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Hi Swanand,<br>
<br>
what we have readily available is the tool to calculate bulk-solvent
mask: is a binary map (0 in protein region and 1 in bulk-solvent
region). Definitions and calculation algorithm are described in <br>
<br>
Jiang, J.-S. & Brünger, A. T. (1994). J. Mol. Biol. 243,
100-115.<br>
<br>
Perhaps other can point something else (if any) but this is all I'm
aware of.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 12/5/14 10:08 AM, Swanand Gore
wrote:<br>
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<div class="moz-cite-prefix">Thanks Pavel!<br>
<br>
Is there a tool to calculate solvent-accessible surface areas
where symmetry-related copies are taken into account and any
area occluded by them is not counted as accessible.<br>
<br>
Regards,<br>
Swanand<br>
<br>
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<blockquote cite="mid:5481EC23.1090407@lbl.gov" type="cite">
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Hi Swanand,<br>
<br>
yes:<br>
<br>
iotbx.show_distances your.pdb > all_distances
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<br>
<br>
will show long list of all distances between pairs including
symmetry related. For symmetry related it will also show the
symmetry operator the relates involved atoms.<br>
<br>
Look implementation for underlying code.<br>
<br>
Type iotbx.show_distances without arguments to see all options.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 12/5/14 8:41 AM, Swanand Gore
wrote:<br>
</div>
<blockquote cite="mid:5481E054.6090406@ebi.ac.uk" type="cite">Hi
All, <br>
<br>
I am sure this has been asked and answered a lot of times... <br>
<br>
Is there a python script somewhere that reads a mmcif file and
for any residue in it, returns a list of residues within a
certain distance of it. And it returns any symmetry-related
copies of residues too within that distance. <br>
<br>
Any pointer greatly appreciated. <br>
<br>
Thanks, <br>
Swanand <br>
<br>
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<br>
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<br>
<br>
<pre class="moz-signature" cols="72">--
Swanand Gore, wwPDB at PDBe-EMBL-EBI, Cambridge
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:swanand@ebi.ac.uk">swanand@ebi.ac.uk</a> ............. <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://pdbe.org">http://pdbe.org</a>
</pre>
</blockquote>
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