1.00  4.83           N  
+ATOM     35  CA  SER A   6       8.653   5.339  15.213  1.00  4.45           C  
+ATOM     36  C   SER A   6       8.769   4.410  14.030  1.00  4.99           C  
+ATOM     37  O   SER A   6       8.733   4.831  12.877  1.00  4.61           O  
+ATOM     38  CB  SER A   6       7.283   5.108  15.930  1.00  5.05           C  
+ATOM     39  OG  SER A   6       6.146   5.113  15.053  1.00  6.39           O  
+ATOM     40  N   ILE A   7       8.892   3.091  14.300  1.00  4.94           N  
+ATOM     41  CA  ILE A   7       8.902   2.051  13.277  1.00  6.33           C  
+ATOM     42  C   ILE A   7       7.613   2.022  12.458  1.00  5.32           C  
+ATOM     43  O   ILE A   7       7.644   1.935  11.236  1.00  6.85           O  
+ATOM     44  CB  ILE A   7       9.210   0.696  13.915  1.00  8.43           C  
+ATOM     45  CG1 ILE A   7      10.706   0.687  14.311  1.00  9.78           C  
+ATOM     46  CG2 ILE A   7       8.869  -0.480  12.968  1.00 11.70           C  
+ATOM     47  CD1 ILE A   7      11.139  -0.531  15.134  1.00  9.92           C  
+ATOM     48  N   VAL A   8       6.437   2.160  13.117  1.00  5.02           N  
+ATOM     49  CA  VAL A   8       5.133   2.251  12.460  1.00  6.93           C  
+ATOM     50  C   VAL A   8       5.066   3.419  11.487  1.00  5.39           C  
+ATOM     51  O   VAL A   8       4.619   3.284  10.349  1.00  6.30           O  
+ATOM     52  CB  VAL A   8       4.013   2.392  13.499  1.00  9.64           C  
+ATOM     53  CG1 VAL A   8       2.674   2.856  12.881  1.00 13.85           C  
+ATOM     54  CG2 VAL A   8       3.807   1.039  14.203  1.00 11.97           C  
+ATOM     55  N   ALA A   9       5.561   4.603  11.904  1.00  3.73           N  
+ATOM     56  CA  ALA A   9       5.593   5.781  11.066  1.00  3.56           C  
+ATOM     57  C   ALA A   9       6.462   5.613   9.825  1.00  4.13           C  
+ATOM     58  O   ALA A   9       6.064   5.996   8.723  1.00  4.36           O  
+ATOM     59  CB  ALA A   9       6.048   6.985  11.906  1.00  4.80           C  
+ATOM     60  N   ARG A  10       7.647   4.976   9.963  1.00  3.73           N  
+ATOM     61  CA  ARG A  10       8.499   4.612   8.843  1.00  3.38           C  
+ATOM     62  C   ARG A  10       7.854   3.632   7.870  1.00  3.47           C  
+ATOM     63  O   ARG A  10       7.907   3.808   6.658  1.00  4.67           O  
+ATOM     64  CB  ARG A  10       9.841   4.010   9.325  1.00  3.95           C  
+ATOM     65  CG  ARG A  10      10.806   3.565   8.198  1.00  4.55           C  
+ATOM     66  CD  ARG A  10      11.252   4.676   7.243  1.00  5.89           C  
+ATOM     67  NE  ARG A  10      12.159   5.572   8.019  1.00  6.20           N  
+ATOM     68  CZ  ARG A  10      12.820   6.616   7.512  1.00  7.52           C  
+ATOM     69  NH1 ARG A  10      12.666   6.960   6.233  1.00 10.68           N  
+ATOM     70  NH2 ARG A  10      13.624   7.329   8.286  1.00  9.48           N  
+ATOM     71  N   SER A  11       7.196   2.575   8.390  1.00  5.19           N  
+ATOM     72  CA  SER A  11       6.481   1.606   7.566  1.00  4.60           C  
+ATOM     73  C   SER A  11       5.350   2.226   6.765  1.00  4.84           C  
+ATOM     74  O   SER A  11       5.209   1.984   5.568  1.00  5.84           O  
+ATOM     75  CB  SER A  11       5.907   0.439   8.404  1.00  5.91           C  
+ATOM     76  OG  SER A  11       6.971  -0.314   8.986  1.00  8.38           O  
+ATOM     77  N   ASN A  12       4.555   3.111   7.401  1.00  3.54           N  
+ATOM     78  CA  ASN A  12       3.526   3.896   6.735  1.00  4.57           C  
+ATOM     79  C   ASN A  12       4.089   4.861   5.690  1.00  4.14           C  
+ATOM     80  O   ASN A  12       3.526   5.027   4.612  1.00  5.52           O  
+ATOM     81  CB  ASN A  12       2.682   4.695   7.759  1.00  6.42           C  
+ATOM     82  CG  ASN A  12       1.855   3.749   8.622  1.00  8.25           C  
+ATOM     83  OD1 ASN A  12       1.587   2.604   8.263  1.00 12.72           O  
