diff --git a/doc/html/.doctrees/contributing.doctree b/doc/html/.doctrees/contributing.doctree
index 6c5f22aa65626ea998f81eae297993d10b278eec..f366d50d132d1436a2df8c5f88c0dcf4e2976e41 100644
Binary files a/doc/html/.doctrees/contributing.doctree and b/doc/html/.doctrees/contributing.doctree differ
diff --git a/doc/html/.doctrees/core/argcheck.doctree b/doc/html/.doctrees/core/argcheck.doctree
index e8ebe02f0f9383e5f8282294b7e64c8590bf3b29..cc6ee6ecf1f02017213224ff911405d18f5f7b71 100644
Binary files a/doc/html/.doctrees/core/argcheck.doctree and b/doc/html/.doctrees/core/argcheck.doctree differ
diff --git a/doc/html/.doctrees/core/index.doctree b/doc/html/.doctrees/core/index.doctree
index e4fa8e5f34e1a8eabba3b9d360ec67a120404836..6bd9c5aa11f20af5893d6a6ceadb6b3f81af93ad 100644
Binary files a/doc/html/.doctrees/core/index.doctree and b/doc/html/.doctrees/core/index.doctree differ
diff --git a/doc/html/.doctrees/environment.pickle b/doc/html/.doctrees/environment.pickle
index 1c33f9ba708dc5bf34314f1cde159d79ecbd5007..44a4e0a1fb1596c3d4b5513a43b67b41b75be1f1 100644
Binary files a/doc/html/.doctrees/environment.pickle and b/doc/html/.doctrees/environment.pickle differ
diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index 3af2c50ce44fc27c35f390a5fcfd6c13ad979373..a0608c2c640cd6939b2234cff2209735817db72f 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -85,7 +85,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Jul 03 10:51, 2014.
+      Last updated on Jul 07 10:40, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/_modules/promod3/core/argcheck.html b/doc/html/_modules/promod3/core/argcheck.html
index 45c289d84de1fd9d5fbf27542595483fda275e34..3d7cfa89c5013e41946992c688b8d2f5ffbde62b 100644
--- a/doc/html/_modules/promod3/core/argcheck.html
+++ b/doc/html/_modules/promod3/core/argcheck.html
@@ -174,7 +174,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Jul 03 10:51, 2014.
+      Last updated on Jul 07 10:40, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt
index 2828fb187ebe8f6b13116d1e3e966d4e824ae3b1..dff3640e9ad87a0749104b2a3126b0a9c51c5f0e 100644
--- a/doc/html/_sources/contributing.txt
+++ b/doc/html/_sources/contributing.txt
@@ -348,7 +348,7 @@ top level :file:`CMakeLists.txt`:
 
 .. code-block:: cmake
   :linenos:
-  :emphasize-lines: 80
+  :emphasize-lines: 83
 
    #-------------------------------------------------------------------------------
    # Author: Bienchen
@@ -360,7 +360,7 @@ top level :file:`CMakeLists.txt`:
    # (if documentation is disabled, there is no doctest, linkcheck at all)
    cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
    set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/cmake_support)
-   
+
    project(PROMOD3 CXX C)
 
    include(PROMOD3)
@@ -406,6 +406,7 @@ top level :file:`CMakeLists.txt`:
    endif()
    find_package(OPENSTRUCTURE 1.4 REQUIRED 
                 COMPONENTS io mol seq seq_alg mol_alg conop)
+   find_package(QMEAN 1.0 REQUIRED)
 
    if (CMAKE_COMPILER_IS_GNUCXX)
      # do not write back into cache, otherwise the compile command line gets
@@ -419,7 +420,8 @@ top level :file:`CMakeLists.txt`:
 
