diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index 55d1bb8bef5c5357a052d139b4f15a1d04ad8e4e..25f32be06c34e046e6b30ed687d71e6321ad772f 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -46,7 +46,8 @@
             
   <h1>All modules for which code is available</h1>
 <ul><li><a href="promod3/core/argcheck.html">promod3.core.argcheck</a></li>
-<li><a href="sm/meld.html">sm.meld</a></li>
+<li><a href="promod3/core/helper.html">promod3.core.helper</a></li>
+<li><a href="promod3/meld.html">promod3.meld</a></li>
 </ul>
 
           </div>
@@ -85,7 +86,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Sep 25 11:22, 2014.
+      Last updated on Oct 16 09:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/_modules/promod3/core/argcheck.html b/doc/html/_modules/promod3/core/argcheck.html
index 334fc4083cb6e5815431d9b89fb4e030b07ae73d..592540390350fb1055b9c63ab0434c83a9e1221d 100644
--- a/doc/html/_modules/promod3/core/argcheck.html
+++ b/doc/html/_modules/promod3/core/argcheck.html
@@ -53,10 +53,7 @@
 
 <span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">sys</span>
 <span class="kn">import</span> <span class="nn">ost</span>
-
-<span class="k">def</span> <span class="nf">_MsgErrorAndExit</span><span class="p">(</span><span class="n">msg</span><span class="p">,</span> <span class="n">exit_status</span><span class="p">):</span>
-    <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">exit_status</span><span class="p">)</span>
+<span class="kn">import</span> <span class="nn">helper</span>
 
 <div class="viewcode-block" id="FileExists"><a class="viewcode-back" href="../../../core/argcheck.html#promod3.core.argcheck.FileExists">[docs]</a><span class="k">def</span> <span class="nf">FileExists</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">exit_status</span><span class="p">,</span> <span class="nb">file</span><span class="p">):</span>
   <span class="sd">&#39;&#39;&#39;</span>
@@ -78,7 +75,7 @@
 <span class="sd">            missing.</span>
 <span class="sd">  &#39;&#39;&#39;</span>
   <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="nb">file</span><span class="p">):</span>
-    <span class="n">_MsgErrorAndExit</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file does not exist: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">),</span>
+    <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file does not exist: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">),</span>
                      <span class="n">exit_status</span><span class="p">)</span>
 </div>
 <div class="viewcode-block" id="FileExtension"><a class="viewcode-back" href="../../../core/argcheck.html#promod3.core.argcheck.FileExtension">[docs]</a><span class="k">def</span> <span class="nf">FileExtension</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">exit_status</span><span class="p">,</span> <span class="nb">file</span><span class="p">,</span> <span class="n">extensions</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
@@ -123,14 +120,16 @@
     <span class="n">filename</span><span class="p">,</span> <span class="n">fileext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
     <span class="k">if</span> <span class="ow">not</span> <span class="n">gz</span><span class="p">:</span>
       <span class="n">extension_string</span> <span class="o">=</span> <span class="s">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
-      <span class="n">_MsgErrorAndExit</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. &#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">)</span><span class="o">+</span>
+      <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. &#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
+                                                                        <span class="nb">file</span><span class="p">)</span><span class="o">+</span>
                        <span class="s">&#39;Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&#39;</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
                        <span class="n">exit_status</span><span class="p">)</span>
   <span class="k">if</span> <span class="n">fileext</span> <span class="o">==</span> <span class="s">&#39;&#39;</span><span class="p">:</span>
     <span class="n">extension_string</span> <span class="o">=</span> <span class="s">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
     <span class="k">if</span> <span class="n">gz</span><span class="p">:</span>
       <span class="n">extension_string</span> <span class="o">+=</span> <span class="s">&#39;, &#39;</span> <span class="o">+</span> <span class="s">&#39;.gz, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span> <span class="o">+</span> <span class="s">&#39;.gz&#39;</span>
-      <span class="n">_MsgErrorAndExit</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. &#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">)</span><span class="o">+</span>
+      <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. &#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
+                                                                        <span class="nb">file</span><span class="p">)</span><span class="o">+</span>
                        <span class="s">&#39;Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&#39;</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
                        <span class="n">exit_status</span><span class="p">)</span>
   <span class="n">fileext</span> <span class="o">=</span> <span class="n">fileext</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
@@ -143,7 +142,8 @@
   <span class="n">extension_string</span> <span class="o">=</span> <span class="s">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
   <span class="k">if</span> <span class="n">gz</span><span class="p">:</span>
     <span class="n">extension_string</span> <span class="o">+=</span> <span class="s">&#39;, &#39;</span> <span class="o">+</span> <span class="s">&#39;.gz, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span> <span class="o">+</span> <span class="s">&#39;.gz&#39;</span>
-  <span class="n">_MsgErrorAndExit</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. &#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">)</span><span class="o">+</span>
+  <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. &#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
+                                                                    <span class="nb">file</span><span class="p">)</span><span class="o">+</span>
                    <span class="s">&#39;Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&#39;</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
                    <span class="n">exit_status</span><span class="p">)</span>
 </div>
@@ -193,7 +193,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Sep 25 11:22, 2014.
+      Last updated on Oct 16 09:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/_sources/core/index.txt b/doc/html/_sources/core/index.txt
index 4ec3a4454ab9ecafa019186d2b6f9a3b665b206e..896ac2e6f2b5724b846046ef6adab708133c0383 100644
--- a/doc/html/_sources/core/index.txt
+++ b/doc/html/_sources/core/index.txt
@@ -4,11 +4,14 @@
 .. module:: promod3.core
   :synopsis: Basic functionality, supporting standard tasks in your code.
   
-This module gathers functions and classes which are not devoted to homology modeling per se but cover standard programming issues.
+This module gathers functions and classes which are not devoted to homology
+modeling per se but cover standard programming issues.
 
 .. toctree:: 
   :maxdepth: 2
   
   argcheck
 
+  helper
+
 ..  LocalWords:  promod se toctree maxdepth argcheck
diff --git a/doc/html/_sources/meld/index.txt b/doc/html/_sources/meld/index.txt
index 148e9702d21b56fadee106c99930b2053775bb89..b90b30a29ef5d31edfaae116dae846ae4ebe5400 100644
--- a/doc/html/_sources/meld/index.txt
+++ b/doc/html/_sources/meld/index.txt
@@ -2,12 +2,98 @@
 ================================================================================
 
 .. module:: promod3.meld
-  :synopsis: Coordinate modeling and sampling
-  
-This module contains functions and classes to model protein structures from sequence.
+  :synopsis: Raw Coordinate Model
+
+.. currentmodule:: promod3.meld
+
+Functionality to build raw (pseudo) models based on a sequence alignment.
+Here is an example of how to build a model from an alignment and a structure.
+
+.. testcode:: meld
+  :hide:
+
+  import os
+  import tempfile
+  from ost import io
+  from promod3 import meld
+
+  aln = io.LoadAlignment('../tests/meld/data/raw-modeling/seq.fasta')
+  template_structure = io.LoadPDB('../tests/meld/data/raw-modeling/gly.pdb',
+                                  restrict_chains='A')
+  aln.AttachView(1, template_structure.Select('peptide=true'))
+  result = meld.BuildRawModel(aln)
+  (fh, fn) = tempfile.mkstemp(suffix='.pdb')
+  io.SavePDB(result.model, fn)
+  os.remove(fn)
+
+.. doctest:: meld
+
+  from ost import io
+  from promod3 import meld
+
+  aln = io.LoadAlignment('seq.fasta')
+  template_structure = io.LoadPDB('gly.pdb', restrict_chains='A')
+  aln.AttachView(1, template_structure.Select('peptide=true'))
+  result = meld.BuildRawModel(aln)
+  io.SavePDB(result.model, 'model.pdb')
+
+
+Raw Coordinate Modeling API
+--------------------------------------------------------------------------------
+
+.. function:: BuildRawModel(alignment, calpha_only=False)
+              BuildRawModel(alignments, calpha_only=False)
+
+  Builds a raw (pseudo) model from the alignment. Can either take a single
+  alignment handle or an alignment handle list. Every list item is treated as a
+  single chain in the final raw model.
+
+  This is a basic protein core modeling algorithm that copies backbone
+  coordinates based on the sequence alignment. For matching residues, the
+  side chain coordinates are also copied. Gaps are ignored. Hydrogen an
+  deuterium atoms are not copied into the model.
+
+  The function tries to reuse as much as possible from the template. Modified
+  residues are treated as follows:
 