+ATOM     84  ND2 ASN A  12       1.391   4.246   9.794  1.00  9.92           N  
+ATOM     85  N   PHE A  13       5.243   5.511   5.979  1.00  3.43           N  
+ATOM     86  CA  PHE A  13       5.953   6.388   5.058  1.00  3.49           C  
+ATOM     87  C   PHE A  13       6.374   5.670   3.781  1.00  3.40           C  
+ATOM     88  O   PHE A  13       6.177   6.176   2.680  1.00  4.07           O  
+ATOM     89  CB  PHE A  13       7.201   6.982   5.781  1.00  5.48           C  
+ATOM     90  CG  PHE A  13       7.975   7.989   4.964  1.00  5.57           C  
+ATOM     91  CD1 PHE A  13       8.957   7.576   4.042  1.00  6.99           C  
+ATOM     92  CD2 PHE A  13       7.727   9.360   5.111  1.00  6.52           C  
+ATOM     93  CE1 PHE A  13       9.600   8.508   3.218  1.00  8.20           C  
+ATOM     94  CE2 PHE A  13       8.396  10.297   4.314  1.00  6.34           C  
+ATOM     95  CZ  PHE A  13       9.292   9.866   3.335  1.00  6.84           C  
+ATOM     96  N   ASN A  14       6.934   4.451   3.911  1.00  3.64           N  
+ATOM     97  CA  ASN A  14       7.340   3.628   2.785  1.00  4.31           C  
+ATOM     98  C   ASN A  14       6.170   3.203   1.900  1.00  3.98           C  
+ATOM     99  O   ASN A  14       6.267   3.250   0.681  1.00  6.22           O  
+ATOM    100  CB  ASN A  14       8.141   2.389   3.256  1.00  5.81           C  
+ATOM    101  CG  ASN A  14       9.498   2.826   3.806  1.00  6.82           C  
+ATOM    102  OD1 ASN A  14      10.007   3.912   3.542  1.00  9.43           O  
+ATOM    103  ND2 ASN A  14      10.145   1.922   4.585  1.00  8.21           N  
+ATOM    104  N   VAL A  15       5.013   2.824   2.494  1.00  3.76           N  
+ATOM    105  CA  VAL A  15       3.788   2.560   1.737  1.00  3.98           C  
+ATOM    106  C   VAL A  15       3.265   3.803   1.032  1.00  3.80           C  
+ATOM    107  O   VAL A  15       2.896   3.764  -0.139  1.00  4.85           O  
+ATOM    108  CB  VAL A  15       2.693   1.938   2.599  1.00  4.71           C  
+ATOM    109  CG1 VAL A  15       1.361   1.800   1.825  1.00  6.67           C  
+ATOM    110  CG2 VAL A  15       3.177   0.544   3.039  1.00  6.26           C  
+ATOM    111  N   CYS A  16       3.274   4.969   1.712  1.00  3.79           N  
+ATOM    112  CA  CYS A  16       2.864   6.239   1.129  1.00  3.54           C  
+ATOM    113  C   CYS A  16       3.718   6.650  -0.072  1.00  3.48           C  
+ATOM    114  O   CYS A  16       3.231   7.265  -1.010  1.00  4.63           O  
+ATOM    115  CB  CYS A  16       2.855   7.367   2.202  1.00  4.58           C  
+ATOM    116  SG  CYS A  16       1.908   8.867   1.760  1.00  0.00           S  
+ATOM    117  N   ARG A  17       5.022   6.292  -0.076  1.00  3.99           N  
+ATOM    118  CA  ARG A  17       5.930   6.534  -1.184  1.00  3.83           C  
+ATOM    119  C   ARG A  17       5.812   5.585  -2.365  1.00  3.79           C  
+ATOM    120  O   ARG A  17       6.301   5.914  -3.443  1.00  5.39           O  
+ATOM    121  CB  ARG A  17       7.400   6.484  -0.701  1.00  4.11           C  
+ATOM    122  CG  ARG A  17       7.776   7.683   0.187  1.00  4.69           C  
+ATOM    123  CD  ARG A  17       7.944   8.995  -0.584  1.00  5.10           C  
+ATOM    124  NE  ARG A  17       9.234   8.890  -1.326  1.00  4.71           N  
+ATOM    125  CZ  ARG A  17       9.543   9.583  -2.428  1.00  5.28           C  
+ATOM    126  NH1 ARG A  17       8.671  10.381  -3.038  1.00  6.67           N  
+ATOM    127  NH2 ARG A  17      10.776   9.474  -2.924  1.00  6.41           N  
+ATOM    128  N   LEU A  18       5.148   4.416  -2.231  1.00  4.70           N  
+ATOM    129  CA  LEU A  18       4.996   3.463  -3.327  1.00  5.46           C  
+ATOM    130  C   LEU A  18       4.342   3.996  -4.610  1.00  5.13           C  
+ATOM    131  O   LEU A  18       4.869   3.695  -5.680  1.00  5.55           O  
+ATOM    132  CB  LEU A  18       4.208   2.196  -2.900  1.00  6.47           C  
+ATOM    133  CG  LEU A  18       4.950   1.171  -2.026  1.00  7.43           C  
