diff --git a/run_af2/doc/html/.buildinfo b/run_af2/doc/html/.buildinfo
index 81f8203bc8c5479c9199bf1d76fb1313b9939b47..26582485d21a3feb4ac48645e7aa0b0eb9dccfe3 100644
--- a/run_af2/doc/html/.buildinfo
+++ b/run_af2/doc/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 34c58de7082695529d0703a29c210ffe
+config: 05a61d3931a722ab5f48da6f21b28fc2
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/run_af2/doc/html/.doctrees/environment.pickle b/run_af2/doc/html/.doctrees/environment.pickle
index 283ced44059f7a6f4cc1b951af2f899adf31d79c..d1385e49856c4fb4a9c1fc0bd46b5470cccf3d82 100644
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diff --git a/run_af2/doc/html/.doctrees/index.doctree b/run_af2/doc/html/.doctrees/index.doctree
index c0a74647a68cd54ec3f973b079f3109ae5d18233..a084148078ece811a5735b8737b27a60ec5499e2 100644
Binary files a/run_af2/doc/html/.doctrees/index.doctree and b/run_af2/doc/html/.doctrees/index.doctree differ
diff --git a/run_af2/doc/html/.doctrees/run_singularity.doctree b/run_af2/doc/html/.doctrees/run_singularity.doctree
index 74e585ceeb602c8d9484561449465216d9902049..3c1faf793ed736d9b1cd43764e6f8101f04a6e5c 100644
Binary files a/run_af2/doc/html/.doctrees/run_singularity.doctree and b/run_af2/doc/html/.doctrees/run_singularity.doctree differ
diff --git a/run_af2/doc/html/_shared.html b/run_af2/doc/html/_shared.html
index 1545cd6a3b7e6f6d78053c820a4ffd9cba717c4d..706f53e8ab3d54a70254f7f5809f256f30ade2f6 100644
--- a/run_af2/doc/html/_shared.html
+++ b/run_af2/doc/html/_shared.html
@@ -5,10 +5,10 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>_shared &#8212; af2@scicore/run_af2 4.0.2 documentation</title>
+    <title>_shared &#8212; af2@scicore/run_af2 4.1.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=649a27d8" />
     <link rel="stylesheet" type="text/css" href="_static/sphinxdoc.css?v=d59dc883" />
-    <script src="_static/documentation_options.js?v=a084f797"></script>
+    <script src="_static/documentation_options.js?v=42d1b3bd"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="genindex.html" />
@@ -31,7 +31,7 @@
         <li class="right" >
           <a href="index.html" title="Welcome to af2@scicore/run_af2’s documentation!"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.0.2 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.1.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">_shared</a></li> 
       </ul>
     </div>  
@@ -142,7 +142,7 @@ and run tests on input with the <a class="reference external" href="https://docs
         <li class="right" >
           <a href="index.html" title="Welcome to af2@scicore/run_af2’s documentation!"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.0.2 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.1.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">_shared</a></li> 
       </ul>
     </div>
diff --git a/run_af2/doc/html/_static/documentation_options.js b/run_af2/doc/html/_static/documentation_options.js
index 0a85d848e7e0f3a609a9220edbc64e4ce0ca20fe..6b898ef27bd16a3eabe3271a6322db94b5fe03f4 100644
--- a/run_af2/doc/html/_static/documentation_options.js
+++ b/run_af2/doc/html/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '4.0.2',
+    VERSION: '4.1.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/run_af2/doc/html/genindex.html b/run_af2/doc/html/genindex.html
index 985af54dbcf94a90f439039aca9a64341fd41ad8..c50cc3c6bae02296f691c63b4fafcedd0171ccd3 100644
--- a/run_af2/doc/html/genindex.html
+++ b/run_af2/doc/html/genindex.html
@@ -4,10 +4,10 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Index &#8212; af2@scicore/run_af2 4.0.2 documentation</title>
+    <title>Index &#8212; af2@scicore/run_af2 4.1.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=649a27d8" />
     <link rel="stylesheet" type="text/css" href="_static/sphinxdoc.css?v=d59dc883" />
-    <script src="_static/documentation_options.js?v=a084f797"></script>
+    <script src="_static/documentation_options.js?v=42d1b3bd"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="#" />
@@ -22,7 +22,7 @@
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.0.2 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.1.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Index</a></li> 
       </ul>
     </div>  
@@ -130,7 +130,7 @@
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.0.2 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.1.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Index</a></li> 
       </ul>
     </div>
diff --git a/run_af2/doc/html/index.html b/run_af2/doc/html/index.html
index c3b7fa608e34c16a72388f2e89891e84f43328bb..62b96070c8bb2bc57b2f4e2415a830bb033a77bb 100644
--- a/run_af2/doc/html/index.html
+++ b/run_af2/doc/html/index.html
@@ -5,10 +5,10 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Welcome to af2@scicore/run_af2’s documentation! &#8212; af2@scicore/run_af2 4.0.2 documentation</title>
+    <title>Welcome to af2@scicore/run_af2’s documentation! &#8212; af2@scicore/run_af2 4.1.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=649a27d8" />
     <link rel="stylesheet" type="text/css" href="_static/sphinxdoc.css?v=d59dc883" />
-    <script src="_static/documentation_options.js?v=a084f797"></script>
+    <script src="_static/documentation_options.js?v=42d1b3bd"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="genindex.html" />
@@ -27,7 +27,7 @@
         <li class="right" >
           <a href="_shared.html" title="_shared"
              accesskey="N">next</a> |</li>
-        <li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 4.0.2 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 4.1.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Welcome to af2&#64;scicore/run_af2’s documentation!</a></li> 
       </ul>
     </div>  
@@ -39,7 +39,7 @@
             
   <section id="welcome-to-af2-scicore-run-af2-s-documentation">
 <h1>Welcome to af2&#64;scicore/run_af2’s documentation!<a class="headerlink" href="#welcome-to-af2-scicore-run-af2-s-documentation" title="Link to this heading">¶</a></h1>
-<p>You are reading the documentation for version 4.0 (release 4.0.2)
+<p>You are reading the documentation for version 4.1 (release 4.1.0)
 of <strong>run_af2</strong>.</p>
 <p><strong>run_af2</strong> is a Python package to run the <a class="reference external" href="https://github.com/deepmind/alphafold">AlphaFold 2 (AF2) pipeline</a> on the sciCORE cluster.</p>
