diff --git a/doc/container/singularity.rst b/doc/container/singularity.rst
index 5079e263ad6f6879aad7d1ee47c6fd65b3981aa2..16af7e051382508f764bddb533647d423db67fd7 100644
--- a/doc/container/singularity.rst
+++ b/doc/container/singularity.rst
@@ -36,6 +36,8 @@ Fire the local Registry and push the promod image to it:
   sudo docker tag promod localhost:5000/promod
   sudo docker push localhost:5000/promod
 
+If port 5000 is already taken on your machine, use a different ``<PORT>`` by
+using the flag ``-p <PORT>:5000`` and ``localhost:<PORT>`` in these commands.
 Make sure, that on top of your Singularity recipe you have something like:
 
 .. code-block:: bash
@@ -71,7 +73,24 @@ To get help on how to run it:
 
 .. code-block:: bash
 
-  singularity run --app Notebook <IMAGE> --help
+  singularity help --app Notebook <IMAGE>
+
+Within the notebook you can test OST, ProMod3 and nglview as follows:
+
+.. code-block:: python
+
+  from ost import io
+  from promod3 import loop
+  import nglview
+
+  # generate backbone with dihedrals of a helix and store it
+  sequence = "HELLYEAH"
+  bb_list = loop.BackboneList(sequence)
+  io.SavePDB(bb_list.ToEntity(), "test.pdb")
+
+  # display stored file
+  view = nglview.show_file("test.pdb")
+  view
 
 
 The Compound Library
diff --git a/doc/html/_sources/container/singularity.txt b/doc/html/_sources/container/singularity.txt
index 5079e263ad6f6879aad7d1ee47c6fd65b3981aa2..16af7e051382508f764bddb533647d423db67fd7 100644
--- a/doc/html/_sources/container/singularity.txt
+++ b/doc/html/_sources/container/singularity.txt
@@ -36,6 +36,8 @@ Fire the local Registry and push the promod image to it:
   sudo docker tag promod localhost:5000/promod
   sudo docker push localhost:5000/promod
 
+If port 5000 is already taken on your machine, use a different ``<PORT>`` by
+using the flag ``-p <PORT>:5000`` and ``localhost:<PORT>`` in these commands.
 Make sure, that on top of your Singularity recipe you have something like:
 
 .. code-block:: bash
@@ -71,7 +73,24 @@ To get help on how to run it:
 
 .. code-block:: bash
 
-  singularity run --app Notebook <IMAGE> --help
+  singularity help --app Notebook <IMAGE>
+
+Within the notebook you can test OST, ProMod3 and nglview as follows:
+
+.. code-block:: python
+
+  from ost import io
+  from promod3 import loop
+  import nglview
+
+  # generate backbone with dihedrals of a helix and store it
+  sequence = "HELLYEAH"
+  bb_list = loop.BackboneList(sequence)
+  io.SavePDB(bb_list.ToEntity(), "test.pdb")
+
+  # display stored file
+  view = nglview.show_file("test.pdb")
+  view
 