+ATOM    134  CD1 LEU A  18       3.955   0.076  -1.601  1.00  8.70           C  
+ATOM    135  CD2 LEU A  18       6.147   0.549  -2.760  1.00  9.39           C  
+ATOM    136  N   PRO A  19       3.254   4.780  -4.621  1.00  4.28           N  
+ATOM    137  CA  PRO A  19       2.734   5.368  -5.849  1.00  5.38           C  
+ATOM    138  C   PRO A  19       3.551   6.545  -6.354  1.00  6.30           C  
+ATOM    139  O   PRO A  19       3.236   7.055  -7.422  1.00  9.62           O  
+ATOM    140  CB  PRO A  19       1.282   5.773  -5.523  1.00  5.87           C  
+ATOM    141  CG  PRO A  19       1.141   5.751  -3.996  1.00  6.47           C  
+ATOM    142  CD  PRO A  19       2.336   4.948  -3.491  1.00  6.45           C  
+ATOM    143  N   GLY A  20       4.580   7.018  -5.617  1.00  4.94           N  
+ATOM    144  CA  GLY A  20       5.391   8.149  -6.052  1.00  5.39           C  
+ATOM    145  C   GLY A  20       5.046   9.438  -5.377  1.00  5.03           C  
+ATOM    146  O   GLY A  20       5.551  10.488  -5.751  1.00  7.34           O  
+ATOM    147  N   THR A  21       4.191   9.388  -4.333  1.00  4.10           N  
+ATOM    148  CA  THR A  21       3.790  10.539  -3.524  1.00  3.94           C  
+ATOM    149  C   THR A  21       4.994  11.363  -3.054  1.00  3.96           C  
+ATOM    150  O   THR A  21       5.943  10.768  -2.527  1.00  5.82           O  
+ATOM    151  CB  THR A  21       2.992  10.121  -2.295  1.00  4.13           C  
+ATOM    152  OG1 THR A  21       1.942   9.232  -2.646  1.00  5.45           O  
+ATOM    153  CG2 THR A  21       2.311  11.309  -1.618  1.00  5.41           C  
+ATOM    154  N   PRO A  22       5.091  12.685  -3.239  1.00  5.04           N  
+ATOM    155  CA  PRO A  22       6.160  13.520  -2.704  1.00  4.69           C  
+ATOM    156  C   PRO A  22       6.462  13.281  -1.237  1.00  4.19           C  
+ATOM    157  O   PRO A  22       5.532  13.092  -0.455  1.00  4.47           O  
+ATOM    158  CB  PRO A  22       5.692  14.964  -2.949  1.00  7.12           C  
+ATOM    159  CG  PRO A  22       4.707  14.888  -4.116  1.00  7.03           C  
+ATOM    160  CD  PRO A  22       4.163  13.460  -4.064  1.00  4.90           C  
+ATOM    161  N   GLU A  23       7.740  13.333  -0.819  1.00  5.16           N  
+ATOM    162  CA  GLU A  23       8.148  13.128   0.559  1.00  5.31           C  
+ATOM    163  C   GLU A  23       7.491  14.077   1.558  1.00  4.11           C  
+ATOM    164  O   GLU A  23       7.185  13.710   2.684  1.00  5.11           O  
+ATOM    165  CB  GLU A  23       9.680  13.256   0.670  1.00  6.16           C  
+ATOM    166  CG  GLU A  23      10.443  12.079   0.026  1.00  7.48           C  
+ATOM    167  CD  GLU A  23      11.929  12.078   0.378  1.00  9.40           C  
+ATOM    168  OE1 GLU A  23      12.463  13.127   0.815  1.00 10.40           O  
+ATOM    169  OE2 GLU A  23      12.523  10.979   0.229  1.00 13.32           O  
+ATOM    170  N   ALA A  24       7.250  15.342   1.137  1.00  4.56           N  
+ATOM    171  CA  ALA A  24       6.603  16.363   1.942  1.00  4.49           C  
+ATOM    172  C   ALA A  24       5.181  15.997   2.372  1.00  4.10           C  
+ATOM    173  O   ALA A  24       4.780  16.226   3.504  1.00  5.64           O  
+ATOM    174  CB  ALA A  24       6.614  17.716   1.196  1.00  5.80           C  
+ATOM    175  N   ILE A  25       4.393  15.365   1.471  1.00  0.00           N  
+ATOM    176  CA  ILE A  25       3.059  14.858   1.782  1.00  0.00           C  
+ATOM    177  C   ILE A  25       3.119  13.764   2.814  1.00  0.00           C  
+ATOM    178  O   ILE A  25       2.340  13.713   3.763  1.00  0.00           O  
+ATOM    179  CB  ILE A  25       2.395  14.297   0.537  1.00  0.00           C  
+ATOM    180  CG1 ILE A  25       2.067  15.452  -0.425  1.00  0.00           C  
+ATOM    181  CG2 ILE A  25       1.147  13.432   0.873  1.00  0.00           C  
+ATOM    182  CD1 ILE A  25       1.425  14.937  -1.710  1.00  0.00           C  
+ATOM    183  N   CYS A  26       4.092  12.856   2.643  1.00  0.00           N  