-.. toctree:: 
-  :maxdepth: 2
+    - Selenium methionine residues are converted to methionine
+
+    - Side chains which contain all atoms of the parent amino acid, e.g.
+      phosphoserine are copied as a whole with the modifications stripped off.
+
+  Residue numbers are set such that missing residue in gaps are honoured and
+  subsequent loop modeling can insert new residues without having to
+  renumber.
   
-  loop
-  rawmodel
+  The returned :class:`RawModelingResult` stores the obtained raw model as well
+  as information about insertions and deletions in the gaps list.
+
+  :param calpha_only: If true, only Calpha atoms will be copied. Side chains
+                      and other backbone atoms are completely ignored.
+  :raises: A :exc:`RuntimeError` when the second sequence does not have an
+     attached structure
+
+.. class:: RawModelingResult
+
+  Holds the result of raw model building. Incredibly minimalistic for now. Will
+  most likely grow a few more members over time to, e.g. to store a detailed
+  report.
+
+  .. attribute:: model
+
+    The resulting model.
+
+    :type: :class:`~ost.mol.EntityHandle`
+
+  .. attribute:: gaps
+
+    List of gaps in the model that could not be copied from the template. These
+    gaps may be the result of insertions/deletions in the alignment or due to
+    missing or incomplete backbone coordinates in the template structure.
+
+
+    :type: :class:`StructuralGapList`
+
+
+..  LocalWords:  currentmodule promod aln AttachView BuildRawModel pdb calpha
+..  LocalWords:  RawModelingResult StructuralGapList
diff --git a/doc/html/_sources/meld/loop.txt b/doc/html/_sources/meld/loop.txt
deleted file mode 100644
index 0b015ed7e75fc8aa02f09e2291f9c599a7eb8ef7..0000000000000000000000000000000000000000
--- a/doc/html/_sources/meld/loop.txt
+++ /dev/null
@@ -1,153 +0,0 @@
-Loop Modeling
-================================================================================
-
-.. currentmodule:: sm.meld
-
-
-Loop Modeling API
---------------------------------------------------------------------------------
-
-.. class:: LoopCandidate(gap, bb_list)
-
-  A loop candidate holds the coordinates of the four backbone atoms for a given 
-  peptide fragment as well as the sequence.
-  
-  :param gap: The structural gap 
-  :type gap: :class:`StructuralGap`
-  
-  :param bb_list: List of peptide backbone coordinates
-  :type bb_list: :class:`BackboneList`
-  
-  .. method:: InsertInto(entity)
-
-    Inserts the loop candidate into the given entity. This honours the start and 
-    end point stored in the gap. Missing residues and atoms will be inserted 
-    into the structure.
-    
-    
-    :param entity:
-    :type  entity: :class:`~ost.mol.EntityHandle`
-    :returns: True on success, false if the insertion failed
-    :rtype: bool
-
-  .. method:: RmsdTo(entity)
-  
-    Calculates the RMSD to the corresponding backbone fragment in *entity*. 
-    Raises a RuntimeError if not all backbone atoms exist.
-    
-    :param entity:
-    :type  entity: :class:`~ost.mol.EntityHandle`
-    :rtype: float
-
-  .. method:: ToEntity()
-    
-    Returns an entity holding this backbone fragment. Residue numbers go from 
-    gap.start to gap.end.
-    
-    :rtype: :class:`~ost.mol.EntityHandle`
-
-
-  .. attribute:: allatom_score
-     
-    If set, the allatom_score of this fragment
-  
-  
-  
-  .. attribute:: clash_bb_score
-     
-    The clash score of the loop candidate with sidechain atoms
-  
-  
-  
-  .. attribute:: clash_score
-  
-    The sum of backbone and sidechain clash scores
-  
-  
-  
-  .. attribute:: clash_sc_score
-    
-    Clash score with sidechain atoms
-  
-  
-  
-  .. attribute:: coords
-   
-    Access to the actual coordinates
-    
-    :type: :class:`BackboneList`
-  
-  
-  
-  .. attribute:: correl
-    
-    Correlation with density
-  
-  
-  
-  .. attribute:: gap
-    
-    The structural gap
-  
-  
-  
-  .. attribute:: packing_score
-    
-    Packing score of this loop candidate
-  
-  
-  
-  .. attribute:: reduced_score
-   
-    Reduced score
-  
-  
-  
-  .. attribute:: score
-    
-    Total score of this loop candidate.
-  
-  
-  
-  .. attribute:: torsion_score
-    
-    Torsion score of this loop candidate
-  
-
-.. class:: LoopCandidates(model)
-  
-  A list of loop candidates with a few helper methods to make your life easier. 
-  The candidates are supposed to be loop candidates for the same gap. However, 
-  they are not required to have the same start and end position, e.g. due to 
-  extension of the gap. 
-  
-  :param model: The model the candidates are for.
-  
-  :type model: :class:`~ost.mol.EntityHandle`
-
-  .. method:: Add(candidate)
-  
-    Add a new candidate
-    :param candidate:
-    :type  candidate: :class:`LoopCandidate`
-
-  .. method:: SortByCorrel([, increasing])
-    
-    Sort loop candidates by correlation score
-    
-    :param increasing: If true, the candidates are sorted in increasing order
-    :type  increasing: bool
-
-  .. method:: SortByScore([, increasing])
-
-    Sort loop canditates by total score
-    
-    :param increasing: If true, the candidates are sorted in increasing order
-    :type  increasing: bool
-
-
-  .. attribute:: model
-    
-    The model the candidates are for
-  
-    :type: :class:`~ost.mol.EntityHandle`
diff --git a/doc/html/_sources/meld/rawmodel.txt b/doc/html/_sources/meld/rawmodel.txt
deleted file mode 100644
index 312c68562c977b61d9f30258108f96b6fbe56591..0000000000000000000000000000000000000000
--- a/doc/html/_sources/meld/rawmodel.txt
+++ /dev/null
@@ -1,80 +0,0 @@
-Raw Coordinate Modeling
-================================================================================
-
-.. currentmodule:: sm.meld
-
-Introduction
---------------------------------------------------------------------------------
-
-Contains function to build raw (pseudo) models based on a sequence alignment. Here is an example of how to build a model from an alignment and a structure.
-
-.. code-block:: python
-  
-  from promod3 import meld
-  
-  aln=io.LoadAlignment('parwise.fasta')
-  template_structure=io.LoadPDB('1ake.pdb', restrict_chains='A')
-  aln.AttachView(1, template_structure.Select('peptide=true'))
-  result=meld.BuildRawModel(aln)
-  io.SavePDB(result.model, 'model.pdb')
-  print 'remaining gaps:'
-  for gap in result.gaps:
-    print ' * %s' % str(gap)
-
-
-Raw Coordinate Modeling API
---------------------------------------------------------------------------------
-
-.. function:: BuildRawModel(alignment, calpha_only=False)
-              BuildRawModel(alignments, calpha_only=False)
-
-  Builds a raw (pseudo) model from the alignment.
-  Can either take a single alignment handle or an alignment handle list.
-  Every list item is treated as a single chain in the final raw model.
-  
-  This is a basic protein core modeling algorithm that copies backbone 
-  coordinates based on the sequence alignment. For matching residues, the 
-  sidechain coordinates are also copied. Gaps are ignored. Hydrogen an deuterium 
-  atoms are not copied into the model.
-  
-  The function tries to reuse as much as possible from the template. Modified 
-  residues are treated as follows:
-  
-    - Selenium methionine residues are converted to methionines
-    
-    - Sidechains which contain all atoms of the parent amino acid, e.g. 
-      phosphoserine are copied as a whole with the modifications stripped off.
-    
-  Residue numbers are set such that missing residue in gaps are honored and 
-  subsequent loop modeling can insert new residues without having to 
-  renumber.
-  
-  The returned :class:`RawModelingResult` stores the obtained raw model as well 
-  as information about insertions and deletions in the gaps list.
-  
-  :param calpha_only: If true, only Calpha atoms will be copied. Sidechains and 
-     other backbone atoms are completely ignored.
-  :raises: A :exc:`RuntimeError` when the second sequence does not have an 
-     attached structure
-
-.. class:: RawModelingResult
-
-  Holds the result of raw model building. Incredibly minimalistic for now. Will 
-  most likely grow a few more members over time to, e.g. to store a detailed 
-  report.
-  
-  .. attribute:: model
-  
-    The resulting model.
-    
-    :type: :class:`~ost.mol.EntityHandle`
-  
-  .. attribute:: gaps
-    
-    List of gaps in the model that could not be copied from the template. These 
-    gaps may be the result of insertions/deletions in the alignment or due to 
-    missing or incomplete backbone coordinates in the template structure.
-    
-    
-    :type: :class:`StructuralGapList`
-    
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index 1104805e43f56c44b8399d655d5dd3a6154e3dd3..d29ed22750b76d52d47d637f7c61008ee7494ca8 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -26,7 +26,7 @@
     <link rel="top" title="ProMod3 0 documentation" href="index.html" />
     <link rel="up" title="Documentation For Developes" href="developers.html" />
     <link rel="next" title="Contributing" href="contributing.html" />
-    <link rel="prev" title="Raw Coordinate Modeling" href="meld/rawmodel.html" /> 
+    <link rel="prev" title="meld - Coordinate modeling" href="meld/index.html" /> 
   </head>
   <body>
     <div class="related">
@@ -42,7 +42,7 @@
           <a href="contributing.html" title="Contributing"
              accesskey="N">next</a> |</li>
         <li class="right" >
-          <a href="meld/rawmodel.html" title="Raw Coordinate Modeling"
+          <a href="meld/index.html" title="meld - Coordinate modeling"
              accesskey="P">previous</a> |</li>
         <li><a href="index.html">ProMod3 0 documentation</a> &raquo;</li>
           <li><a href="developers.html" accesskey="U">Documentation For Developes</a> &raquo;</li> 
@@ -164,8 +164,8 @@ builder</li>
 </ul>
 