 <p>The package comes with two major parts: userland commands to just execute the
@@ -124,7 +124,7 @@ Python modules is here:</p>
         <li class="right" >
           <a href="_shared.html" title="_shared"
              >next</a> |</li>
-        <li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 4.0.2 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 4.1.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Welcome to af2&#64;scicore/run_af2’s documentation!</a></li> 
       </ul>
     </div>
diff --git a/run_af2/doc/html/objects.inv b/run_af2/doc/html/objects.inv
index 177d6eebfe3f8c32ecf9754b230f0bf60640a1e4..0ae131860101ddec4772a193191a9c5cb50171e7 100644
Binary files a/run_af2/doc/html/objects.inv and b/run_af2/doc/html/objects.inv differ
diff --git a/run_af2/doc/html/py-modindex.html b/run_af2/doc/html/py-modindex.html
index 77dc3958014d747dd67b4314209bebc0f08aac96..ae9fe25595ef704f9693e8ba0878380924a2436f 100644
--- a/run_af2/doc/html/py-modindex.html
+++ b/run_af2/doc/html/py-modindex.html
@@ -4,10 +4,10 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Python Module Index &#8212; af2@scicore/run_af2 4.0.2 documentation</title>
+    <title>Python Module Index &#8212; af2@scicore/run_af2 4.1.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=649a27d8" />
     <link rel="stylesheet" type="text/css" href="_static/sphinxdoc.css?v=d59dc883" />
-    <script src="_static/documentation_options.js?v=a084f797"></script>
+    <script src="_static/documentation_options.js?v=42d1b3bd"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="genindex.html" />
@@ -25,7 +25,7 @@
         <li class="right" >
           <a href="#" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.0.2 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.1.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Python Module Index</a></li> 
       </ul>
     </div>  
@@ -94,7 +94,7 @@
         <li class="right" >
           <a href="#" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.0.2 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.1.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Python Module Index</a></li> 
       </ul>
     </div>
diff --git a/run_af2/doc/html/run_singularity.html b/run_af2/doc/html/run_singularity.html
index 86a7155cc1106bb5e19ff1e15e7600e87b2c1496..bbab9ff0dfd263efeb51e22685055eb03b145534 100644
--- a/run_af2/doc/html/run_singularity.html
+++ b/run_af2/doc/html/run_singularity.html
@@ -5,10 +5,10 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>run_singularity &#8212; af2@scicore/run_af2 4.0.2 documentation</title>
+    <title>run_singularity &#8212; af2@scicore/run_af2 4.1.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=649a27d8" />
     <link rel="stylesheet" type="text/css" href="_static/sphinxdoc.css?v=d59dc883" />
-    <script src="_static/documentation_options.js?v=a084f797"></script>
+    <script src="_static/documentation_options.js?v=42d1b3bd"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="genindex.html" />
@@ -27,7 +27,7 @@
         <li class="right" >
           <a href="_shared.html" title="_shared"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.0.2 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.1.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">run_singularity</a></li> 
       </ul>
     </div>  
@@ -53,7 +53,7 @@
 
 <dl class="py function">
 <dt class="sig sig-object py" id="run_af2.run_singularity.run_af2_singularity_image">
-<span class="sig-prename descclassname"><span class="pre">run_af2.run_singularity.</span></span><span class="sig-name descname"><span class="pre">run_af2_singularity_image</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fasta_files</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_template_date</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_gpu</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">db_preset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'full_dbs'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model_preset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'monomer'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_precomputed_msas</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_run_relax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_gpu_relax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_multimer_predictions_per_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">af2_image_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">af2_image_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/home/schwede/GROUP/alphafold_data/'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">snglrty_bin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/usr/bin/singularity'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tmpdir_var</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'TMPDIR'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_arg_list</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/AF2params/frozen_230815T000000/'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniref90_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/UniProt/latest/uniref/uniref90/uniref90.fasta'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mgnify_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/MGnify/frozen_230815T000000/mgnify/mgy_clusters_2022_05.fa'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bfd_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/BFD/frozen_210805T085238/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">small_bfd_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/BFD_small/frozen_210812T135116/bfd-first_non_consensus_sequences.fasta'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniref30_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/AF_UniProt/frozen_221115T101000/uniref/uniref30/UniRef30_2021_03'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniprot_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/UniProt/latest/knowledgebase/complete/uniprot.fasta'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb70_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/PDB70/frozen_210805T142857/pdb70'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb_seqres_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/PDB/latest/derived_data/pdb_seqres.txt'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">template_mmcif_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/PDB/latest/data/structures/all/mmcif_files/'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">obsolete_pdbs_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/PDB/latest/data/status/obsolete.dat'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#run_af2.run_singularity.run_af2_singularity_image" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">run_af2.run_singularity.