+ATOM    184  CA  CYS A  26       4.311  11.762   3.553  1.00  0.00           C  
+ATOM    185  C   CYS A  26       4.647  12.226   4.966  1.00  0.00           C  
+ATOM    186  O   CYS A  26       4.108  11.689   5.919  1.00  0.00           O  
+ATOM    187  CB  CYS A  26       5.440  10.845   3.055  1.00  0.00           C  
+ATOM    188  SG  CYS A  26       5.263  10.218   1.382  1.00  0.00           S  
+ATOM    189  N   ALA A  27       5.487  13.282   5.125  1.00  0.00           N  
+ATOM    190  CA  ALA A  27       5.803  13.900   6.406  1.00  0.00           C  
+ATOM    191  C   ALA A  27       4.561  14.357   7.177  1.00  0.00           C  
+ATOM    192  O   ALA A  27       4.384  14.077   8.358  1.00  0.00           O  
+ATOM    193  CB  ALA A  27       6.730  15.122   6.168  1.00  0.00           C  
+ATOM    194  N   THR A  28       3.634  15.017   6.455  1.00  0.00           N  
+ATOM    195  CA  THR A  28       2.321  15.445   6.937  1.00  0.00           C  
+ATOM    196  C   THR A  28       1.408  14.292   7.325  1.00  0.00           C  
+ATOM    197  O   THR A  28       0.716  14.344   8.336  1.00  0.00           O  
+ATOM    198  CB  THR A  28       1.627  16.339   5.912  1.00  0.00           C  
+ATOM    199  OG1 THR A  28       2.410  17.506   5.704  1.00  0.00           O  
+ATOM    200  CG2 THR A  28       0.253  16.829   6.388  1.00  0.00           C  
+ATOM    201  N   TYR A  29       1.380  13.210   6.520  1.00  0.00           N  
+ATOM    202  CA  TYR A  29       0.556  12.034   6.755  1.00  0.00           C  
+ATOM    203  C   TYR A  29       1.029  11.150   7.922  1.00  0.00           C  
+ATOM    204  O   TYR A  29       0.220  10.589   8.656  1.00  0.00           O  
+ATOM    205  CB  TYR A  29       0.432  11.213   5.436  1.00  0.00           C  
+ATOM    206  CG  TYR A  29      -0.619  10.131   5.521  1.00  0.00           C  
+ATOM    207  CD1 TYR A  29      -0.249   8.777   5.596  1.00  0.00           C  
+ATOM    208  CD2 TYR A  29      -1.986  10.458   5.550  1.00  0.00           C  
+ATOM    209  CE1 TYR A  29      -1.222   7.776   5.727  1.00  0.00           C  
+ATOM    210  CE2 TYR A  29      -2.961   9.454   5.658  1.00  0.00           C  
+ATOM    211  CZ  TYR A  29      -2.576   8.113   5.749  1.00  0.00           C  
+ATOM    212  OH  TYR A  29      -3.541   7.091   5.857  1.00  0.00           O  
+ATOM    213  N   THR A  30       2.361  10.976   8.099  1.00  0.00           N  
+ATOM    214  CA  THR A  30       2.919   9.964   9.002  1.00  0.00           C  
+ATOM    215  C   THR A  30       3.692  10.502  10.184  1.00  0.00           C  
+ATOM    216  O   THR A  30       4.081   9.745  11.071  1.00  0.00           O  
+ATOM    217  CB  THR A  30       3.865   8.993   8.298  1.00  0.00           C  
+ATOM    218  OG1 THR A  30       4.991   9.632   7.711  1.00  0.00           O  
+ATOM    219  CG2 THR A  30       3.100   8.329   7.156  1.00  0.00           C  
+ATOM    220  N   GLY A  31       3.953  11.821  10.249  1.00  4.99           N  
+ATOM    221  CA  GLY A  31       4.745  12.407  11.324  1.00  5.50           C  
+ATOM    222  C   GLY A  31       6.234  12.247  11.157  1.00  4.19           C  
+ATOM    223  O   GLY A  31       7.005  12.647  12.019  1.00  6.12           O  
+ATOM    224  N   CYS A  32       6.696  11.661  10.031  1.00  4.30           N  
+ATOM    225  CA  CYS A  32       8.098  11.698   9.639  1.00  4.89           C  
+ATOM    226  C   CYS A  32       8.497  13.099   9.220  1.00  5.50           C  
+ATOM    227  O   CYS A  32       7.656  13.930   8.904  1.00  5.82           O  
+ATOM    228  CB  CYS A  32       8.466  10.716   8.500  1.00  4.66           C  
+ATOM    229  SG  CYS A  32       8.024   8.992   8.876  1.00  0.00           S  
+ATOM    230  N   ILE A  33       9.798  13.416   9.221  1.00  6.02           N  
+ATOM    231  CA  ILE A  33      10.261  14.745   8.877  1.00  5.24           C  
+ATOM    232  C   ILE A  33      11.307  14.643   7.792  1.00  5.16           C  