   <h4>Previous topic</h4>
-  <p class="topless"><a href="meld/rawmodel.html"
-                        title="previous chapter">Raw Coordinate Modeling</a></p>
+  <p class="topless"><a href="meld/index.html"
+                        title="previous chapter"><tt class="docutils literal"><span class="pre">meld</span></tt> - Coordinate modeling</a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="contributing.html"
                         title="next chapter">Contributing</a></p>
@@ -204,7 +204,7 @@ builder</li>
           <a href="contributing.html" title="Contributing"
              >next</a> |</li>
         <li class="right" >
-          <a href="meld/rawmodel.html" title="Raw Coordinate Modeling"
+          <a href="meld/index.html" title="meld - Coordinate modeling"
              >previous</a> |</li>
         <li><a href="index.html">ProMod3 0 documentation</a> &raquo;</li>
           <li><a href="developers.html" >Documentation For Developes</a> &raquo;</li> 
@@ -212,7 +212,7 @@ builder</li>
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Sep 25 11:22, 2014.
+      Last updated on Oct 16 09:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 15117151827e6038321e4d9f8a9b8a9a3094d9fd..fb2834449dfa3b851ec0159a0be9bd5767e01755 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -127,7 +127,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Sep 18 15:50, 2014.
+      Last updated on Oct 16 09:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index dd5d620840f960a7dbbef11cca3e6a77b04db738..c07a094c1f0f6375d4483dc7e303224abc9d405a 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -795,7 +795,7 @@ contributions to web pages using ProMod3.</p>
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Sep 25 11:22, 2014.
+      Last updated on Oct 16 09:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/core/argcheck.html b/doc/html/core/argcheck.html
index e75d016e4ef73dc11f2d0f03f7aa6ab380092fae..1a628fdbbbc2c1c1c41d848a128b8f5d34dcfd21 100644
--- a/doc/html/core/argcheck.html
+++ b/doc/html/core/argcheck.html
@@ -25,7 +25,7 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <link rel="top" title="ProMod3 0 documentation" href="../index.html" />
     <link rel="up" title="core - ProMod3 core functionality" href="index.html" />
-    <link rel="next" title="meld - Coordinate modeling" href="../meld/index.html" />
+    <link rel="next" title="helper - Shared functionality for the everything" href="helper.html" />
     <link rel="prev" title="core - ProMod3 core functionality" href="index.html" /> 
   </head>
   <body>
@@ -39,7 +39,7 @@
           <a href="../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="right" >
-          <a href="../meld/index.html" title="meld - Coordinate modeling"
+          <a href="helper.html" title="helper - Shared functionality for the everything"
              accesskey="N">next</a> |</li>
         <li class="right" >
           <a href="index.html" title="core - ProMod3 core functionality"
@@ -95,11 +95,11 @@ fixed and only needs a <em>prefix</em> describing the specimen of file.</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>prefix</strong> (<tt class="xref py py-class docutils literal"><span class="pre">str</span></tt>) &#8211; String to put in front of the failure-message
+<li><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">str</span></tt></a>) &#8211; String to put in front of the failure-message
 &#8220;file does not exist: <tt class="docutils literal"><span class="pre">file</span></tt>&#8221;.</li>
-<li><strong>exit_status</strong> (<tt class="xref py py-class docutils literal"><span class="pre">int</span></tt>) &#8211; Exit code on missing file, ends up in <tt class="docutils literal"><span class="pre">$?</span></tt> in the
+<li><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) &#8211; Exit code on missing file, ends up in <tt class="docutils literal"><span class="pre">$?</span></tt> in the
 shell. <tt class="docutils literal"><span class="pre">0</span></tt> is traditionally reserved to successful commands.</li>
-<li><strong>file</strong> (<tt class="xref py py-class docutils literal"><span class="pre">str</span></tt>) &#8211; Path including file name to be checked.</li>
+<li><strong>file</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">str</span></tt></a>) &#8211; Path including file name to be checked.</li>
 </ul>
 </td>
 </tr>
@@ -129,20 +129,20 @@ function terminates the script.</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>prefix</strong> (<tt class="xref py py-class docutils literal"><span class="pre">str</span></tt>) &#8211; String to put in front of the failure-message
+<li><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">str</span></tt></a>) &#8211; String to put in front of the failure-message
 &#8220;file extension not supported: <tt class="docutils literal"><span class="pre">file</span></tt>&#8221;.</li>
-<li><strong>exit_status</strong> (<tt class="xref py py-class docutils literal"><span class="pre">int</span></tt>) &#8211; Exit code on missing file, ends up in <tt class="docutils literal"><span class="pre">$?</span></tt> in the
+<li><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) &#8211; Exit code on missing file, ends up in <tt class="docutils literal"><span class="pre">$?</span></tt> in the
 shell. <tt class="docutils literal"><span class="pre">0</span></tt> is traditionally reserved to successful commands.</li>
-<li><strong>file</strong> (<tt class="xref py py-class docutils literal"><span class="pre">str</span></tt>) &#8211; Path including file name to be checked.</li>
-<li><strong>extensions</strong> (<tt class="xref py py-class docutils literal"><span class="pre">list</span></tt>) &#8211; List of strings without a leading &#8221;.&#8221;.</li>
-<li><strong>gz</strong> (<tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt>) &#8211; Indicates whether to check for an additional &#8220;gz&#8221; extension.</li>
+<li><strong>file</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">str</span></tt></a>) &#8211; Path including file name to be checked.</li>
+<li><strong>extensions</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a>) &#8211; List of strings without a leading &#8221;.&#8221;.</li>
+<li><strong>gz</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) &#8211; Indicates whether to check for an additional &#8220;gz&#8221; extension.</li>
 </ul>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">(base name of <tt class="docutils literal"><span class="pre">file</span></tt> (<tt class="xref py py-class docutils literal"><span class="pre">str</span></tt>), extension of file without a
-&#8221;.gz&#8221; (<tt class="xref py py-class docutils literal"><span class="pre">str</span></tt>), flag to indicate an additional &#8221;.gz&#8221;
-(<tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt>)) <strong>if</strong> <tt class="docutils literal"><span class="pre">gz</span></tt> is set, (base name of <tt class="docutils literal"><span class="pre">file</span></tt>
-(<tt class="xref py py-class docutils literal"><span class="pre">str</span></tt>), extension of file) <strong>if not</strong>.</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">(base name of <tt class="docutils literal"><span class="pre">file</span></tt> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">str</span></tt></a>), extension of file without a
+&#8221;.gz&#8221; (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">str</span></tt></a>), flag to indicate an additional &#8221;.gz&#8221;
+(<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>)) <strong>if</strong> <tt class="docutils literal"><span class="pre">gz</span></tt> is set, (base name of <tt class="docutils literal"><span class="pre">file</span></tt>
+(<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">str</span></tt></a>), extension of file) <strong>if not</strong>.</p>
 </td>
 </tr>
 </tbody>
@@ -171,8 +171,8 @@ shell. <tt class="docutils literal"><span class="pre">0</span></tt> is tradition
   <p class="topless"><a href="index.html"
                         title="previous chapter"><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 core functionality</a></p>
   <h4>Next topic</h4>
-  <p class="topless"><a href="../meld/index.html"
-                        title="next chapter"><tt class="docutils literal"><span class="pre">meld</span></tt> - Coordinate modeling</a></p>
+  <p class="topless"><a href="helper.html"
+                        title="next chapter"><tt class="docutils literal"><span class="pre">helper</span></tt> - Shared functionality for the everything</a></p>
   <h3>This Page</h3>
   <ul class="this-page-menu">
     <li><a href="../_sources/core/argcheck.txt"
@@ -205,7 +205,7 @@ shell. <tt class="docutils literal"><span class="pre">0</span></tt> is tradition
           <a href="../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="right" >
-          <a href="../meld/index.html" title="meld - Coordinate modeling"
+          <a href="helper.html" title="helper - Shared functionality for the everything"
              >next</a> |</li>
         <li class="right" >
           <a href="index.html" title="core - ProMod3 core functionality"
@@ -217,7 +217,7 @@ shell. <tt class="docutils literal"><span class="pre">0</span></tt> is tradition
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Sep 18 15:50, 2014.
+      Last updated on Oct 16 09:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 34e940facadd8833d2a3ecf696901df65759e316..0f1d5a6abf8889372a81ecad14605c453217a411 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -56,7 +56,8 @@
             
