From: Cezary Czaplewski <czarek@chem.univ.gda.pl>
Date: Fri, 28 Feb 2020 07:24:23 +0000 (+0100)
Subject: dock tutorial
X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=commitdiff_plain;h=d818722a1fbd1ccd64f5c744afae35f303e82025;p=django_unres.git

dock tutorial
---

diff --git a/django_simple/todo/templates/base.html b/django_simple/todo/templates/base.html
index b40095b..63d29ac 100644
--- a/django_simple/todo/templates/base.html
+++ b/django_simple/todo/templates/base.html
@@ -27,6 +27,7 @@
     </div>
     <ul class="nav navbar-nav" >
       <li><a href="/tutorial">Tutorial</a></li>
+      <li><a href="/tutorial_dock">UNRES-Dock tutorial</a></li>
       <li><a href="/input">Input data</a></li>
       <li><a href="/output">Output files</a></li>
       <li><a href="/changelog">Changelog</a></li>
diff --git a/django_simple/todo/templates/tutorial_dock.html b/django_simple/todo/templates/tutorial_dock.html
new file mode 100644
index 0000000..652cfa9
--- /dev/null
+++ b/django_simple/todo/templates/tutorial_dock.html
@@ -0,0 +1,183 @@
+{% extends "base.html" %}
+
+{% load i18n lazysignup_tags %}
+{% block content %}
+
+<h4>
+In order to submit a UNRES-Dock job you need to provide its name:</h4>
+<p>
+<img src="static/name.png" style="border:2px solid blueviolet">
+<p>
+<h4>and choose DOCK as the type of simulation:</h4>
+<p>
+<img src="static/dock1.png" style="border:2px solid blueviolet">
+<p>
+UNRES-Dock 
+utilizes multiplexed replica exchange MD simulation (MREMD) with
+24 random starting structures of a complex, with diverse orientations of monomers.
+The monomers are placed to interact weakly with each other, the smallest
+periodic-box size prohibiting interactions between a molecule with its image
+is estimated. A set of log-Gaussian restraints are imposed on both
+monomers for protein-protein docking, and only on the first monomer for
+protein-peptide docking.
+<p>
+Use the "Save & submit" button to start calculations.
+<img src="static/submit.png" style="border:2px solid blueviolet">
+<p>
+Use the "Refresh" button to check the status of a simulation:
+<p>
+<img src="static/refresh.png" style="border:2px solid blueviolet">
+<p>
+until
+<img src="static/done.png" style="border:2px solid blueviolet">
+<p>
+
+After the server job has been submitted the "waiting in the queue to start"
+message will be displayed in the status field, which will subsequently
+change to "running", "postprocessing", and "done".  While the job has the
+"running" status, the percentage of job accomplishment is displayed.  It
+should be noted that the "100%" accomplishment refers to the production
+phase of a job, after which the postprocessing phase is triggered which also
+takes some time and whose progress is not monitored.  The page is
+autorefreshed every 30 sec.  <p> Any single job can by accessed later (for
+at least 14 days) using the address of the web page displayed after job
+submission: e.g. 
+http://unres-server.chem.ug.edu.pl/details1/570cf15fc638493893ece1f011ea0182/984/
+<br> Registered users can save all their jobs and access them later after
+logging in.  Note that the results will be available for a limited period of
+time, depending on the storage space availability (at least 30 days).  <p>
+
+<h4>You can use "Load example data" button before submitting calculations to
+try an example docking:</h4>
+
+
+<h4><li>
+Docking simulation for two chains of Drosophila Insulin-Like Peptide 5
+(PDB code:2WFU) </h4>  
+<div>
+    <fieldset class="majorpoints">
+        <legend class="majorpointslegend"
+            style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
+    
+    <div class="hiders" style="display:none" >
+<img src="static/dock2.png" style="border:2px solid blueviolet">
+<p>
+<p>
+After a UNRES-Dock MREMD run is accomplished, the same data
+as for regules MREMD run is shown:
+a table showing replica-exchange statistics
+(a), plots of histograms of UNRES energy for each temperature (b), a plot of
+energy vs. temperature (c), a temperature-colored scatter plot of energy vs. RMSD
+(d), and the temperature-colored cumulative plot of rmsd vs. step number for all replicas
+(e), and a cumulative plot of walk of the replicas in temperature space (f). 
+The colors corresponding to replica temperatures are shown in panel (c),
+while different replicas are colored from black to yellow in panel (f).
