display boostrap grid correction

[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 35b8dba..6e9bbde 100644 (file)
--- 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">
 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: 
 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.
 <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>
 <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>
 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>
 <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>
     
     <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">
 
 
 <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>
 <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>
 
 </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
 <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>
 </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
 <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>
 

@@ -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.
 
 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>

-$('.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{
     }else{

-        $(this).find('.majorpointslegend').text('Show');
+        $(this.parentNode).find('.majorpointslegend').text('Show');

     }    
 });
 </script>
     }    
 });
 </script>