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-Tutorial
+<h4>
+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 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>
+<img src="static/refresh.png" style="border:2px solid blueviolet">
+<p>
+until
+<img src="static/done.png" style="border:2px solid blueviolet">
+<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.
+<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>
+<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 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 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>
+
+<hr>
+<h4><li>Molecular dynamics of IGG-binding domain from streptococcal protein G
+(PDB code:1IGD) starting from the native structure</h4>
+<div>
+ <fieldset class="majorpoints">
+ <legend class="majorpointslegend"
+ style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
+
+ <div class="hiders" style="display:none" >
+
+<p>
+<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,
+RMSD, fraction of native contacts, and CA fluctuations:
+<p>
+<a href="static/md1.png"><img src="static/md1.png" width="300px"></a>
+<a href="static/md2.png"><img src="static/md2.png" width="300px"></a>
+<a href="static/md3.png"><img src="static/md3.png" width="300px"></a>
+<a href="static/md4.png"><img src="static/md4.png" width="300px"></a>
+<a href="static/md5.png"><img src="static/md5.png" width="300px"></a>
+<a href="static/md6.png"><img src="static/md6.png" width="300px"></a>
+<a href="static/md7.png"><img src="static/md7.png" width="300px"></a>
+<a href="static/md8.png"><img src="static/md8.png" width="300px"></a>
+<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 example.
+</div>
+</div>
+<hr>
+<h4><li>
+Replica exchange molecular dynamics of Trp-Cage miniprotein (PDB
+code:1L2Y) starting from the extended chain </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/remd.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/remd1.png"><img src="static/remd1.png" width="300px"></a>
+<a href="static/remd2.png"><img src="static/remd2.png" width="300px"></a>
+<a href="static/remd3.png"><img src="static/remd3.png" width="300px"></a>
+<a href="static/remd4.png"><img src="static/remd4.png" width="300px"></a>
+<a href="static/remd5.png"><img src="static/remd5.png" width="300px"></a>
+<a href="static/remd6.png"><img src="static/remd6.png" width="300px"></a>
+<a href="static/remd7.png"><img src="static/remd7.png" width="300px"></a>
+<a href="static/remd8.png"><img src="static/remd8.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. 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>
+
+
+</div>
+</div>
+<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.
+
+<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>
+$('.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>
+
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projects / django_unres.git / blobdiff