</span></span><span class="sig-name descname"><span class="pre">run_af2_singularity_image</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fasta_files</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_template_date</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_gpu</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">db_preset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'full_dbs'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model_preset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'monomer'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_precomputed_msas</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_gpu_relax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_multimer_predictions_per_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">af2_image_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">af2_image_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/home/schwede/GROUP/alphafold_data/'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">snglrty_bin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/usr/bin/singularity'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tmpdir_var</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'TMPDIR'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_arg_list</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/AF2params/frozen_230815T000000/'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniref90_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/UniProt/latest/uniref/uniref90/uniref90.fasta'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mgnify_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/MGnify/frozen_230815T000000/mgnify/mgy_clusters_2022_05.fa'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bfd_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/BFD/frozen_210805T085238/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">small_bfd_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/BFD_small/frozen_210812T135116/bfd-first_non_consensus_sequences.fasta'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniref30_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/AF_UniProt/frozen_221115T101000/uniref/uniref30/UniRef30_2021_03'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniprot_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/UniProt/latest/knowledgebase/complete/uniprot.fasta'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb70_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/PDB70/frozen_210805T142857/pdb70'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb_seqres_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/PDB/latest/derived_data/pdb_seqres.txt'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">template_mmcif_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/PDB/latest/data/structures/all/mmcif_files/'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">obsolete_pdbs_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/PDB/latest/data/status/obsolete.dat'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#run_af2.run_singularity.run_af2_singularity_image" title="Link to this definition">¶</a></dt>
 <dd><p>Run the AlphaFold 2 Singularity image on host.</p>
 <p>The keyword arguments all come with defaults to run on the sciCORE cluster.</p>
 <p>If the Singularity container fails, a <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#RuntimeError" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> will be
@@ -79,10 +79,6 @@ templates are included.</p></li>
 parameter in AF2.</p></li>
 <li><p><strong>use_precomputed_msas</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Use existing MSAs from cwd. Corresponds to the
 use_precomputed_msas parameter in AF2.</p></li>
-<li><p><strong>no_run_relax</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Disable relaxation at the end of modelling.
-Corresponds to AF2’s no_run_relax parameter but works
-oppositely, True means no relaxation, False means
-relaxation.</p></li>
 <li><p><strong>use_gpu_relax</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Run relaxation on GPU. Corresponds to the
 use_gpu_relax parameter in AF2.</p></li>
 <li><p><strong>num_multimer_predictions_per_model</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – In multimer mode, no. of
@@ -202,7 +198,7 @@ in AF2.</p></li>
         <li class="right" >
           <a href="_shared.html" title="_shared"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.0.2 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.1.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">run_singularity</a></li> 
       </ul>
     </div>
diff --git a/run_af2/doc/html/search.html b/run_af2/doc/html/search.html
index d065deadfe1d405f4bd940f2f11f7d3290c8582a..a12120bd6dec7c639f6b6e0fae3e528beb9bb7e0 100644
--- a/run_af2/doc/html/search.html
+++ b/run_af2/doc/html/search.html
@@ -4,11 +4,11 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Search &#8212; af2@scicore/run_af2 4.0.2 documentation</title>
+    <title>Search &#8212; af2@scicore/run_af2 4.1.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=649a27d8" />
     <link rel="stylesheet" type="text/css" href="_static/sphinxdoc.css?v=d59dc883" />
     
-    <script src="_static/documentation_options.js?v=a084f797"></script>
+    <script src="_static/documentation_options.js?v=42d1b3bd"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/searchtools.js"></script>
@@ -28,7 +28,7 @@
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.0.2 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.1.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Search</a></li> 
       </ul>
     </div>  
@@ -88,7 +88,7 @@
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.0.2 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 4.1.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Search</a></li> 
       </ul>
     </div>
diff --git a/run_af2/doc/html/searchindex.js b/run_af2/doc/html/searchindex.js
index 7734b6bda4915c439d51890819dc6d7381dd0c3a..7f9f16ed9bd475d61f366bcb6f61662528cb7d39 100644
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