+ATOM    233  O   ILE A  33      11.935  13.604   7.599  1.00  7.19           O  
+ATOM    234  CB  ILE A  33      10.816  15.514  10.075  1.00  5.49           C  
+ATOM    235  CG1 ILE A  33      12.052  14.827  10.704  1.00  6.85           C  
+ATOM    236  CG2 ILE A  33       9.672  15.686  11.098  1.00  6.45           C  
+ATOM    237  CD1 ILE A  33      12.736  15.667  11.788  1.00  8.94           C  
+ATOM    238  N   ILE A  34      11.516  15.749   7.050  1.00  5.52           N  
+ATOM    239  CA  ILE A  34      12.542  15.857   6.033  1.00  6.82           C  
+ATOM    240  C   ILE A  34      13.537  16.862   6.551  1.00  6.92           C  
+ATOM    241  O   ILE A  34      13.163  17.970   6.943  1.00  9.22           O  
+ATOM    242  CB  ILE A  34      12.013  16.367   4.696  1.00  8.11           C  
+ATOM    243  CG1 ILE A  34      10.931  15.424   4.143  1.00  9.59           C  
+ATOM    244  CG2 ILE A  34      13.166  16.514   3.671  1.00  9.73           C  
+ATOM    245  CD1 ILE A  34      10.163  16.046   2.978  1.00 13.41           C  
+ATOM    246  N   ILE A  35      14.832  16.507   6.576  1.00  7.06           N  
+ATOM    247  CA  ILE A  35      15.900  17.397   6.990  1.00  7.52           C  
+ATOM    248  C   ILE A  35      16.895  17.555   5.839  1.00  6.63           C  
+ATOM    249  O   ILE A  35      17.010  16.646   5.004  1.00  7.90           O  
+ATOM    250  CB  ILE A  35      16.627  16.933   8.255  1.00  8.07           C  
+ATOM    251  CG1 ILE A  35      17.345  15.572   8.080  1.00  9.41           C  
+ATOM    252  CG2 ILE A  35      15.604  16.934   9.413  1.00  9.46           C  
+ATOM    253  CD1 ILE A  35      18.269  15.211   9.249  1.00  9.85           C  
+ATOM    254  N   PRO A  36      17.632  18.673   5.737  1.00  8.07           N  
+ATOM    255  CA  PRO A  36      18.637  18.871   4.698  1.00  8.78           C  
+ATOM    256  C   PRO A  36      19.884  18.038   4.926  1.00  8.31           C  
+ATOM    257  O   PRO A  36      20.550  17.686   3.959  1.00  9.09           O  
+ATOM    258  CB  PRO A  36      18.968  20.380   4.711  1.00  9.67           C  
+ATOM    259  CG  PRO A  36      18.247  20.998   5.919  1.00 10.15           C  
+ATOM    260  CD  PRO A  36      17.388  19.886   6.520  1.00  9.53           C  
+ATOM    261  N   GLY A  37      20.245  17.766   6.197  1.00  8.48           N  
+ATOM    262  CA  GLY A  37      21.414  16.968   6.556  1.00  9.20           C  
+ATOM    263  C   GLY A  37      21.179  15.482   6.482  1.00 10.41           C  
+ATOM    264  O   GLY A  37      20.178  15.006   5.955  1.00 12.06           O  
+ATOM    265  N   ALA A  38      22.111  14.681   7.026  1.00  9.24           N  
+ATOM    266  CA  ALA A  38      22.015  13.238   6.986  1.00  9.24           C  
+ATOM    267  C   ALA A  38      21.913  12.606   8.360  1.00  9.60           C  
+ATOM    268  O   ALA A  38      21.810  11.395   8.492  1.00 13.65           O  
+ATOM    269  CB  ALA A  38      23.257  12.706   6.258  1.00 10.43           C  
+ATOM    270  N   THR A  39      21.883  13.426   9.424  1.00  8.70           N  
+ATOM    271  CA  THR A  39      21.990  12.912  10.778  1.00  9.46           C  
+ATOM    272  C   THR A  39      20.683  13.187  11.461  1.00  8.32           C  
+ATOM    273  O   THR A  39      20.381  14.325  11.828  1.00  9.89           O  
+ATOM    274  CB  THR A  39      23.118  13.577  11.552  1.00 10.72           C  
+ATOM    275  OG1 THR A  39      24.344  13.437  10.849  1.00 11.66           O  
+ATOM    276  CG2 THR A  39      23.326  12.909  12.915  1.00 11.81           C  
+ATOM    277  N   CYS A  40      19.839  12.153  11.616  1.00  7.64           N  
+ATOM    278  CA  CYS A  40      18.549  12.273  12.271  1.00  8.05           C  
+ATOM    279  C   CYS A  40      18.683  12.470  13.782  1.00  7.63           C  
+ATOM    280  O   CYS A  40      19.553  11.848  14.390  1.00  9.64           O  
+ATOM    281  CB  CYS A  40      17.636  11.060  11.978  1.00  7.80           C  
+ATOM    282  SG  CYS A  40      17.219  10.907  10.214  1.00  0.00           S  