   <div class="section" id="module-promod3.core">
 <span id="core-promod3-core-functionality"></span><h1><a class="reference internal" href="#module-promod3.core" title="promod3.core: Basic functionality, supporting standard tasks in your code."><tt class="xref py py-mod docutils literal"><span class="pre">core</span></tt></a> - ProMod3 core functionality<a class="headerlink" href="#module-promod3.core" title="Permalink to this headline">¶</a></h1>
-<p>This module gathers functions and classes which are not devoted to homology modeling per se but cover standard programming issues.</p>
+<p>This module gathers functions and classes which are not devoted to homology
+modeling per se but cover standard programming issues.</p>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="argcheck.html"><tt class="docutils literal"><span class="pre">argcheck</span></tt> - Standard tests for command line arguments</a><ul>
@@ -64,6 +65,11 @@
 <li class="toctree-l2"><a class="reference internal" href="argcheck.html#file-tests">File Tests</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="helper.html"><tt class="docutils literal"><span class="pre">helper</span></tt> - Shared functionality for the everything</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="helper.html#introduction">Introduction</a></li>
+<li class="toctree-l2"><a class="reference internal" href="helper.html#messages">Messages</a></li>
+</ul>
+</li>
 </ul>
 </div>
 </div>
@@ -123,7 +129,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Sep 18 15:50, 2014.
+      Last updated on Oct 16 09:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 62874d5948d7c5dc0269c94925e6b7add3c23e91..f999557c69bb510223f004b05548e27be2a74d75 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -59,11 +59,11 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="core/index.html"><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 core functionality</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="core/argcheck.html"><tt class="docutils literal"><span class="pre">argcheck</span></tt> - Standard tests for command line arguments</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/helper.html"><tt class="docutils literal"><span class="pre">helper</span></tt> - Shared functionality for the everything</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="meld/index.html"><tt class="docutils literal"><span class="pre">meld</span></tt> - Coordinate modeling</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="meld/loop.html">Loop Modeling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="meld/rawmodel.html">Raw Coordinate Modeling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="meld/index.html#raw-coordinate-modeling-api">Raw Coordinate Modeling API</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="buildsystem.html">Building ProMod3</a><ul>
@@ -140,7 +140,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Sep 25 11:22, 2014.
+      Last updated on Oct 16 09:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 873f86cb88c47efb4b5aaf240adb09cd1ced1257..00249f62eaf8438f2d207f09fc0cfcb5ddac3de9 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -49,69 +49,19 @@
 <h1 id="index">Index</h1>
 
 <div class="genindex-jumpbox">
- <a href="#A"><strong>A</strong></a>
- | <a href="#B"><strong>B</strong></a>
- | <a href="#C"><strong>C</strong></a>
+ <a href="#B"><strong>B</strong></a>
  | <a href="#F"><strong>F</strong></a>
  | <a href="#G"><strong>G</strong></a>
- | <a href="#I"><strong>I</strong></a>
- | <a href="#L"><strong>L</strong></a>
  | <a href="#M"><strong>M</strong></a>
  | <a href="#P"><strong>P</strong></a>
  | <a href="#R"><strong>R</strong></a>
- | <a href="#S"><strong>S</strong></a>
- | <a href="#T"><strong>T</strong></a>
  
