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

{% extends "base.html" %}

{% load i18n lazysignup_tags %}
{% block content %}

<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>
The following three types of simulations can be run with the UNRES server: 
local minimization, molecular dynamics and replica exchange molecular dynamics:
<p>
<img src="static/types.png" style="border:2px solid blueviolet">
<p>
Use the "Save & submit" button to start calculations.
<img src="static/submit.png" style="border:2px solid blueviolet">
<p>
Use the "Refresh" button to check the status of a 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>
After the server job has been submitted the "waiting in the queue to
start" message will be displayed in the status field, which will subsequently change
to "running",  "postprocessing", and "done". While the job has the "running" 
status, the percentage of job accomplishment is displayed.
It should be noted that the "100%" accomplishment refers to the production
phase of a job, after which the postprocessing phase is triggered which also takes
some time (up to several minutes when making a movie from an MD trajectory is 
requested) and whose progress is not monitored. The page is autorefreshed every 30 sec.
<p>
Any single job can by accessed later using the address of the web page
displayed after job submission: e.g. 
http://unres-server.chem.ug.edu.pl/details1/570cf15fc638493893ece1f011ea0182/984/
<br>
Registered users can save all their jobs and access them later after logging in.
<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 the selected protein (1BDD) is input.
<p>
<img src="static/min.png" style="border:2px solid blueviolet">


After energy minimization is accomplished, the UNRES model of the protein, 
its total UNRES energy and superposition on starting structure are displayed.
The interactive <a href="https://github.com/arose/ngl">NGL Viewer</a> is employed, which enables the users to manipulate the 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 the "Directory" link.
</div>
</div>

<h4><li>Molecular dynamics of IGG-binding domain from streptococcal protein G
(PDB code:1IGD) starting from the experimental 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>
After the MD simulation is accomplished temperature histogram, 
plots of UNRES energy, RMSD from the experimental structure, fraction of native
contacts, and radius of gyration vs. time, a movie of the trajectory, and 
CA-atom fluctuations are displayed.
<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 the reference structure is provided, as in this example.
</div>
</div>
<h4><li>
Replica exchange molecular dynamics of the 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>
<p>
After a (M)REMD run is accomplished, a table showing replica-exchange statistics
(a), plots of histograms of UNRES energy for each temperature (b), a plot of
energy vs. temperature (c), a temperature-colored scatter plot of energy vs. RMSD
(d), and the temperature-colored cumulative plot of rmsd vs. step number for all replicas
(e), and a cumulative plot of walk of the replicas in temperature space (f) are
displayed. The colors corresponding to replica temperatures are shown in panel (c),
while different replicas are colored from black to yellow in panel (f).
<p>
<a href="static/remd1.png"><img src="static/remd1.png" width="300px"></a>(a)
<a href="static/remd2.png"><img src="static/remd2.png" width="300px"></a>(b)
<a href="static/remd3.png"><img src="static/remd3.png" width="300px"></a>(c)
<a href="static/remd6.png"><img src="static/remd6.png" width="300px"></a>(d)
<a href="static/remd7.png"><img src="static/remd7.png" width="300px"></a>(e)
<a href="static/remd8.png"><img src="static/remd8.png" width="300px"></a>(f)
<p>
The weighted histogram analysis method (WHAM) is applied to compute the
probabilities of the obtained conformations to occur at particular
temperatures and, consequently, the plots of heat capacity (g) and ensemble-averaged RMSD (h) as a functions
of temperature; these are shown in the respective graphs. 
<p>
<a href="static/remd4.png"><img src="static/remd4.png" width="300px"></a>(g)
<a href="static/remd5.png"><img src="static/remd5.png" width="300px"></a>(h)
<p>
Note! Panels are labeled in this tutorial only and labels are not displayed 
in the outputs from real server jobs.
<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.
<p>
<a href="static/remd9.png"><img src="static/remd9.png" width="300px"></a>

<p>


</div>
</div>
</ol>
<hr>
Advanced mode enables the user to change more parameters for each type of
simulation. Separate examples are provided (use the <i>Load example data</i> button as
in the 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 the selected protein (1EI0) and the OPT-WTFSA-2
force field are selected:  
<p>
<img src="static/min_adv.png" style="border:2px solid blueviolet">

After the minimization is accomplished, the UNRES model of 1EI0 protein
with two disulfide bonds as read from the respective PDB file, 
its total UNRES energy and superposition on the starting structure are displayed:
<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 the 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" >
In this example the PDB code of the selected protein (1L2Y) and 
option to write trajectory as a PDB file are selected, saving trajectory 
as a PDB file allows its 3D visualisation by NGL Viewer in addition to
the 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>
After the MD simulation is accomplished temperature histogram, 
plots of UNRES energy, RMSD from the experimental structure, fraction of native
contacts, and radius of gyration vs. time, and a movie of the trajectory are displayed.
<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>
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 the 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. The Berendsen thermostat
was employed and the resulting conformational ensemble was clustered 
at the temperature of 290K. 
This is a full-blown structure-prediction run, but shorter
compared to the UNRES runs during the CASP exercises.

<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>


The output items are the same as those discussed with the Basic mode Example 3.
<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_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>
<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>
<p>
The final models are shown using NGL Viewer.
PDB files can be downloaded by clicking on the <i>Download</i> button.
The 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>
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 SAXS 1 example</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>

The output items are the same as those displayed with the Basic mode example 3.
Additionaly the input reference distance distribution and 
distance distributions for 5 final models are plotted.
<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/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>
<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>
<p>
Finally models.
<p>
<a href="static/saxs12.png"><img src="static/saxs12.png" width="300px"></a>
<p>
Comparison of the input distance distributions with those calculated from the 5 models.
<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 SAXS 2 example</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 a short (50 energy evaluations)
initial minimization is requested.
The distance distribution has been downloaded from the SASBDB database (the SASDA25 entry).

<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>

The input items are the same as those in the Advanced mode Example 2.
<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_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>
<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>
<p>
Final models.
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>
Comparison of the input distance distributions with those calculated from the 5 models.
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>


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{% endblock %}