tutorial update and other changes

preminim=50 for saxs example 2

diff --git a/django_simple/todo/templates/changelog.html b/django_simple/todo/templates/changelog.html
index 1c159b0..9507fc8 100644 (file)
--- a/django_simple/todo/templates/changelog.html
+++ b/django_simple/todo/templates/changelog.html
@@ -34,6 +34,14 @@
  NGL Viewer added for 3D display of structures and trajectories.
  </dd>
 
+<dt>29.01.2018</dt>
+ <dd>
+ Random initial SEED value.<br>
+ Second SAXS example in advance mode for the central
+ portion of Factor H (PDB code: 2KMS).<br>
+ Extension and update of the Tutorial.
+ </dd>
+
  
 </dl>
               

diff --git a/django_simple/todo/templates/tutorial.html b/django_simple/todo/templates/tutorial.html
index e073eb7..e271941 100644 (file)
--- a/django_simple/todo/templates/tutorial.html
+++ b/django_simple/todo/templates/tutorial.html
@@ -25,7 +25,7 @@ until
 <p>
 The job status information will start from the "waiting in the queue to
 start", then "running" and finally "postprocessing" before "done".
-Autorefresh is active every 30 sec.
+Postprocessing do not count to 100%. Autorefresh is active every 30 sec.
 <p>
 Any single job can by accessed later using the adress of the web page
 displayed after job submission: 
@@ -61,7 +61,6 @@ can be viewed/download by clicking on "Directory" link.
 </div>
 </div>
 
-<hr>
 <h4><li>Molecular dynamics of IGG-binding domain from streptococcal protein G
 (PDB code:1IGD) starting from the native structure</h4>
 <div>
@@ -75,7 +74,8 @@ can be viewed/download by clicking on "Directory" link.
 <img src="static/md.png" style="border:2px solid blueviolet">
 <p>
 The results of md simulations show temperature histogram, 
-potential energy changes, evolution of radius of gyration,
+potential energy changes, movie generated from trajectory,
+evolution of radius of gyration,
 RMSD, fraction of native contacts, and CA fluctuations:
 <p>
 <a href="static/md1.png"><img src="static/md1.png" width="300px"></a>
@@ -92,7 +92,6 @@ comparison of CA fluctuations to Bfactor is presented
 only when reference structure is provided as in this example.
 </div>
 </div>
-<hr>
 <h4><li>
 Replica exchange molecular dynamics of Trp-Cage miniprotein (PDB
 code:1L2Y) starting from the extended chain </h4>  
@@ -123,7 +122,8 @@ 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. PDB files can be downloaded by clicking on the picture.
+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/remd9.png"><img src="static/remd9.png" width="300px"></a>
 
@@ -132,14 +132,149 @@ and refined. PDB files can be downloaded by clicking on the picture.
 