 </div>
-<h2 id="A">A</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidates.Add">Add() (sm.meld.LoopCandidates method)</a>
-  </dt>
-
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidate.allatom_score">allatom_score (sm.meld.LoopCandidate attribute)</a>
-  </dt>
-
-  </dl></td>
-</tr></table>
-
 <h2 id="B">B</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="meld/rawmodel.html#sm.meld.BuildRawModel">BuildRawModel() (in module sm.meld)</a>
-  </dt>
-
-  </dl></td>
-</tr></table>
-
-<h2 id="C">C</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidate.clash_bb_score">clash_bb_score (sm.meld.LoopCandidate attribute)</a>
-  </dt>
-
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidate.clash_sc_score">clash_sc_score (sm.meld.LoopCandidate attribute)</a>
-  </dt>
-
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidate.clash_score">clash_score (sm.meld.LoopCandidate attribute)</a>
-  </dt>
-
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidate.coords">coords (sm.meld.LoopCandidate attribute)</a>
-  </dt>
-
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidate.correl">correl (sm.meld.LoopCandidate attribute)</a>
+  <dt><a href="meld/index.html#promod3.meld.BuildRawModel">BuildRawModel() (in module promod3.meld)</a>
   </dt>
 
   </dl></td>
@@ -137,39 +87,7 @@
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidate.gap">gap (sm.meld.LoopCandidate attribute)</a>
-  </dt>
-
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="meld/rawmodel.html#sm.meld.RawModelingResult.gaps">gaps (sm.meld.RawModelingResult attribute)</a>
-  </dt>
-
-  </dl></td>
-</tr></table>
-
-<h2 id="I">I</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidate.InsertInto">InsertInto() (sm.meld.LoopCandidate method)</a>
-  </dt>
-
-  </dl></td>
-</tr></table>
-
-<h2 id="L">L</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidate">LoopCandidate (class in sm.meld)</a>
-  </dt>
-
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidates">LoopCandidates (class in sm.meld)</a>
+  <dt><a href="meld/index.html#promod3.meld.RawModelingResult.gaps">gaps (promod3.meld.RawModelingResult attribute)</a>
   </dt>
 
   </dl></td>
@@ -205,15 +123,13 @@
   </dt>
 
       
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidates.model">model (sm.meld.LoopCandidates attribute)</a>
+  <dt><a href="meld/index.html#promod3.meld.RawModelingResult.model">model (promod3.meld.RawModelingResult attribute)</a>
   </dt>
 
-      <dd><dl>
-        
-  <dt><a href="meld/rawmodel.html#sm.meld.RawModelingResult.model">(sm.meld.RawModelingResult attribute)</a>
+      
+  <dt><a href="core/helper.html#promod3.core.helper.MsgErrorAndExit">MsgErrorAndExit() (in module promod3.core.helper)</a>
   </dt>
 
-      </dl></dd>
   </dl></td>
 </tr></table>
 
@@ -221,10 +137,6 @@
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidate.packing_score">packing_score (sm.meld.LoopCandidate attribute)</a>
-  </dt>
-
-      
   <dt><a href="core/index.html#module-promod3.core">promod3.core (module)</a>
   </dt>
 
@@ -241,53 +153,7 @@
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="meld/rawmodel.html#sm.meld.RawModelingResult">RawModelingResult (class in sm.meld)</a>
-  </dt>
-
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidate.reduced_score">reduced_score (sm.meld.LoopCandidate attribute)</a>
-  </dt>
-
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidate.RmsdTo">RmsdTo() (sm.meld.LoopCandidate method)</a>
-  </dt>
-
-  </dl></td>
-</tr></table>
-
-<h2 id="S">S</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidate.score">score (sm.meld.LoopCandidate attribute)</a>
-  </dt>
-
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidates.SortByCorrel">SortByCorrel() (sm.meld.LoopCandidates method)</a>
-  </dt>
-
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidates.SortByScore">SortByScore() (sm.meld.LoopCandidates method)</a>
-  </dt>
-
-  </dl></td>
-</tr></table>
-
-<h2 id="T">T</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidate.ToEntity">ToEntity() (sm.meld.LoopCandidate method)</a>
-  </dt>
-
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="meld/loop.html#sm.meld.LoopCandidate.torsion_score">torsion_score (sm.meld.LoopCandidate attribute)</a>
+  <dt><a href="meld/index.html#promod3.meld.RawModelingResult">RawModelingResult (class in promod3.meld)</a>
   </dt>
 
   </dl></td>
@@ -334,7 +200,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Sep 25 11:22, 2014.
+      Last updated on Oct 16 09:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/index.html b/doc/html/index.html
index de372cdc663e3f328c84468a401834cab57580a8..728d4c3131da60adb60b6894859717ea708927eb 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -132,7 +132,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Sep 25 11:22, 2014.
+      Last updated on Oct 16 09:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/meld/index.html b/doc/html/meld/index.html
index 6dd1af16b259e784215f0bf39303fd6ad4de4d3d..0f71bc8f67df5016a6aecc0450597170a46c5178 100644
--- a/doc/html/meld/index.html
+++ b/doc/html/meld/index.html
@@ -25,8 +25,8 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <link rel="top" title="ProMod3 0 documentation" href="../index.html" />
     <link rel="up" title="Documentation For Developes" href="../developers.html" />
-    <link rel="next" title="Loop Modeling" href="loop.html" />
-    <link rel="prev" title="argcheck - Standard tests for command line arguments" href="../core/argcheck.html" /> 
+    <link rel="next" title="Building ProMod3" href="../buildsystem.html" />
+    <link rel="prev" title="helper - Shared functionality for the everything" href="../core/helper.html" /> 
   </head>
   <body>
     <div class="related">
@@ -39,10 +39,10 @@
           <a href="../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="right" >
-          <a href="loop.html" title="Loop Modeling"
+          <a href="../buildsystem.html" title="Building ProMod3"
              accesskey="N">next</a> |</li>
         <li class="right" >
-          <a href="../core/argcheck.html" title="argcheck - Standard tests for command line arguments"
+          <a href="../core/helper.html" title="helper - Shared functionality for the everything"
              accesskey="P">previous</a> |</li>
         <li><a href="../index.html">ProMod3 0 documentation</a> &raquo;</li>
           <li><a href="../developers.html" accesskey="U">Documentation For Developes</a> &raquo;</li> 
@@ -55,20 +55,99 @@
           <div class="body">
             