+ATOM    283  N   PRO A  41      17.894  13.320  14.440  1.00  8.00           N  
+ATOM    284  CA  PRO A  41      17.922  13.457  15.891  1.00  8.96           C  
+ATOM    285  C   PRO A  41      17.385  12.227  16.604  1.00  9.06           C  
+ATOM    286  O   PRO A  41      16.722  11.388  16.007  1.00  8.82           O  
+ATOM    287  CB  PRO A  41      17.063  14.703  16.156  1.00 10.39           C  
+ATOM    288  CG  PRO A  41      16.065  14.729  14.998  1.00 10.99           C  
+ATOM    289  CD  PRO A  41      16.862  14.158  13.828  1.00 10.49           C  
+ATOM    290  N   GLY A  42      17.676  12.109  17.918  1.00  7.55           N  
+ATOM    291  CA  GLY A  42      17.326  10.939  18.720  1.00  8.00           C  
+ATOM    292  C   GLY A  42      15.854  10.667  18.936  1.00  7.22           C  
+ATOM    293  O   GLY A  42      15.487   9.550  19.270  1.00  8.41           O  
+ATOM    294  N   ASP A  43      14.968  11.663  18.745  1.00  5.54           N  
+ATOM    295  CA  ASP A  43      13.534  11.508  18.861  1.00  5.85           C  
+ATOM    296  C   ASP A  43      12.885  11.230  17.500  1.00  5.87           C  
+ATOM    297  O   ASP A  43      11.689  10.973  17.400  1.00  7.29           O  
+ATOM    298  CB  ASP A  43      12.926  12.754  19.574  1.00  6.72           C  
+ATOM    299  CG  ASP A  43      13.238  14.092  18.910  1.00  8.59           C  
+ATOM    300  OD1 ASP A  43      14.277  14.195  18.201  1.00  9.59           O  
+ATOM    301  OD2 ASP A  43      12.454  15.039  19.151  1.00 11.45           O  
+ATOM    302  N   TYR A  44      13.695  11.172  16.422  1.00  5.22           N  
+ATOM    303  CA  TYR A  44      13.256  10.771  15.100  1.00  5.56           C  
+ATOM    304  C   TYR A  44      14.244   9.740  14.605  1.00  4.61           C  
+ATOM    305  O   TYR A  44      14.900   9.896  13.577  1.00  6.04           O  
+ATOM    306  CB  TYR A  44      13.176  11.942  14.089  1.00  5.41           C  
+ATOM    307  CG  TYR A  44      12.025  12.846  14.397  1.00  5.34           C  
+ATOM    308  CD1 TYR A  44      12.132  13.887  15.332  1.00  6.59           C  
+ATOM    309  CD2 TYR A  44      10.800  12.641  13.747  1.00  5.94           C  
+ATOM    310  CE1 TYR A  44      11.027  14.699  15.622  1.00  5.97           C  
+ATOM    311  CE2 TYR A  44       9.696  13.450  14.036  1.00  5.17           C  
+ATOM    312  CZ  TYR A  44       9.812  14.487  14.966  1.00  5.96           C  
+ATOM    313  OH  TYR A  44       8.695  15.301  15.229  1.00  8.60           O  
+ATOM    314  N   ALA A  45      14.374   8.640  15.366  1.00  4.76           N  
+ATOM    315  CA  ALA A  45      15.454   7.695  15.240  1.00  5.89           C  
+ATOM    316  C   ALA A  45      15.168   6.534  14.284  1.00  6.67           C  
+ATOM    317  O   ALA A  45      15.991   5.643  14.126  1.00  7.56           O  
+ATOM    318  CB  ALA A  45      15.705   7.115  16.649  1.00  6.82           C  
+ATOM    319  N   ASN A  46      13.980   6.516  13.642  1.00  5.80           N  
+ATOM    320  CA  ASN A  46      13.548   5.423  12.792  1.00  6.15           C  
+ATOM    321  C   ASN A  46      13.271   5.858  11.325  1.00  6.61           C  
+ATOM    322  O   ASN A  46      13.555   7.019  10.928  1.00  7.18           O  
+ATOM    323  CB  ASN A  46      12.273   4.785  13.398  1.00  7.27           C  
+ATOM    324  CG  ASN A  46      12.512   4.269  14.812  1.00  7.98           C  
+ATOM    325  OD1 ASN A  46      11.887   4.710  15.772  1.00 11.00           O  
+ATOM    326  ND2 ASN A  46      13.406   3.262  14.967  1.00 10.32           N  
+ATOM    327  OXT ASN A  46      12.762   5.007  10.548  1.00  0.00           O  
+TER     328      ASN A  46                                                      
+END   
diff --git a/modelling/doc/algorithms.rst b/modelling/doc/algorithms.rst
index c9db60f1f7f57dc8ac74e00d8db94b9cb018c4be..5545a9acfd90270e035ef0cbf2c45b6ffe5a1088 100644
--- a/modelling/doc/algorithms.rst
+++ b/modelling/doc/algorithms.rst
@@ -308,7 +308,7 @@ iteration.
 