 
 The Compound Library
diff --git a/doc/html/container/singularity.html b/doc/html/container/singularity.html
index d3581fe64d2b761ef18aa06316c963d1c47571c4..e6ef2d40ea1dfcb5ac2d6e7457ef5edd730c25d6 100644
--- a/doc/html/container/singularity.html
+++ b/doc/html/container/singularity.html
@@ -57,7 +57,9 @@ sudo docker tag promod localhost:5000/promod
 sudo docker push localhost:5000/promod
 </pre></div>
 </div>
-<p>Make sure, that on top of your Singularity recipe you have something like:</p>
+<p>If port 5000 is already taken on your machine, use a different <code class="docutils literal"><span class="pre">&lt;PORT&gt;</span></code> by
+using the flag <code class="docutils literal"><span class="pre">-p</span> <span class="pre">&lt;PORT&gt;:5000</span></code> and <code class="docutils literal"><span class="pre">localhost:&lt;PORT&gt;</span></code> in these commands.
+Make sure, that on top of your Singularity recipe you have something like:</p>
 <div class="highlight-bash"><div class="highlight"><pre><span></span>BootStrap: docker
 Registry: http://localhost:5000
 Namespace:
@@ -81,7 +83,22 @@ E.g. to run scripts with pm:</p>
 </div>
 <p>The jupyter notebook is setup as an app in the container.
 To get help on how to run it:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity run --app Notebook &lt;IMAGE&gt; --help
+<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity <span class="nb">help</span> --app Notebook &lt;IMAGE&gt;
+</pre></div>
+</div>
+<p>Within the notebook you can test OST, ProMod3 and nglview as follows:</p>
+<div class="highlight-python"><div class="highlight"><pre><span></span><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">loop</span>
+<span class="kn">import</span> <span class="nn">nglview</span>
+
+<span class="c1"># generate backbone with dihedrals of a helix and store it</span>
+<span class="n">sequence</span> <span class="o">=</span> <span class="s2">&quot;HELLYEAH&quot;</span>
+<span class="n">bb_list</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneList</span><span class="p">(</span><span class="n">sequence</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">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s2">&quot;test.pdb&quot;</span><span class="p">)</span>
+
+<span class="c1"># display stored file</span>
+<span class="n">view</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_file</span><span class="p">(</span><span class="s2">&quot;test.pdb&quot;</span><span class="p">)</span>
+<span class="n">view</span>
 </pre></div>
 </div>
 </div>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index e1c5ff506a9a7a8823d27608488d58c7dd5905d5..0526fe4e70ec80cc440a08f0b2f0c0139e787535 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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,13,15,25,26],enable_mm:2,enable_ss:2,enclos:[20,29,35],encod:0,encount:[29,34],end:[0,1,2,4,8,10,11,13,16,20,21,22,26,28,29,31,35,38],end_resnum:35,end_transl:4,endian:37,energi:[0,3,8,10,18,25,32,34,35,36,39,41,44,45,46,47,49,50,52],energy_funct:[0,36],enforc:[0,3,21,31,34,35,36,39,40,41],engin:19,enough:[8,16,25,26,35,37],ensur:[2,8,18,31,35,37],ent:[0,13,21,25,26,33,36,42],ent_seq:42,enter:[35,45],entiti:[8,13,14,20,21,22,26,28,33,35,42,47],entityhandl:[13,21,22,26,33,35,36,40],entityview:[26,27,28,33,35],entri:[0,3,8,14,25,26,31,32,33,36,41,47,50],enumer:[8,10,21,25,26,28,31,35,40,47,49,50,51],env:[8,18,21,25,28,32,33,35,36,39,40,41,42],env_po:[32,36],env_structur:[21,40],environ:[1,3,8,21,28,29,31,32,34,35,36,37,39],epsilon:[10,25,36,52],equal:[28,34,39,41,44,50],equidist:51,equival:[28,35,39,41],error:[0,11,13,14,26,32,35,37],especi:28,estim:[10,28,33,34,38,41,44,49,50,51],etc:[1,3,8,16,22,26,31,40],evalu:[4,