 </div>
 </div>
+</ol>
 <hr>
 Advanced mode allows for changes of more parameters of each type of
 simulation. Separate examples are provided (use <i>Load example data</i> button as
-in Basic mode): minimization of 1EI0 with
-dissulfide bonds, MD simulations of 1L2Y starting from extended chain
-and multiplexed replica exchange simulations of 5G3Q:B (CASP12 target T0882) 
-starting form extended chain with secondary structure restraints predicted
-by PSIPRED and Berendsen thermostat.
+in Basic mode): 
+<ol>
+<h4><li>
+Minimization of the P8MTCP1 disulfide-bonded helical hairpin miniprotein
+(PDB code: 1EI0).</h4>
+<div>
+    <fieldset class="majorpoints">
+        <legend class="majorpointslegend"
+            style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
+    
+    <div class="hiders" style="display:none" >
+<p>
+In this example the PDB code of selected protein (1EI0) and opt-wtfsa-2
+force field are selected:  
+<p>
+<img src="static/min_adv.png" style="border:2px solid blueviolet">
+
+The results of local minimizations show the UNRES model of 1EI0 protein
+with two dissulfide bonds as read from pdb, 
+its total UNRES energy and overlap on starting structure:
+<p>
+<a href="static/min_adv1.png"><img src="static/min_adv1.png" width="300px"></a>
+<a href="static/min_adv2.png"><img src="static/min_adv2.png" width="300px"></a>
+<a href="static/min_adv3.png"><img src="static/min_adv3.png" width="300px"></a>
+
+    </div>
+</div>
+
+<h4><li>
+Canonical MD simulations of Trp-Cage miniprotein (PDB code:1L2Y) 
+starting from extended chain.</h4>
+<div>
+    <fieldset class="majorpoints">
+        <legend class="majorpointslegend"
+            style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
+    
+    <div class="hiders" style="display:none" >
+In this example the PDB code of selected protein (1L2Y) and 
+option to write trajectory as pdb are selected, saving trajectory 
+as pdb allows its 3D visualisation in NGL Viewer in addtion to
+movie which is always generated from the MD trajectory 
+<p>
+<img src="static/md_adv.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/md_adv0.png" style="border:2px solid blueviolet">
+<p>
+The results of md simulations show temperature histogram, 
+potential energy changes, movie generated from trajectory,
+trajectory visualization in NGL Viewer,
+evolution of radius of gyration,
+RMSD, fraction of native contacts:
+<p>
+<a href="static/md_adv1.png"><img src="static/md_adv1.png" width="300px"></a>
+<a href="static/md_adv2.png"><img src="static/md_adv2.png" width="300px"></a>
+<a href="static/md_adv3.png"><img src="static/md_adv3.png" width="300px"></a>
+<a href="static/md_adv4.png"><img src="static/md_adv4.png" width="300px"></a>
+<a href="static/md_adv5.png"><img src="static/md_adv5.png" width="300px"></a>
+<a href="static/md_adv6.png"><img src="static/md_adv6.png" width="300px"></a>
+<a href="static/md_adv7.png"><img src="static/md_adv7.png" width="300px"></a>
+<p>
+Evolution of RMSD and fraction of native contacts 
+is shown only when reference structure is provided as in this example.
+The CA fluctuations are not analyzed for start from the extended structure
+because of large scale conformational changes during folding.
+
+    </div>
+</div>
+
+
+<h4><li>
+MREMD simulations of 5G3Q:B (CASP12 target T0882)</h4>
+ 
+<div>
+    <fieldset class="majorpoints">
+        <legend class="majorpointslegend"
+            style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
+    
+    <div class="hiders" style="display:none" >
+This simulation starts from extended chain, 2000000 steps for each of 16
+replicas (8 temperatures with multiplexing 2)
+are run and secondary structure restraints predicted by PSIPRED and 
+obtained at the CASP12 time when the experimental 5G3Q structure
+was not included in the PDB database are used. Berendsen thermostat
+and clustering temperature 290K are selected. 
+This is a full-blown structure-prediction run, but shorter
+in comparison to UNRES runs during CASP.
+
+<p>
+<img src="static/remd_adv.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/remd_adv01.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/remd_adv02.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/remd_adv03.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/remd_adv1.png"><img src="static/remd_adv1.png" width="300px"></a>
+<a href="static/remd_adv2.png"><img src="static/remd_adv2.png" width="300px"></a>
+<a href="static/remd_adv3.png"><img src="static/remd_adv3.png" width="300px"></a>
+<a href="static/remd_adv4.png"><img src="static/remd_adv4.png" width="300px"></a>
+<a href="static/remd_adv5.png"><img src="static/remd_adv5.png" width="300px"></a>
+<a href="static/remd_adv6.png"><img src="static/remd_adv6.png" width="300px"></a>
+<a href="static/remd_adv7.png"><img src="static/remd_adv7.png" width="300px"></a>
+<a href="static/remd_adv8.png"><img src="static/remd_adv8.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. Models are shown using NGL Viewer.
+PDB files can be downloaded by clicking on the <i>Download</i> button.
+RMSD of model 1 
+from the experimental structure is 3.6 A and 
+the GDT TS is 58.8 %
+
+<p>
+<a href="static/remd_adv9.png"><img src="static/remd_adv9.png" width="300px"></a>
+
+<p>
+
+
+    </div>
+</div>
+
 