   <div class="section" id="module-promod3.meld">
-<span id="meld-coordinate-modeling"></span><h1><a class="reference internal" href="#module-promod3.meld" title="promod3.meld: Coordinate modeling and sampling"><tt class="xref py py-mod docutils literal"><span class="pre">meld</span></tt></a> - Coordinate modeling<a class="headerlink" href="#module-promod3.meld" title="Permalink to this headline">¶</a></h1>
-<p>This module contains functions and classes to model protein structures from sequence.</p>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="loop.html">Loop Modeling</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="loop.html#loop-modeling-api">Loop Modeling API</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="rawmodel.html">Raw Coordinate Modeling</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="rawmodel.html#introduction">Introduction</a></li>
-<li class="toctree-l2"><a class="reference internal" href="rawmodel.html#raw-coordinate-modeling-api">Raw Coordinate Modeling API</a></li>
-</ul>
-</li>
+<span id="meld-coordinate-modeling"></span><h1><a class="reference internal" href="#module-promod3.meld" title="promod3.meld: Raw Coordinate Model"><tt class="xref py py-mod docutils literal"><span class="pre">meld</span></tt></a> - Coordinate modeling<a class="headerlink" href="#module-promod3.meld" title="Permalink to this headline">¶</a></h1>
+<p>Functionality to build raw (pseudo) models based on a sequence alignment.
+Here is an example of how to build a model from an alignment and a structure.</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">meld</span>
+
+<span class="n">aln</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadAlignment</span><span class="p">(</span><span class="s">&#39;seq.fasta&#39;</span><span class="p">)</span>
+<span class="n">template_structure</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">&#39;gly.pdb&#39;</span><span class="p">,</span> <span class="n">restrict_chains</span><span class="o">=</span><span class="s">&#39;A&#39;</span><span class="p">)</span>
+<span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">template_structure</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">&#39;peptide=true&#39;</span><span class="p">))</span>
+<span class="n">result</span> <span class="o">=</span> <span class="n">meld</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="s">&#39;model.pdb&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+<div class="section" id="raw-coordinate-modeling-api">
+<h2>Raw Coordinate Modeling API<a class="headerlink" href="#raw-coordinate-modeling-api" title="Permalink to this headline">¶</a></h2>
+<dl class="function">
+<dt id="promod3.meld.BuildRawModel">
+<tt class="descclassname">promod3.meld.</tt><tt class="descname">BuildRawModel</tt><big>(</big><em>alignment</em>, <em>calpha_only=False</em><big>)</big><a class="headerlink" href="#promod3.meld.BuildRawModel" title="Permalink to this definition">¶</a></dt>
+<dt>
+<tt class="descclassname">promod3.meld.</tt><tt class="descname">BuildRawModel</tt><big>(</big><em>alignments</em>, <em>calpha_only=False</em><big>)</big></dt>
+<dd><p>Builds a raw (pseudo) model from the alignment. Can either take a single
+alignment handle or an alignment handle list. Every list item is treated as a
+single chain in the final raw model.</p>
+<p>This is a basic protein core modeling algorithm that copies backbone
+coordinates based on the sequence alignment. For matching residues, the
+side chain coordinates are also copied. Gaps are ignored. Hydrogen an
+deuterium atoms are not copied into the model.</p>
+<p>The function tries to reuse as much as possible from the template. Modified
+residues are treated as follows:</p>
+<blockquote>
+<div><ul class="simple">
+<li>Selenium methionine residues are converted to methionine</li>
+<li>Side chains which contain all atoms of the parent amino acid, e.g.
+phosphoserine are copied as a whole with the modifications stripped off.</li>
 </ul>
+</div></blockquote>
+<p>Residue numbers are set such that missing residue in gaps are honoured and
+subsequent loop modeling can insert new residues without having to
+renumber.</p>
+<p>The returned <a class="reference internal" href="#promod3.meld.RawModelingResult" title="promod3.meld.RawModelingResult"><tt class="xref py py-class docutils literal"><span class="pre">RawModelingResult</span></tt></a> stores the obtained raw model as well
+as information about insertions and deletions in the gaps list.</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>calpha_only</strong> &#8211; If true, only Calpha atoms will be copied. Side chains
+and other backbone atoms are completely ignored.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body">A <tt class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></tt> when the second sequence does not have an
+attached structure</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="class">
+<dt id="promod3.meld.RawModelingResult">
+<em class="property">class </em><tt class="descclassname">promod3.meld.</tt><tt class="descname">RawModelingResult</tt><a class="headerlink" href="#promod3.meld.RawModelingResult" title="Permalink to this definition">¶</a></dt>
+<dd><p>Holds the result of raw model building. Incredibly minimalistic for now. Will
+most likely grow a few more members over time to, e.g. to store a detailed
+report.</p>
+<dl class="attribute">
+<dt id="promod3.meld.RawModelingResult.model">
+<tt class="descname">model</tt><a class="headerlink" href="#promod3.meld.RawModelingResult.model" title="Permalink to this definition">¶</a></dt>
+<dd><p>The resulting model.</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="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.3.3)"><tt class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></tt></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.meld.RawModelingResult.gaps">
+<tt class="descname">gaps</tt><a class="headerlink" href="#promod3.meld.RawModelingResult.gaps" title="Permalink to this definition">¶</a></dt>
+<dd><p>List of gaps in the model that could not be copied from the template. These
+gaps may be the result of insertions/deletions in the alignment or due to
+missing or incomplete backbone coordinates in the template structure.</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"><tt class="xref py py-class docutils literal"><span class="pre">StructuralGapList</span></tt></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
 </div>
 </div>
 
