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helper_nmr.php
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helper_nmr.php
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<?php # (jEdit options) :folding=explicit:collapseFolds=1:
/*****************************************************************************
Welcome/start page for MP3, with hints for new users about how to proceed.
*****************************************************************************/
// We use a uniquely named wrapper class to avoid re-defining display(), etc.
class helper_nmr_delegate extends BasicDelegate {
#{{{ display - creates the UI for this page
############################################################################
/**
* Context is not used.
*/
function display($context)
{
echo $this->pageHeader("Evaluate NMR structure", "helper_nmr");
?>
<div class='feature'>
We currently have no tutorials for NMR structures, but many of the principles of analyzing crystal structures still apply.
See our
<a href='http://kinemage.biochem.duke.edu/teaching/workshop/CSHL2012/' target='_blank'>2012 Cold Spring Harbor tutorial on MolProbity</a>
as well as our <a href='<?php echo makeEventURL("onGoto", "helper_xray.php") ?>'>guide to analyzing X-ray structures</a>.
</div>
Use this guide to help you evaluate the reliablity of a structural model determined by Nuclear Magnetic Resonance (NMR) spectroscopy --
not all parts of all structures (published or not) are correct,
and the errors could impact the biological conclusion you wish to draw.
<ol>
<li><b><?php echo "<a href='".makeEventURL("onCall", "upload_setup.php")."'>Choose a structure</a>"; ?>:</b>
You need the coordinates for your model in PDB format.
You can upload a file directly from your computer, or search for one at the
<a href='http://www.pdb.org/' target='blank'>Protein Data Bank</a> or the
<a href='http://ndbserver.rutgers.edu/' target='blank'>Nucleic Acid Data Bank</a>.
</li>
<li><b><?php echo "<a href='".makeEventURL("onCall", "reduce_setup.php")."'>Add hydrogens (usually unnecessary)</a>"; ?>:</b>
Explicit hydrogens are needed for many of MolProbity's analyses to function correctly, but
structures determined by NMR almost always include them.
</li>
<li><b><?php echo "<a href='".makeEventURL("onCall", "aacgeom_setup.php")."'>Analyze sterics & geometry for single models</a>"; ?>:</b>
Most NMR structures are reported as ensembles of models.
At the moment, MolProbity has limited tools for analyzing ensembles,
but it can easily analyze each model individually.
<p>Don't be daunted by the array of <b>options</b> here --
MolProbity automatically selects appropriate settings for your structure,
so it's not necessary for you to change them unless you want to.
Running all the various analyses may take a few minutes, so please be patient.
<p>The <b>all-atom contact</b> analysis is concerned with steric interactions inside the model.
Non-(H)bonded atoms with substantial (e.g. >0.4Å) van der Waals overlap
are errors in the model; the energetic cost is enormous relative the stability of a macromolecule.
The clashscore is the number of these overlaps per 1000 atoms; smaller numbers are better.
You can see the individual clashes in the multi-criterion kinemage as hot pink spikes,
which is useful for seeing if the errors affect your region(s) of interest.
<p>The <b>geometric</b> analyses are also good indicators of potential errors in the model.
Ramachandran and rotamer outliers flag very unusual conformations of the protein backbone or sidechains, respectively.
A few of these may be genuine, but in most cases they are mistakes.
Cβ deviations indicate net distortion of bond angles around the Cα,
which can be diagnostic of a backwards sidechain.
For nucleic acids, the perpendicular distance from the base to the phosphate
is strongly correlated with the pucker of the ribose ring, making it a useful aid to fitting.
<p>Don't be dismayed -- <b>all structures have a few problems!</b>
These tools can help structural biologists reduce the number of problems in their structures, however,
and can help other scientists know whether a particular model offers a believable view of a specific area.
</li>
<li><b><?php echo "<a href='".makeEventURL("onCall", "ens_aacgeom_setup.php")."'>Analyze sterics & geometry for the ensemble</a>"; ?>:</b>
At the moment, MolProbity has limited tools for analyzing ensembles.
It can produce multi-model multi-criterion kinemages, but not much else (yet).
Feature requests to Jeremy Block (jeremy.block@duke.edu).
</li>
<li><b><?php echo "<a href='".makeEventURL("onGoto", "file_browser.php")."'>Download files</a>"; ?>:</b>
Before you leave, you may want to download some of the files you've created,
like the PDB file with hydrogens added, or the multi-criterion kinemage.
You can also review the results you've obtained using the
<?php echo "<a href='".makeEventURL("onGoto", "notebook_main.php")."'>lab notebook</a>"; ?>.
</li>
<li><b><?php echo "<a href='".makeEventURL("onGoto", "logout.php")."'>Log out</a>"; ?>:</b>
This will permanenty remove your files from our server, freeing up space for other users.
</li>
</ol>
<?php
echo $this->pageFooter();
}
#}}}########################################################################
#{{{ a_function_definition - sumary_statement_goes_here
############################################################################
/**
* Documentation for this function.
*/
//function someFunctionName() {}
#}}}########################################################################
}//end of class definition
?>