    # basic environment
    include_directories(${Boost_INCLUDE_DIRS}
-                       ${OST_INCLUDE_DIR})
+                       ${OST_INCLUDE_DIR}
+                       ${QMEAN_INCLUDE_DIR})
 
    set(FILES_TO_BE_REMOVED ${PROJECT_BINARY_DIR}/stage)
    set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES
@@ -429,9 +431,11 @@ top level :file:`CMakeLists.txt`:
    ## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt
    add_subdirectory(config)
    add_subdirectory(core)
+   add_subdirectory(meld)
    add_subdirectory(sidechains)
    add_subdirectory(scripts)
    add_subdirectory(actions)
+   add_subdirectory(extras)
    if(NOT DISABLE_DOCUMENTATION)
      add_changelog_to_doc(FILE "${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG")
      add_subdirectory(doc)
@@ -440,11 +444,12 @@ top level :file:`CMakeLists.txt`:
    ## report setup
    message(STATUS "PROMOD3 will be built with the following options:\n"
            "   OpenStructure (-DOST_ROOT) : ${OST_ROOT}\n"
+           "   QMEAN         (-DQMEAN_ROOT) : ${QMEAN_ROOT}\n"
            "   Optimized     (-DOPTIMIZE) : ${_OPT}\n"
            "   Python                     : ${PYTHON_BINARY}\n")
 
 All that needs to be done for |cmake| to recognise your module is adding its
-directory as shown in line 80.
+directory as shown in line 83.
 
 This was the final step to set up the build system. Running |cmake| at this
 point would create the build environment in place. But building software in
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index be1669cdb06ab01b97fcfa067fc8d24ac3da6144..f3e8ab05ff4a55f448aaafec108e1ddb5dbc92fb 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -197,7 +197,7 @@ builder</li>
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Jul 03 10:51, 2014.
+      Last updated on Jul 07 09:50, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index e1db7225f623ca8074e68e55ec4e198bf5ae05c6..5fd2f52ba779ba2eb2b3754615a91e275e78c2ee 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -445,7 +445,12 @@ top level <tt class="file docutils literal"><span class="pre">CMakeLists.txt</sp
 89
 90
 91
-92</pre></div></td><td class="code"><div class="highlight"><pre> <span class="c">#-------------------------------------------------------------------------------</span>
+92
+93
+94
+95
+96
+97</pre></div></td><td class="code"><div class="highlight"><pre> <span class="c">#-------------------------------------------------------------------------------</span>
  <span class="c"># Author: Bienchen</span>
  <span class="c">#-------------------------------------------------------------------------------</span>
  <span class="c"># Options to CMake:</span>
@@ -501,6 +506,7 @@ top level <tt class="file docutils literal"><span class="pre">CMakeLists.txt</sp
  <span class="nb">endif</span><span class="p">()</span>
  <span class="nb">find_package</span><span class="p">(</span><span class="s">OPENSTRUCTURE</span> <span class="s">1.4</span> <span class="s">REQUIRED</span>
               <span class="s">COMPONENTS</span> <span class="s">io</span> <span class="s">mol</span> <span class="s">seq</span> <span class="s">seq_alg</span> <span class="s">mol_alg</span> <span class="s">conop</span><span class="p">)</span>
+ <span class="nb">find_package</span><span class="p">(</span><span class="s">QMEAN</span> <span class="s">1.0</span> <span class="s">REQUIRED</span><span class="p">)</span>
 
  <span class="nb">if</span> <span class="p">(</span><span class="s">CMAKE_COMPILER_IS_GNUCXX</span><span class="p">)</span>
    <span class="c"># do not write back into cache, otherwise the compile command line gets</span>
@@ -514,7 +520,8 @@ top level <tt class="file docutils literal"><span class="pre">CMakeLists.txt</sp
 
  <span class="c"># basic environment</span>
  <span class="nb">include_directories</span><span class="p">(</span><span class="o">${</span><span class="nv">Boost_INCLUDE_DIRS</span><span class="o">}</span>
-                     <span class="o">${</span><span class="nv">OST_INCLUDE_DIR</span><span class="o">}</span><span class="p">)</span>
+                     <span class="o">${</span><span class="nv">OST_INCLUDE_DIR</span><span class="o">}</span>
+                     <span class="o">${</span><span class="nv">QMEAN_INCLUDE_DIR</span><span class="o">}</span><span class="p">)</span>
 