 .. method:: FindMotifs(query, target_positions, hash_tresh=0.4, \
                        distance_thresh=1.0, refine_thresh=0.7, \
-                       flags=list())
+                       flags=list(), swap_thresh=False)
 
   Performs the detection and refinement stages of the geometric hashing 
   algorithm. 
@@ -322,6 +322,10 @@ iteration.
                         constructor. If you didn't provide anything there,
                         this can be ignored. Only the actual coordinates
                         matter in this case.
+  :param swap_thresh: *hash_thresh* and *refine_thresh* refer to fraction of
+                      covered positions in *query*. When setting this to
+                      True, they refer to the fraction of covered positions
+                      in *target_positions*.
 
   :returns:             All found matches
 
diff --git a/modelling/pymod/export_motif_finder.cc b/modelling/pymod/export_motif_finder.cc
index e966af4463beeb2fa304f9cb611bba0d5f89f003..c711e12a9629662b2d76de7c8c243c49663b94f9 100644
--- a/modelling/pymod/export_motif_finder.cc
+++ b/modelling/pymod/export_motif_finder.cc
@@ -69,7 +69,8 @@ boost::python::list WrapFindMotifs(const MotifQuery& query,
                                    Real hash_thresh,
                                    Real distance_thresh,
                                    Real refine_thresh,
-                                   const boost::python::list& flags) {
+                                   const boost::python::list& flags,
+                                   bool swap_thresh) {
 
   std::vector<int> v_flags;
   promod3::core::ConvertListToVector(flags, v_flags);
@@ -78,7 +79,8 @@ boost::python::list WrapFindMotifs(const MotifQuery& query,
                                                 hash_thresh,
                                                 distance_thresh,
                                                 refine_thresh,
-                                                v_flags);
+                                                v_flags,
+                                                swap_thresh);
   list return_list;
   for(std::vector<MotifMatch>::iterator it = v_result.begin();
       it != v_result.end(); ++it) {
@@ -153,5 +155,6 @@ void export_motif_finder() {
                                       arg("hash_thresh")=0.4,
                                       arg("distance_thresh")=1.0,
                                       arg("refine_thresh")=0.7,
-                                      arg("flags")=boost::python::list()));
+                                      arg("flags")=boost::python::list(),
+                                      arg("swap_thresh")=false));
 }
diff --git a/modelling/src/motif_finder.cc b/modelling/src/motif_finder.cc
index 61c62f075a3a4d16799c4df34af1bccaf70c2cb1..2ec8d756037187a2ddc96778b9d49dc2c7186f9f 100644
--- a/modelling/src/motif_finder.cc
+++ b/modelling/src/motif_finder.cc
@@ -172,20 +172,29 @@ struct InitialHits{
 struct Accumulator{
 
   Accumulator(const promod3::modelling::MotifQuery& query, 
-              Real coverage_thresh) {
+              Real coverage_thresh, int fix_thresh) {
 
     int n = 0;
     for(uint i = 0; i < query.GetN(); ++i) {
       range_start.push_back(n);
-      uint32_t query_size = query.GetQuerySize(i);
-      uint32_t n_triangles = query.GetNTriangles(i);
-      uint16_t thresh = std::ceil((query_size-3) * coverage_thresh);
-      for(uint j = 0; j < n_triangles; ++j) {
-        thresholds.push_back(thresh);
-      }
-      n += n_triangles;
+      n += query.GetNTriangles(i);
     }
     accumulator.assign(n, 0);
+
+    if(fix_thresh < 0) {
+      // default: thresholds depend on sizes of query
+      for(uint i = 0; i < query.GetN(); ++i) {
+        uint32_t query_size = query.GetQuerySize(i);
+        uint32_t n_triangles = query.GetNTriangles(i);
+        uint16_t thresh = std::ceil((query_size-3) * coverage_thresh);
+        for(uint j = 0; j < n_triangles; ++j) {
+          thresholds.push_back(thresh);
+        }
+      }
+    } else {
+      // assign fix thresh for each triangle
+      thresholds.assign(n, fix_thresh);
+    }
   }
 
