switch for respa, D aminoacids, saxs tutorial, license

[django_unres.git] / django_simple / todo / templates / tutorial.html

diff --git a/django_simple/todo/templates/tutorial.html b/django_simple/todo/templates/tutorial.html
index d59175c..6e9bbde 100644 (file)
--- a/django_simple/todo/templates/tutorial.html
+++ b/django_simple/todo/templates/tutorial.html
@@ -122,7 +122,7 @@ of temperature are shown. Replica exchanges are analyzed.
 <p>
 Finally cluster analysis is performed to select 5 families of conformations,
 and representative model from each family is converted to all-atom
 <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. 
+and refined. PDB files can be downloaded by clicking on the picture.

 <p>
 <a href="static/remd9.png"><img src="static/remd9.png" width="300px"></a>
 
 <p>
 <a href="static/remd9.png"><img src="static/remd9.png" width="300px"></a>
 

@@ -138,6 +138,60 @@ dissulfide bonds, MD simulations of 1L2Y starting from extended chain
 and replica exchange simulations of 1E0G starting form extended chain 
 using new UNRES force field and Berendsen thermostat.
 
 and replica exchange simulations of 1E0G starting form extended chain 
 using new UNRES force field and Berendsen thermostat.
 

+<hr>
+<h4><li>
+Distance distribution restrained (simulated SAXS data)
+replica exchange molecular dynamics of 
+Bacteriocin CbnXY (PDB code:5UJQ) starting from the extended chain.
+<br>
+(Use <i>Load example SAXS data</i> button in advanced mode)
+</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/saxs1.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/saxs2.png" style="border:2px solid blueviolet">
+<p>
+
+Plots of histograms of UNRES energy for each temperature, and
+energy vs temperature are presented.
+The weighted histogram analysis (WHAM) is applied to compute the
+probabilities of the obtained conformations to occur at particular
+temperatures, plots of heat capacity and average RMSD as a functions
+of temperature are shown. Replica exchanges are analyzed.
+<p>
+<a href="static/saxs3.png"><img src="static/saxs3.png" width="300px"></a>
+<a href="static/sasx4.png"><img src="static/saxs4.png" width="300px"></a>
+<a href="static/saxs5.png"><img src="static/saxs5.png" width="300px"></a>
+<a href="static/saxs6.png"><img src="static/saxs6.png" width="300px"></a>
+<a href="static/saxs7.png"><img src="static/saxs7.png" width="300px"></a>
+<a href="static/saxs8.png"><img src="static/saxs8.png" width="300px"></a>
+<a href="static/saxs9.png"><img src="static/saxs9.png" width="300px"></a>
+<a href="static/saxs10.png"><img src="static/saxs10.png" width="300px"></a>
+<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. 
+<p>
+<a href="static/saxs12.png"><img src="static/saxs12.png" width="300px"></a>
+
+<p>
+Additionaly the input reference distance distribution and 
+distance distributions for 5 final models are plotted.
+<p>
+<a href="static/saxs11.png"><img src="static/saxs11.png" width="300px"></a>
+
+
+</div>
+</div>
+
+

 <script src="/static/jquery.min.js"></script>
 
 <script>
 <script src="/static/jquery.min.js"></script>
 
 <script>