@@ -78,12 +157,20 @@
       </div>
       <div class="sphinxsidebar">
         <div class="sphinxsidebarwrapper">
+  <h3><a href="../index.html">Table Of Contents</a></h3>
+  <ul>
+<li><a class="reference internal" href="#"><tt class="docutils literal"><span class="pre">meld</span></tt> - Coordinate modeling</a><ul>
+<li><a class="reference internal" href="#raw-coordinate-modeling-api">Raw Coordinate Modeling API</a></li>
+</ul>
+</li>
+</ul>
+
   <h4>Previous topic</h4>
-  <p class="topless"><a href="../core/argcheck.html"
-                        title="previous chapter"><tt class="docutils literal"><span class="pre">argcheck</span></tt> - Standard tests for command line arguments</a></p>
+  <p class="topless"><a href="../core/helper.html"
+                        title="previous chapter"><tt class="docutils literal"><span class="pre">helper</span></tt> - Shared functionality for the everything</a></p>
   <h4>Next topic</h4>
-  <p class="topless"><a href="loop.html"
-                        title="next chapter">Loop Modeling</a></p>
+  <p class="topless"><a href="../buildsystem.html"
+                        title="next chapter">Building ProMod3</a></p>
   <h3>This Page</h3>
   <ul class="this-page-menu">
     <li><a href="../_sources/meld/index.txt"
@@ -116,10 +203,10 @@
           <a href="../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="right" >
-          <a href="loop.html" title="Loop Modeling"
+          <a href="../buildsystem.html" title="Building ProMod3"
              >next</a> |</li>
         <li class="right" >
-          <a href="../core/argcheck.html" title="argcheck - Standard tests for command line arguments"
+          <a href="../core/helper.html" title="helper - Shared functionality for the everything"
              >previous</a> |</li>
         <li><a href="../index.html">ProMod3 0 documentation</a> &raquo;</li>
           <li><a href="../developers.html" >Documentation For Developes</a> &raquo;</li> 
@@ -127,7 +214,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Sep 18 16:17, 2014.
+      Last updated on Oct 16 09:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/meld/loop.html b/doc/html/meld/loop.html
deleted file mode 100644
index 75bbf7696bd9945724adf37f6172b12d7c957d5e..0000000000000000000000000000000000000000
--- a/doc/html/meld/loop.html
+++ /dev/null
@@ -1,345 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    
-    <title>Loop Modeling &mdash; ProMod3 0 documentation</title>
-    
-    <link rel="stylesheet" href="../_static/default.css" type="text/css" />
-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    
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-      <h3>Navigation</h3>
-      <ul>
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-          <a href="../genindex.html" title="General Index"
-             accesskey="I">index</a></li>
-        <li class="right" >
-          <a href="../py-modindex.html" title="Python Module Index"
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-          <li><a href="../developers.html" >Documentation For Developes</a> &raquo;</li>
-          <li><a href="index.html" accesskey="U"><tt class="docutils literal"><span class="pre">meld</span></tt> - Coordinate modeling</a> &raquo;</li> 
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-      <div class="documentwrapper">
-        <div class="bodywrapper">
-          <div class="body">
-            
-  <div class="section" id="loop-modeling">
-<h1>Loop Modeling<a class="headerlink" href="#loop-modeling" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="loop-modeling-api">
-<h2>Loop Modeling API<a class="headerlink" href="#loop-modeling-api" title="Permalink to this headline">¶</a></h2>
-<dl class="class">
-<dt id="sm.meld.LoopCandidate">
-<em class="property">class </em><tt class="descclassname">sm.meld.</tt><tt class="descname">LoopCandidate</tt><big>(</big><em>gap</em>, <em>bb_list</em><big>)</big><a class="headerlink" href="#sm.meld.LoopCandidate" title="Permalink to this definition">¶</a></dt>
-<dd><p>A loop candidate holds the coordinates of the four backbone atoms for a given
-peptide fragment as well as the sequence.</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"><ul class="first last simple">
-<li><strong>gap</strong> (<tt class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></tt>) &#8211; The structural gap</li>
-<li><strong>bb_list</strong> (<tt class="xref py py-class docutils literal"><span class="pre">BackboneList</span></tt>) &#8211; List of peptide backbone coordinates</li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-<dl class="method">
-<dt id="sm.meld.LoopCandidate.InsertInto">
-<tt class="descname">InsertInto</tt><big>(</big><em>entity</em><big>)</big><a class="headerlink" href="#sm.meld.LoopCandidate.InsertInto" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inserts the loop candidate into the given entity. This honours the start and
-end point stored in the gap. Missing residues and atoms will be inserted
-into the structure.</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>entity</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.3.3)"><tt class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></tt></a>) &#8211; </td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">True on success, false if the insertion failed</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">bool</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="sm.meld.LoopCandidate.RmsdTo">
-<tt class="descname">RmsdTo</tt><big>(</big><em>entity</em><big>)</big><a class="headerlink" href="#sm.meld.LoopCandidate.RmsdTo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calculates the RMSD to the corresponding backbone fragment in <em>entity</em>.
-Raises a RuntimeError if not all backbone atoms exist.</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>entity</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.3.3)"><tt class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></tt></a>) &#8211; </td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">float</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="sm.meld.LoopCandidate.ToEntity">
-<tt class="descname">ToEntity</tt><big>(</big><big>)</big><a class="headerlink" href="#sm.meld.LoopCandidate.ToEntity" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns an entity holding this backbone fragment. Residue numbers go from
-gap.start to gap.end.</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">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.3.3)"><tt class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></tt></a></td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="sm.meld.LoopCandidate.allatom_score">
-<tt class="descname">allatom_score</tt><a class="headerlink" href="#sm.meld.LoopCandidate.allatom_score" title="Permalink to this definition">¶</a></dt>
-<dd><p>If set, the allatom_score of this fragment</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="sm.meld.LoopCandidate.clash_bb_score">
-<tt class="descname">clash_bb_score</tt><a class="headerlink" href="#sm.meld.LoopCandidate.clash_bb_score" title="Permalink to this definition">¶</a></dt>
-<dd><p>The clash score of the loop candidate with sidechain atoms</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="sm.meld.LoopCandidate.clash_score">
-<tt class="descname">clash_score</tt><a class="headerlink" href="#sm.meld.LoopCandidate.clash_score" title="Permalink to this definition">¶</a></dt>
-<dd><p>The sum of backbone and sidechain clash scores</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="sm.meld.LoopCandidate.clash_sc_score">
-<tt class="descname">clash_sc_score</tt><a class="headerlink" href="#sm.meld.LoopCandidate.clash_sc_score" title="Permalink to this definition">¶</a></dt>
-<dd><p>Clash score with sidechain atoms</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="sm.meld.LoopCandidate.coords">
-<tt class="descname">coords</tt><a class="headerlink" href="#sm.meld.LoopCandidate.coords" title="Permalink to this definition">¶</a></dt>
-<dd><p>Access to the actual coordinates</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"><tt class="xref py py-class docutils literal"><span class="pre">BackboneList</span></tt></td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="sm.meld.LoopCandidate.correl">
-<tt class="descname">correl</tt><a class="headerlink" href="#sm.meld.LoopCandidate.correl" title="Permalink to this definition">¶</a></dt>
-<dd><p>Correlation with density</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="sm.meld.LoopCandidate.gap">
-<tt class="descname">gap</tt><a class="headerlink" href="#sm.meld.LoopCandidate.gap" title="Permalink to this definition">¶</a></dt>
-<dd><p>The structural gap</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="sm.meld.LoopCandidate.packing_score">
-<tt class="descname">packing_score</tt><a class="headerlink" href="#sm.meld.LoopCandidate.packing_score" title="Permalink to this definition">¶</a></dt>
-<dd><p>Packing score of this loop candidate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="sm.meld.LoopCandidate.reduced_score">
-<tt class="descname">reduced_score</tt><a class="headerlink" href="#sm.meld.LoopCandidate.reduced_score" title="Permalink to this definition">¶</a></dt>
-<dd><p>Reduced score</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="sm.meld.LoopCandidate.score">
-<tt class="descname">score</tt><a class="headerlink" href="#sm.meld.LoopCandidate.score" title="Permalink to this definition">¶</a></dt>
-<dd><p>Total score of this loop candidate.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="sm.meld.LoopCandidate.torsion_score">
-<tt class="descname">torsion_score</tt><a class="headerlink" href="#sm.meld.LoopCandidate.torsion_score" title="Permalink to this definition">¶</a></dt>
-<dd><p>Torsion score of this loop candidate</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="sm.meld.LoopCandidates">
-<em class="property">class </em><tt class="descclassname">sm.meld.</tt><tt class="descname">LoopCandidates</tt><big>(</big><em>model</em><big>)</big><a class="headerlink" href="#sm.meld.LoopCandidates" title="Permalink to this definition">¶</a></dt>
-<dd><p>A list of loop candidates with a few helper methods to make your life easier.
-The candidates are supposed to be loop candidates for the same gap. However,
-they are not required to have the same start and end position, e.g. due to
-extension of the gap.</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>model</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.3.3)"><tt class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></tt></a>) &#8211; The model the candidates are for.</td>
-</tr>
-</tbody>
-</table>
-<dl class="method">
-<dt id="sm.meld.LoopCandidates.Add">
-<tt class="descname">Add</tt><big>(</big><em>candidate</em><big>)</big><a class="headerlink" href="#sm.meld.LoopCandidates.Add" title="Permalink to this definition">¶</a></dt>
-<dd><p>Add a new candidate
-:param candidate:
-:type  candidate: <a class="reference internal" href="#sm.meld.LoopCandidate" title="sm.meld.LoopCandidate"><tt class="xref py py-class docutils literal"><span class="pre">LoopCandidate</span></tt></a></p>
-</dd></dl>
-
