X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Ftemplates%2Ftutorial.html;h=6e9bbdee3dd3f6f475e69a1c6bcd13c9aa293260;hb=56e79678d88f1b25b4c15ce3ac8047b6fa6faa35;hp=35b8dba122f2b7e659b0220d8529f1785835ef1b;hpb=0f5d683edc824468ab5da53d015b39e91fe2766d;p=django_unres.git

diff --git a/django_simple/todo/templates/tutorial.html b/django_simple/todo/templates/tutorial.html
index 35b8dba..6e9bbde 100644
--- a/django_simple/todo/templates/tutorial.html
+++ b/django_simple/todo/templates/tutorial.html
@@ -7,13 +7,14 @@
 In order to submit a job you need to provide its name:</h4>
 <p>
 <img src="static/name.png" style="border:2px solid blueviolet">
-
+<p>
 UNRES server allows three types of simulations: 
-local minimization, molecular dynamics, replica exchange molecular dynamics:
+local minimization, molecular dynamics and replica exchange molecular dynamics:
 <p>
 <img src="static/types.png" style="border:2px solid blueviolet">
 <p>
 Use "Save & submit" button to start calculations.
+<img src="static/submit.png" style="border:2px solid blueviolet">
 <p>
 Use "Refresh" button to check the status of simulation:
 <p>
@@ -22,10 +23,17 @@ Use "Refresh" button to check the status of simulation:
 until
 <img src="static/done.png" style="border:2px solid blueviolet">
 <p>
-
-
-<h4>Use "Load example data" button before submitting calculations 
-to try all examples listed below:</h4>
+The job status information will start from the "waiting in the queue to
+start", then "running" and finally "postprocessing" before "done".
+<p>
+Any single job can by accessed later using the adress of the web page
+displayed after job submission: 
+http://unres-server.chem.ug.edu.pl/details1/570cf15fc638493893ece1f011ea0182/984/
+<br>
+Registered users can save all their jobs and access them  after login.
+<p>
+<h4>You can use "Load example data" button before submitting calculations 
+to try examples listed below:</h4>
 <p>
 <ol>
 <h4><li>Local minimization of protein A (PDB code:1BDD) structure</h4>
@@ -36,14 +44,19 @@ to try all examples listed below:</h4>
     
     <div class="hiders" style="display:none" >
 <p>
+In this example only the PDB code of selected protein (1BDD) is provided
+<p>
 <img src="static/min.png" style="border:2px solid blueviolet">
 
 
-The results of local minimizations show the UNRES model, its total energy 
-and overlap on starting structure:
+The results of local minimizations show the UNRES model of 1BDD protein, 
+its total UNRES energy and overlap on starting structure:
 <p>
 <a href="static/min1.png"><img src="static/min1.png" width="300px"></a>
 <a href="static/min2.png"><img src="static/min2.png" width="300px"></a>
+<p>
+All files generated during calculations 
+can be viewed/download by clicking on "Directory" link.
 </div>
 </div>
 
@@ -75,7 +88,7 @@ RMSD, fraction of native contacts, and CA fluctuations:
 <p>
 Evolution of RMSD, fraction of native contacts and 
 comparison of CA fluctuations to Bfactor is presented
-only when reference structure is provided as in this case.
+only when reference structure is provided as in this example.
 </div>
 </div>
 <hr>
@@ -109,7 +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
-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>
 
@@ -125,15 +138,69 @@ 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.
 
+<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>
-$('.majorpoints').click(function(){
-    $(this).find('.hiders').toggle();
-    if($(this).find('.majorpointslegend').text()=='Show'){
-        $(this).find('.majorpointslegend').text('Hide');
+$('.majorpointslegend').click(function(){
+    $(this.parentNode).find('.hiders').toggle();
+    if($(this.parentNode).find('.majorpointslegend').text()=='Show'){
+        $(this.parentNode).find('.majorpointslegend').text('Hide');
     }else{
-        $(this).find('.majorpointslegend').text('Show');
+        $(this.parentNode).find('.majorpointslegend').text('Show');
     }    
 });
 </script>