 
@@ -416,9 +425,9 @@ void GetInitialAlignment(const promod3::core::EMat3X& query_pos,
 bool RefineInitialHit(const promod3::modelling::MotifQuery& query,  
                       const promod3::core::EMat3X& target_pos, 
                       const std::vector<int>& target_flags,
-                      Real dist_thresh, Real refine_thresh, int query_idx, 
-                      int query_triangle_idx, int target_p1, int target_p2, 
-                      int target_p3, geom::Mat4& mat, 
+                      Real dist_thresh, Real refine_thresh, bool swap_thresh,
+                      int query_idx, int query_triangle_idx, int target_p1,
+                      int target_p2, int target_p3, geom::Mat4& mat, 
                       std::vector<std::pair<int, int> >& alignment) {
 
   // the query is only available as geom::Vec3List. This makes sense from a 
@@ -527,8 +536,14 @@ bool RefineInitialHit(const promod3::modelling::MotifQuery& query,
   }
 
   // check whether enough positions are superposed
-  if(static_cast<Real>(alignment.size()) / query_n < refine_thresh) {
-    return false;
+  if(swap_thresh) {
+    if(static_cast<Real>(alignment.size()) / target_pos.cols() < refine_thresh) {
+      return false;
+    }
+  } else {
+    if(static_cast<Real>(alignment.size()) / query_n < refine_thresh) {
+      return false;
+    }
   }
 
   // chain together the final transformation matrix
@@ -546,7 +561,7 @@ void RefineInitialHits(const InitialHits& initial_hits,
                        const promod3::modelling::MotifQuery& query,
                        const promod3::core::EMat3X& target_pos, 
                        const std::vector<int>& flags, Real dist_thresh,
-                       Real refine_thresh,
+                       Real refine_thresh, bool swap_thresh,
                        std::vector<promod3::modelling::MotifMatch>& results) {
 
 
@@ -562,9 +577,9 @@ void RefineInitialHits(const InitialHits& initial_hits,
     for(auto it = initial_hits.initial_hits[query_idx].begin();
         it != initial_hits.initial_hits[query_idx].end(); ++it) {
       if(RefineInitialHit(query, target_pos, flags, dist_thresh, 
-                          refine_thresh, query_idx, it->triangle_idx, 
-                          it->target_p1, it->target_p2, it->target_p3, 
-                          mat, aln)) {
+                          refine_thresh, swap_thresh, query_idx,
+                          it->triangle_idx,  it->target_p1, it->target_p2,
+                          it->target_p3, mat, aln)) {
         // only add the result if its unique
         bool already_there = false;
         for(uint res_idx = 0; res_idx < query_results.size(); ++res_idx) {
@@ -1302,7 +1317,8 @@ std::vector<MotifMatch> FindMotifs(const MotifQuery& query,
                                    Real hash_thresh, 
                                    Real distance_thresh,
                                    Real refine_thresh,
-                                   const std::vector<int>& flags) {
+                                   const std::vector<int>& flags,
+                                   bool swap_thresh) {
 
   promod3::core::ScopedTimerPtr prof = promod3::core::StaticRuntimeProfiler::StartScoped(
                                 "FindMotifs::FindMotifs", 2);
@@ -1345,7 +1361,11 @@ std::vector<MotifMatch> FindMotifs(const MotifQuery& query,
 
   // fetch hash map and setup accumulator
   const MotifHasherMap& map = query.data_->map;
-  Accumulator accumulator(query, hash_thresh);
+  int acc_thresh = -1;
+  if(swap_thresh) {
+    acc_thresh = std::ceil((n_target-3) * hash_thresh);
+  }
+  Accumulator accumulator(query, hash_thresh, acc_thresh);
     
   for(int p1 = 0; p1 < n_target; ++p1) {
     for(int p2 = p1+1; p2 < n_target; ++p2) {
@@ -1421,7 +1441,7 @@ std::vector<MotifMatch> FindMotifs(const MotifQuery& query,
   }
 
   RefineInitialHits(initial_hits, query, eigen_positions, flags, 
-                    distance_thresh, refine_thresh, results);
+                    distance_thresh, refine_thresh, swap_thresh, results);
 
   return results;
 }
diff --git a/modelling/src/motif_finder.hh b/modelling/src/motif_finder.hh
index 729911202fffe9bb1747eae516c40fbbca448223..10806f1423df66b9f920285264e3805c77ba51ac 100644
--- a/modelling/src/motif_finder.hh
+++ b/modelling/src/motif_finder.hh
@@ -105,7 +105,8 @@ std::vector<MotifMatch> FindMotifs(const MotifQuery& query,
                                    Real hash_thresh = 0.4,
                                    Real distance_thresh = 1.0,
                                    Real refine_thresh = 0.7,
-                                   const std::vector<int>& flags = std::vector<int>());
+                                   const std::vector<int>& flags = std::vector<int>(),
+                                   bool swap_thresh=false);
 
 
 }} // ns