8,32,35,39,40,41],evaluategromacsposrul:9,even:[2,8,10,20,22,25,29,35],event:[20,28],eventu:13,ever:[16,34],everi:[0,1,8,10,13,21,22,26,27,28,31,32,34,35,36,39,40,41,44,46,49,50,51,52],everyth:[1,2,3,7,8],evolut:38,evolv:42,exact:[0,7,10,13,37],exactli:[2,10,26,28,31,35,40,44,49],exampl:[0,1,2,3,8,11,13,16,17,18,20,21,23,25,26,27,28,30],example_reconstruct:47,exce:[39,41],exceed:[26,29],except:[0,3,13,20,26,29,34,35],exclud:[8,20,26],exclus:[1,8,20,25],exec:7,execut:0,exercis:20,exisit:17,exist:[0,1,2,4,8,10,11,13,14,16,21,22,26,31,32,33,34,35,37,39,40,41,48,49,51],exit:[0,1,11,13],exit_cod:1,exit_statu:11,exot:8,exp:34,expect:[1,3,7,21,25,26,35,36,40,44,50,52],expens:26,experiment:35,explain:[1,8],explan:8,explicit:2,explicitli:20,explor:38,exponenti:34,exponentialcool:34,expos:26,express:[20,44],ext:11,extend:[1,4,8,16,17,24,26,28],extendatcterm:29,extendatnterm:29,extended_search:[31,35],extens:[0,3,11,13,29,35],extension_penalti:29,extent:26,extern:[3,4,5,8,34],external_script:[3,8],extra:[2,3,8,16,22,37,48],extra_bin:26,extra_force_field:35,extract:[8,9,21,22,23,25,26,27,28,30,31,32,34,35,36,39,40,41,44,50],extractbackbon:21,extractloopposit:25,extractstatist:27,extrem:[22,28],f_i:26,f_idx:40,f_vinaparticl:49,facilit:28,factor:[10,25,34,49],fail:[0,1,8,11,14,22,31,32,35],failur:[0,8,11,13,20,35,51],fall:32,fallback:51,fals:[1,8,10,11,13,22,25,26,29,31,34,35,36,44,47,49,50],fantast:8,far:[31,35],fast:[0,9,18,19,21,25,26,27,37,39,40,41,51],fasta:[0,13,30,35],faster:[10,25,26,32,33,40],fastest:[32,35],favor:33,favourit:1,fed:[4,16],fedora:8,fee:20,feed:[4,21,31],feel:[8,16],fellow:8,fetch:[13,16,18,28],few:[2,8,16,25,37,42],ff_aa:25,ff_aa_on:25,ff_aa_two:25,ff_ala:25,ff_arg:25,ff_asn:25,ff_asp:25,ff_cy:25,ff_cys2:25,ff_gln:25,ff_glu:25,ff_gly:25,ff_hisd:25,ff_hise:25,ff_ile:25,ff_leu:25,ff_lookup:[25,32,35],ff_lookup_charmm:37,ff_ly:25,ff_met:25,ff_phe:25,ff_pro:25,ff_ser:25,ff_thr:25,ff_trp:25,ff_tyr:25,ff_val:25,ff_xxx:25,field:[20,35,37,51],fifti:20,figur:16,file:[0,1,2,3,4,5,8],filecheck:16,fileexist:11,fileextens:11,filegzip:11,filenam:[0,8,11,13,25,26,27,28,37,39,41,48,51],filenotfound:33,fill:[4,8,13,16,23,26,29,30,31,33,35],fillfromdatabas:[31,35],fillfrommontecarlosampl:[31,35],fillloopsbydatabas:35,fillloopsbymontecarlo:35,filo:40,filtercandid:33,filtercandidateswithsc:33,final_model:[30,35],find:[3,4,7,8,10,16,21,23],findatom:28,findchain:42,findeigen3:20,findmotif:28,findwithin:[8,28],fine:8,finish:52,fire:[1,7],first:[0,1,8,10,13,16,18,21,22,25,26,27,28,29,31,32,34,35,36,39,40,41,43,44,47,49,50,51],fit:[16,20,22,26,30,31],fix:[3,8,11,16,25,32,36,37,39,41],fix_cterm:32,fix_nterm:32,fix_surrounding_hydrogen:25,flag1:4,flag2:4,flag:[0,2,4,8,10,11,13,22,26,28,35,36,49,50],flanking_rot_angle_on:22,flanking_rot_angle_two:22,fletch:[26,47],fletcher:35,flexibl:[0,19,36,44,47,49,50,52],flip:51,flood:26,fluorin:49,flush:[1,16],fold:38,folder:[2,4,8,16,18,37],follow:[0,1,2,4,5,8,10,11,16,18,20,22,23,25,26,28,29,30,31,35,36,37,39,41,47,49,50,51],fontsiz:27,forbidden:8,forc:[25,32,35],force_const:[25,32],forcefield:23,forcefieldaminoacid:25,forcefieldbondinfo:25,forcefieldconnect:25,forcefieldharmonicangleinfo:25,forcefieldharmonicimproperinfo:25,forcefieldljpairinfo:25,forcefieldlookup:[25,32,35,37],forcefieldperiodicdihedralinfo:25,forcefieldureybradleyangleinfo:25,forg:16,forget:[1,8],form:[14,20,24,25,26,30,35,40,51],formal:[31,32,49,51],format:[0,5,13,20,26,48],formula:33,forward:16,found:[1,3,4,8,11,13,16,19,21,23,26,28,31,32,33,34,35,36,44,46,49,51],foundat:1,four:[9,34],fraction:[26,28,32,34],frag_db:[23,26,31,37],frag_length:[23,26,28],frag_map:26,frag_po:[23,26,28],frag_residu:[23,26],frag_seq:[23,26],frag_siz:26,fragdb:[23,24,26,31,35,37],fragger:[13,23,26,28,34,35],fragger_handl:[13,35],fragger_map:26,fraggerhandl:[0,13,26,28,35],fraggermap:[26,28],fragment:[0,3,9,13,22,23,24],fragment_db:35,fragment_handl:28,fragment_info:26,fragment_length:[26,28],fragmentinfo:[26,31],fragments_per_posit:28,fragmentsampl:34,frame:[3,16,35,36],frame_energi:49,frame_residu:[45,47],frameresidu:[45,49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6,40,42],updatedistribut:27,updateposit:[25,32],upon:[26,32,34],upper:28,urei:25,urey_bradley_angl:25,usabl:16,usag:[0,3,10,13,24,26,31,32,36],use_amber_ff:35,use_bbdep_lib:36,use_frm:36,use_full_extend:35,use_scoring_extend:35,user:[1,5,8,19,28,53],userlevel:1,usr:[2,5,7,8],usual:[1,2,4,8,13,14,16,22,31,35,39],utilis:[8,16],v_size:37,val:[27,49],valid:[0,10,16,22,26,29,34,35,36,48,51],valin:49,valu:[2,10,11,13,21,22,25,26,28,31,34,35,37,39,40,41,44,47,49,50,51,52],valueerror:[28,35],vanish:40,varadarajan:38,vari:[4,37],variabl:[1,2,8,14,18,25,33,35,37],variant:[25,31],variou:[1,2,4,16,30],vec3:[9,21,22,26,32,33,43,44,49],vec3list:[28,49],vector:[25,27,28,31,37,49],verbal:20,verbos:1,veri:[1,8,11,16,25,28,35,37],verif:13,verifi:[1,11,16],version:[2,3,5,8,16,20,26,35,37,48,49],vertic:28,via:[1,5,8,13,15,25],view:[13,16,27,35,40],vina:[3,38],vinaparticletyp:[49,50],vinarotamerconstructor:50,virtual:8,visibl:36,vision:38,visual:18,volum:5,wai:[1,2,4,5,8,16,22,23,25,31,41,47,49],wait:8,walk:[1,8],want:[1,2,3,8,15,16,22,26,28,31,32,35,40,49,50,51,52,53],warn:[8,16,35],warranti:20,watch:8,web:[2,8],weight:[3,26,28,31,34,35,39,41],weird:[28,32,47],well:[0,4,16,21,27,28,29,31,35,37,41,47,50,51],went:[0,8],were:[16,26,31,35],wester:38,wether:10,what:[1,8,11,13,16,23,26,36,40],when:[1,3,4,5,8,10,13,14,21,22,25,26,27,28,29,31,34,35,36,37,38,40,41,44,47,48,49,50,51],whenev:[8,21,31,40],where:[0,1,3,4,5,8,10,11,13,14,16,20,21,22,25,26,27,31,35,37,39,40,41,48,49,50,51],wherea:26,wherev:20,whether:[3,5,8,10,11,13,20,22,25,26,31,32,34,36,39,40,41,49,50,51],which:[0,1,4,8,9,11,12,13,16,18,20,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,49,50,51],whistl:8,whitespac:0,who:[10,47],whole:[1,2,8,16,20,22,26,35,49],whom:20,why:[1,16],width:[10,37,47],wild:4,window:28,window_length:28,wise:4,wish:[2,17,27,35],with_aa:31,with_db:31,within:[2,3,4,8,14,16,20,21,25,28,29,33,35,36,39,41,51],without:[0,1,3,4,8,11,13,20,25,29,32,35,40,51],wolfson:[28,38],won:[0,35,36,50],word:4,work:[1,2,4,5,7,8,14,16,18,20,25,29,35,37,50],worldwid:20,worst:16,worth:53,would:[1,2,8,11,22,26,27,44,49],wrap:26,wrapper:[1,4,8,15,35],write:0,writebasetyp:37,writemagicnumb:37,writetypes:37,writeversionnumb:37,written:[8,20,37],wrong:[2,13],wwpdb:5,www:20,xlabel:27,xlim:27,xml:8,xxx:[22,49],xxx_num_atom:21,xxx_num_hydrogen:21,year:1,yet:[26,31,35],ylabel:27,ylim:27,you:[0,1,2,3,4,5,7,8,10,11,13,14,15,16,18,20,21,22,23,25,26,27,28,30,31,32,34,35,36,37,39,40,41,47,48,49,50,51,52,53],your:[1,2,4,5,7],your_modul:[8,16],yourself:[2,8,10,16,35,50],yyyi:20,zero:[0,26,28,35,51],zhou2005:[26,38],zhou:38,zip:[26,47]},titles:["ProMod3 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Actions","<code class=\"docutils literal\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3&#8216;s Share Of CMake","Docker","ProMod3 and Containers","Singularity","Contributing","Geometry functions","Graph Minimizer","<code class=\"docutils literal\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"docutils literal\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","ProMod3 Setup","Documentation For Developers","Getting Started","ProMod3","License","Handling All Atom Positions","Representing Loops","<code class=\"docutils literal\"><span class=\"pre\">loop</span></code> - Loop Handling","Loading Precomputed Objects","Generate <code class=\"docutils literal\"><span class=\"pre\">ost.mol.mm</span></code> systems","Structural Data","Sampling Dihedral Angles","Modelling Algorithms","Handling Gaps","<code class=\"docutils literal\"><span class=\"pre\">modelling</span></code> - Protein Modelling","Handling Loop Candidates","Fitting Loops Into Gaps","Model Checking","Generating Loops De Novo","Modelling Pipeline","Sidechain Reconstruction","Using Binary Files In ProMod3","References","All Atom Scorers","Backbone Score Environment","Backbone Scorers","<code class=\"docutils literal\"><span class=\"pre\">scoring</span></code> - Loop Scoring","Other Scoring Functions","Disulfid Bond Evaluation","Frame - The Rigid Part","Rotamer Graph","<code class=\"docutils literal\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Loading Rotamer Libraries","Representing Sidechains - Rotamers &amp; Co.","Rotamer Constructor","Rotamer Library","Subrotamer Optimization","Contributing","Documentation For Users"],titleterms:{"class":[21,22,26,27,29,31,36,39,40,41],"default":35,"function":[4,9,11,12,29,36,40,43,49,50],acid:[21,25,27],action:[0,1,4,5,7,8],actiontestcas:1,algorithm:28,all:[21,32,39],allatomclashscor:39,allatomenv:21,allatomenvposit:21,allatominteractionscor:39,allatomoverallscor:39,allatompackingscor:39,allatomposit:21,allatomscor:39,amino:[21,25,27],angl:27,api:1,argument:13,atom:[21,32,39],backbon:[32,40,41,51],backbonelist:22,backboneoverallscor:41,backbonescor:41,backbonescoreenv:40,base:[26,39,41],baseclass:50,binari:37,block:[28,49],bond:44,branch:16,build:[0,2,5,7,35,49],can:49,candid:31,cbetascor:41,cbpackingscor:41,ccd:32,chain:26,changelog:3,check:33,clashscor:41,closer:34,cmake:[1,2,4,16],code:37,command:13,compound:[5,7],configur:51,construct:40,constructor:50,contain:6,contribut:[8,53],conveni:40,cooler:34,core:12,creat:[1,25],data:[26,37],databas:26,defin:[26,27],definit:4,depend:[2,51],detect:33,develop:17,dihedr:27,directori:16,distinguish:21,disulfid:44,docker:5,document:[4,8,17,19,54],entri:51,environ:40,evalu:44,everyth:11,exampl:[31,37],execut:1,exisit:37,extend:29,featur:[8,26],file:[11,37],find:26,finder:28,fit:32,forcefield:25,fragment:26,frame:45,from:43,gap:[29,32],gener:[25,34],geometr:26,geometri:9,get:[18,49],git:16,graph:[10,46],group:49,handl:[21,23,29,31,35],have:1,hbondscor:41,header:37,helper:11,hook:16,how:[8,49],imag:[5,7],instal:2,integr:1,introduct:[4,11,13],issu:8,keep:31,kic:32,librari:[5,7,48,51],licens:[8,20],line:13,load:[24,48],lookup:25,loop:[22,23,25,31,32,34,42],loopcandid:31,mainten:4,make:[1,2],messag:11,minim:10,model:[0,18,28,30,31,33,35,47],modul:[4,8],mol:25,molprob:33,motif:28,must:1,non:51,novo:[28,34],object:[24,34,45],optim:52,ost:[5,7,25],other:43,output:1,own:8,pairwis:40,pairwisescor:41,pars:13,parser:13,part:45,parti:8,particl:49,pipelin:[18,35],pm3argpars:13,portabl:37,posit:21,precomput:24,profil:14,promod3:[0,2,4,6,8,12,16,18,19,37],protein:30,psipredpredict:26,punch:33,quick:8,raw:35,reconstruct:36,reducedscor:41,refer:38,relax:32,releas:3,repres:[22,49],rigid:[28,45],ring:33,rotam:[46,48,49,50,51],rotamerconstructor:50,rotamerid:49,run:[1,2,5,7,18],runtim:14,sampl:27,sampler:[27,34],score:[31,40,42,43,49,50],scorer:[8,34,39,41],script:[1,5,7,8],scwrl3:[43,49],scwrl4:49,sequenc:26,setcompoundschemlib:15,setup:16,share:[4,8,11],sidechain:[0,36,47,49],sidechainreconstructiondata:36,sidechainreconstructor:36,singular:7,smallest:49,specif:50,ssagreementscor:41,stage:16,start:[8,18],step:35,structur:[16,26],subclass:1,subrotam:52,system:25,test:[1,4,8,11],test_act:1,third:8,torsion:27,torsionscor:41,track:31,triplet:27,type:51,unit:[1,4,8],user:54,vina:49,write:8,your:8}})
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