 <hr>
 <h4><li>
@@ -147,7 +282,7 @@ 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)
+(Use <i>Load example SAXS 1</i> button in advanced mode)
 </h4>  
 <div>
     <fieldset class="majorpoints">
@@ -190,8 +325,81 @@ distance distributions for 5 final models are plotted.
 <p>
 <a href="static/saxs11.png"><img src="static/saxs11.png" width="300px"></a>
 
+</div>
+</div>
+
+<h4><li>
+Distance distribution restrained (real SAXS data)
+replica exchange molecular dynamics of 
+the central portion of Factor H (PDB code:2KMS).
+<br>
+(Use <i>Load example SAXS 2</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" >
+REMD simulation starts from the experimental NMR structure. Secondary
+structure restraints are used. Only short (50 energy evaluations)
+initial minimization is requested.
+The SASDA25 entry of the SASBDB is used for SAXS distance distribution.
+
+<img src="static/saxs2_1.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/saxs2_2.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/saxs2_3.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/sasx2_4.png"><img src="static/saxs2_4.png" width="300px"></a>
+<a href="static/saxs2_5.png"><img src="static/saxs2_5.png" width="300px"></a>
+<a href="static/saxs2_6.png"><img src="static/saxs2_6.png" width="300px"></a>
+<a href="static/saxs2_7.png"><img src="static/saxs2_7.png" width="300px"></a>
+<a href="static/saxs2_8.png"><img src="static/saxs2_8.png" width="300px"></a>
+<a href="static/saxs2_9.png"><img src="static/saxs2_9.png" width="300px"></a>
+<a href="static/saxs2_10.png"><img src="static/saxs2_10.png" width="300px"></a>
+<a href="static/saxs2_11.png"><img src="static/saxs2_11.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. 
+In the UNRES calculated
+structures, the domains are at a larger angle than
+those in the experimental NMR structure.
+
+<p>
+<a href="static/saxs2_13.png"><img src="static/saxs2_13.png" width="300px"></a>
+
+<p>
+Additionaly the input reference distance distribution and 
+distance distributions for 5 final models are plotted.
+The distance distribution calculated from the
+experimental NMR structure does not fully overlap with that from
+SAXS; in particular, the plot calculated from the 2KMS
+structure decays to 0 quicker than that from SAXS.
+Much better agreement, in
+particular in the long-distance part is obtained
+for structres from the UNRES simulation.
+<p>
+<a href="static/saxs2_12.png"><img src="static/saxs2_12.png" width="300px"></a>
+
 
 </div>
+
 </div>
 
 

diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py
index f91e57c..33276ac 100644 (file)
--- a/django_simple/todo/views.py
+++ b/django_simple/todo/views.py
@@ -518,7 +518,7 @@ def add_remd_a(request,task_id):
         data= {'name':task.name,'pdbid':'2KMS','md_pdbref':True,'md_start':'pdbstart',
         'md_2d':'----EEEEEE-EEEEE-------EEEEEEEEE--EEEEEE-EEEE---EEEEEEEEE-----EEEEEEE-EEE-HHHHH-EEEE-EEEEEEEEE----EEEEEE---EEE-----',
          'md_nstep':200000,'md_lang':'langevin','unres_ff':'FF2','md_seed':-39912345,
-         'remd_cluter_temp':280, 
+         'remd_cluter_temp':280, 'min_maxfun':50,
          'scal_rad':5.0,'wsaxs':1000.0,'saxs_data':
 """0.7100E-00 0.2036E-03
 0.1420E+01 0.4221E-03

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