  <span class="nb">set</span><span class="p">(</span><span class="s">FILES_TO_BE_REMOVED</span> <span class="o">${</span><span class="nv">PROJECT_BINARY_DIR</span><span class="o">}</span><span class="s">/stage</span><span class="p">)</span>
  <span class="nb">set_directory_properties</span><span class="p">(</span><span class="s">PROPERTIES</span> <span class="s">ADDITIONAL_MAKE_CLEAN_FILES</span>
@@ -524,9 +531,11 @@ top level <tt class="file docutils literal"><span class="pre">CMakeLists.txt</sp
  <span class="c">## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt</span>
  <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">config</span><span class="p">)</span>
  <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">core</span><span class="p">)</span>
+ <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">meld</span><span class="p">)</span>
 <span class="hll"> <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">sidechains</span><span class="p">)</span>
 </span> <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">scripts</span><span class="p">)</span>
  <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">actions</span><span class="p">)</span>
+ <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">extras</span><span class="p">)</span>
  <span class="nb">if</span><span class="p">(</span><span class="s">NOT</span> <span class="s">DISABLE_DOCUMENTATION</span><span class="p">)</span>
    <span class="nb">add_changelog_to_doc</span><span class="p">(</span><span class="s">FILE</span> <span class="s2">&quot;${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG&quot;</span><span class="p">)</span>
    <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">doc</span><span class="p">)</span>
@@ -535,12 +544,13 @@ top level <tt class="file docutils literal"><span class="pre">CMakeLists.txt</sp
  <span class="c">## report setup</span>
  <span class="nb">message</span><span class="p">(</span><span class="s">STATUS</span> <span class="s2">&quot;PROMOD3 will be built with the following options:\n&quot;</span>
          <span class="s2">&quot;   OpenStructure (-DOST_ROOT) : ${OST_ROOT}\n&quot;</span>
+         <span class="s2">&quot;   QMEAN         (-DQMEAN_ROOT) : ${QMEAN_ROOT}\n&quot;</span>
          <span class="s2">&quot;   Optimized     (-DOPTIMIZE) : ${_OPT}\n&quot;</span>
          <span class="s2">&quot;   Python                     : ${PYTHON_BINARY}\n&quot;</span><span class="p">)</span>
 </pre></div>
 </td></tr></table></div>
 <p>All that needs to be done for CMake to recognise your module is adding its
-directory as shown in line 80.</p>
+directory as shown in line 83.</p>
 <p>This was the final step to set up the build system. Running CMake at this
 point would create the build environment in place. But building software in
 your code repository has several drawbacks. First of all, it puts all kind of
@@ -697,7 +707,7 @@ you.</p>
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Jun 19 11:36, 2014.
+      Last updated on Jul 07 10:40, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/core/argcheck.html b/doc/html/core/argcheck.html
index 87da7739010efb097ea0c53d4ba03e14c222b70d..6741990a6cfe54153bb54753ac62a08ab5133b71 100644
--- a/doc/html/core/argcheck.html
+++ b/doc/html/core/argcheck.html
@@ -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 Jun 26 16:15, 2014.
+      Last updated on Jul 07 09:50, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 391743016b2fd3ef8b4002ee92b45dd88263f3b1..992edc9e82b9c71fa06eaf623efeb97519aefdc3 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -123,7 +123,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Jun 26 16:15, 2014.
+      Last updated on Jul 07 09:50, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index c03708a1d704e6d5137f5db8851e80e67de9ed5b..f50bf07cc4a387f45be06dfcf076ff093ad94a1c 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -139,7 +139,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Jul 03 10:51, 2014.
+      Last updated on Jul 07 10:40, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 0c7b71b0af48c558bba0c6c54638fef21cf99e76..228223819fc382dfd4dd98ad29bd6cbc6eec9c5e 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -334,7 +334,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Jul 03 10:51, 2014.
+      Last updated on Jul 07 10:40, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/index.html b/doc/html/index.html
index 889a15068d9e12b1cab97df435454daebfca4f46..f6469e9d8676b93dc1b0945c083822929bd55dc6 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -134,7 +134,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Jul 03 10:51, 2014.
+      Last updated on Jul 07 10:40, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index b3827e5dbedc0efb5dbfaa604f7b39003827a4e0..b39703852981793d5c099921721236011bc5dc01 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -113,7 +113,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Jul 03 10:51, 2014.
+      Last updated on Jul 07 10:40, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/search.html b/doc/html/search.html
index 3bb78e7c396b3d3024a74162be7f764f8d3fa089..ef7e789a64f59b9d6de0a370a0c1f24360dc2443 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 Jul 03 10:51, 2014.
+      Last updated on Jul 07 10:40, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index b5660a1565bd0c5d767a5d741627270a5b175713..c1acd1872f521fbeb3ae719aacb58ce889084408 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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