+<p>
+<a href="static/dock3.png"><img src="static/dock3.png" width="300px"></a>(a)
+<a href="static/dock4.png"><img src="static/dock4.png" width="300px"></a>(b)
+<a href="static/dock5.png"><img src="static/dock5.png" width="300px"></a>(c)
+<a href="static/dock6.png"><img src="static/dock6.png" width="300px"></a>(d)
+<a href="static/dock7.png"><img src="static/dock7.png" width="300px"></a>(e)
+<a href="static/dock8.png"><img src="static/dock8.png" width="300px"></a>(f)
+<p>
+The weighted histogram analysis method (WHAM) is applied to compute the
+probabilities of the obtained complexes to occur at particular
+temperatures and, consequently, the plots of heat capacity 
+(g) and ensemble-averaged RMSD (h) as a functions
+of temperature; these are shown in the respective graphs. 
+<p>
+<a href="static/dock9.png"><img src="static/dock9.png" width="300px"></a>(g)
+<a href="static/dock10.png"><img src="static/dock10.png" width="300px"></a>(h)
+<p>
+Note! Panels are labeled in this tutorial only and labels are not displayed 
+in the outputs from real server jobs.
+<p>
+Finally cluster analysis is performed to select 5 families of complexes,
+and representative model from each family is converted to all-atom
+and refined. Models are shown using NGL Viewer.
+PDB files can be downloaded by clicking on the <i>Download</i> button.
+<p>
+<a href="static/dock11.png"><img src="static/dock11.png" width="300px"></a>
+<p>
+DockQ is utilised to measure quality of 5 docked models.
+
+</div>
+</div>
+</ol>
+<hr>
+Advanced mode enables the user to change more parameters for 
+UNRES-Dock. A separate example is provided 
+(use the <i>Load example data</i> button as
+in the Basic mode): 
+
+<h4><li>
+Docking simulation of p97/PNGase complex
+(PDB code:2HPL), there are no restraints imposed on the DDLYG peptide </h4>  
+<div>
+    <fieldset class="majorpoints">
+        <legend class="majorpointslegend"
+            style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
+    
+    <div class="hiders" style="display:none" >
+<img src="static/docka1.png" style="border:2px solid blueviolet">
+<p>
+Only sequence is given for the peptide. No reference structure is provided
+for the complex. <br>
+All temperatures are multiplexed, total number of replicas is 36.
+<p>
+<img src="static/docka2.png" style="border:2px solid blueviolet">
+<p>
+After a UNRES-Dock MREMD run is accomplished without the reference structure, 
+a table showing replica-exchange statistics (a), 
+plots of histograms of UNRES energy for each temperature (b), 
+a plot of energy vs. temperature (c), 
+and a cumulative plot of walk of the replicas in temperature space (d) are
+displayed. The colors corresponding to replica temperatures are shown in panel (c),
+while different replicas are colored from black to yellow in panel (d).
+<p>
+<a href="static/docka3.png"><img src="static/docka3.png" width="300px"></a>(a)
+<a href="static/docka4.png"><img src="static/docka4.png" width="300px"></a>(b)
+<a href="static/docka5.png"><img src="static/docka5.png" width="300px"></a>(c)
+<a href="static/docka7.png"><img src="static/docka7.png" width="300px"></a>(d)
+<p>
+The weighted histogram analysis method (WHAM) is applied to compute the
+probabilities of the obtained complexes to occur at particular
+temperatures and, consequently, the plot of heat capacity (e) 
+as a functions of temperature is shown. 
+<p>
+<a href="static/docka6.png"><img src="static/docka6.png" width="300px"></a>(e)
+<p>
+Note! Panels are labeled in this tutorial only and labels are not displayed 
+in the outputs from real server jobs.
+<p>
+Finally cluster analysis is performed to select 5 families of conformations,
+and representative model from each family is converted to all-atom
+and refined. Models are shown using NGL Viewer.
+PDB files can be downloaded by clicking on the <i>Download</i> button.
+<p>
+<a href="static/docka11.png"><img src="static/docka11.png" width="300px"></a>
+
+<p>
+
+
+</div>
+</div>
+</ol>
+
+
+
+<script src="/static/jquery.min.js"></script>
+
+<script>
+$('.majorpointslegend').click(function(){
+    $(this.parentNode).find('.hiders').toggle();
+    if($(this.parentNode).find('.majorpointslegend').text()=='Show'){
+        $(this.parentNode).find('.majorpointslegend').text('Hide');
+    }else{
+        $(this.parentNode).find('.majorpointslegend').text('Show');
+    }    
+});
+</script>
+
+
+{% endblock %}
diff --git a/django_simple/urls.py b/django_simple/urls.py
index db4afae..848c362 100644
--- a/django_simple/urls.py
+++ b/django_simple/urls.py
@@ -19,6 +19,9 @@ urlpatterns = [
         url(r'^contact', 
             TemplateView.as_view(template_name='contact.html'),
                 name='contact'),
+        url(r'^tutorial_dock', 
+            TemplateView.as_view(template_name='tutorial_dock.html'),
+                name='tutorial_dock'),
         url(r'^tutorial', 
             TemplateView.as_view(template_name='tutorial.html'),
                 name='tutorial'),
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