-<dl class="method">
-<dt id="sm.meld.LoopCandidates.SortByCorrel">
-<tt class="descname">SortByCorrel</tt><big>(</big><span class="optional">[</span><em>increasing</em><span class="optional">]</span><big>)</big><a class="headerlink" href="#sm.meld.LoopCandidates.SortByCorrel" title="Permalink to this definition">¶</a></dt>
-<dd><p>Sort loop candidates by correlation score</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>increasing</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><em>bool</em></a>) &#8211; If true, the candidates are sorted in increasing order</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="sm.meld.LoopCandidates.SortByScore">
-<tt class="descname">SortByScore</tt><big>(</big><span class="optional">[</span><em>increasing</em><span class="optional">]</span><big>)</big><a class="headerlink" href="#sm.meld.LoopCandidates.SortByScore" title="Permalink to this definition">¶</a></dt>
-<dd><p>Sort loop canditates by total score</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>increasing</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><em>bool</em></a>) &#8211; If true, the candidates are sorted in increasing order</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="sm.meld.LoopCandidates.model">
-<tt class="descname">model</tt><a class="headerlink" href="#sm.meld.LoopCandidates.model" title="Permalink to this definition">¶</a></dt>
-<dd><p>The model the candidates are for</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="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.3.3)"><tt class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></tt></a></td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-</dd></dl>
-
-</div>
-</div>
-
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-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../index.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Loop Modeling</a><ul>
-<li><a class="reference internal" href="#loop-modeling-api">Loop Modeling API</a></li>
-</ul>
-</li>
-</ul>
-
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-  <p class="topless"><a href="index.html"
-                        title="previous chapter"><tt class="docutils literal"><span class="pre">meld</span></tt> - Coordinate modeling</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="rawmodel.html"
-                        title="next chapter">Raw Coordinate Modeling</a></p>
-  <h3>This Page</h3>
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diff --git a/doc/html/meld/rawmodel.html b/doc/html/meld/rawmodel.html
deleted file mode 100644
index 79038f458bfc8eb1d4eb82a3824e72570c08f2ae..0000000000000000000000000000000000000000
--- a/doc/html/meld/rawmodel.html
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-            
-  <div class="section" id="raw-coordinate-modeling">
-<h1>Raw Coordinate Modeling<a class="headerlink" href="#raw-coordinate-modeling" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="introduction">
-<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
-<p>Contains function to build raw (pseudo) models based on a sequence alignment. Here is an example of how to build a model from an alignment and a structure.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">meld</span>
-
-<span class="n">aln</span><span class="o">=</span><span class="n">io</span><span class="o">.</span><span class="n">LoadAlignment</span><span class="p">(</span><span class="s">&#39;parwise.fasta&#39;</span><span class="p">)</span>
-<span class="n">template_structure</span><span class="o">=</span><span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">&#39;1ake.pdb&#39;</span><span class="p">,</span> <span class="n">restrict_chains</span><span class="o">=</span><span class="s">&#39;A&#39;</span><span class="p">)</span>
-<span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">template_structure</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">&#39;peptide=true&#39;</span><span class="p">))</span>
-<span class="n">result</span><span class="o">=</span><span class="n">meld</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="s">&#39;model.pdb&#39;</span><span class="p">)</span>
-<span class="k">print</span> <span class="s">&#39;remaining gaps:&#39;</span>
-<span class="k">for</span> <span class="n">gap</span> <span class="ow">in</span> <span class="n">result</span><span class="o">.</span><span class="n">gaps</span><span class="p">:</span>
-  <span class="k">print</span> <span class="s">&#39; * </span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">gap</span><span class="p">)</span>
-</pre></div>
-</div>
-</div>
-<div class="section" id="raw-coordinate-modeling-api">
-<h2>Raw Coordinate Modeling API<a class="headerlink" href="#raw-coordinate-modeling-api" title="Permalink to this headline">¶</a></h2>
-<dl class="function">
-<dt id="sm.meld.BuildRawModel">
-<tt class="descclassname">sm.meld.</tt><tt class="descname">BuildRawModel</tt><big>(</big><em>alignment</em>, <em>calpha_only=False</em><big>)</big><a class="headerlink" href="#sm.meld.BuildRawModel" title="Permalink to this definition">¶</a></dt>
-<dt>
-<tt class="descclassname">sm.meld.</tt><tt class="descname">BuildRawModel</tt><big>(</big><em>alignments</em>, <em>calpha_only=False</em><big>)</big></dt>
-<dd><p>Builds a raw (pseudo) model from the alignment.
-Can either take a single alignment handle or an alignment handle list.
-Every list item is treated as a single chain in the final raw model.</p>
-<p>This is a basic protein core modeling algorithm that copies backbone
-coordinates based on the sequence alignment. For matching residues, the
-sidechain coordinates are also copied. Gaps are ignored. Hydrogen an deuterium
-atoms are not copied into the model.</p>
-<p>The function tries to reuse as much as possible from the template. Modified
-residues are treated as follows:</p>
-<blockquote>
-<div><ul class="simple">
-<li>Selenium methionine residues are converted to methionines</li>
-<li>Sidechains which contain all atoms of the parent amino acid, e.g.
-phosphoserine are copied as a whole with the modifications stripped off.</li>
-</ul>
-</div></blockquote>
-<p>Residue numbers are set such that missing residue in gaps are honored and
-subsequent loop modeling can insert new residues without having to
-renumber.</p>
-<p>The returned <a class="reference internal" href="#sm.meld.RawModelingResult" title="sm.meld.RawModelingResult"><tt class="xref py py-class docutils literal"><span class="pre">RawModelingResult</span></tt></a> stores the obtained raw model as well
-as information about insertions and deletions in the gaps list.</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>calpha_only</strong> &#8211; If true, only Calpha atoms will be copied. Sidechains and
-other backbone atoms are completely ignored.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body">A <tt class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></tt> when the second sequence does not have an
-attached structure</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="class">
-<dt id="sm.meld.RawModelingResult">
-<em class="property">class </em><tt class="descclassname">sm.meld.</tt><tt class="descname">RawModelingResult</tt><a class="headerlink" href="#sm.meld.RawModelingResult" title="Permalink to this definition">¶</a></dt>
-<dd><p>Holds the result of raw model building. Incredibly minimalistic for now. Will
-most likely grow a few more members over time to, e.g. to store a detailed
-report.</p>
-<dl class="attribute">
-<dt id="sm.meld.RawModelingResult.model">
-<tt class="descname">model</tt><a class="headerlink" href="#sm.meld.RawModelingResult.model" title="Permalink to this definition">¶</a></dt>
-<dd><p>The resulting model.</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="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.3.3)"><tt class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></tt></a></td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="sm.meld.RawModelingResult.gaps">
-<tt class="descname">gaps</tt><a class="headerlink" href="#sm.meld.RawModelingResult.gaps" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of gaps in the model that could not be copied from the template. These
-gaps may be the result of insertions/deletions in the alignment or due to
-missing or incomplete backbone coordinates in the template structure.</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"><tt class="xref py py-class docutils literal"><span class="pre">StructuralGapList</span></tt></td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-</dd></dl>
-
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../index.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Raw Coordinate Modeling</a><ul>
-<li><a class="reference internal" href="#introduction">Introduction</a></li>
-<li><a class="reference internal" href="#raw-coordinate-modeling-api">Raw Coordinate Modeling API</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="loop.html"
-                        title="previous chapter">Loop Modeling</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="../buildsystem.html"
-                        title="next chapter">Building ProMod3</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
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diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 5f98c7dd8eb9661333612747ad89492cf38764c1..74174deab424a13c6f3e3035ccaeffedc1a058f7 100644
--- a/doc/html/objects.inv
+++ b/doc/html/objects.inv
@@ -2,5 +2,4 @@
 # Project: ProMod3
 # Version: 0.1
 # The remainder of this file is compressed using zlib.
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diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index d39d332e052bc1adf428453b8673521947e9de41..2fbe71259e595d59d1f39f1349f136e232eb4b37 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -73,7 +73,7 @@
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
        <a href="meld/index.html#module-promod3.meld"><tt class="xref">promod3.meld</tt></a></td><td>
-       <em>Coordinate modeling and sampling</em></td></tr>
+       <em>Raw Coordinate Model</em></td></tr>
    </table>
 
 
@@ -113,7 +113,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Sep 25 11:22, 2014.
+      Last updated on Oct 16 09:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/search.html b/doc/html/search.html
index 72ed3117c048d4a43b05d273560b6fa0274d9330..7f012f8889852082fea816a4d9f89a1d04168153 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -99,7 +99,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Sep 25 11:22, 2014.
+      Last updated on Oct 16 09:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 7aeb31c4266540ce82ed9b7d7c0d4e687769cdf7..4fe49b1d6804d89cb18e206ca7e671794e3140a8 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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diff --git a/doc/html/users.html b/doc/html/users.html
index bfc1fc6897970868976be0c6751cbf9543ddb0e1..23f886887981e1ffe430b323ccc69d2418fbb49d 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
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-      Last updated on Sep 18 15:50, 2014.
+      Last updated on Oct 16 09:31, 2014.
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