Hi Daniel,
If you don't HAVE to use Pymol, something like fPocket, HOLE or
PocketDepth from this list might do what you want:
http://www.vls3d.com/links/bioinformatics/binding-pockets
You might find this list interesting too:
http://www.vls3d.com/links/bioinformatics/peptides-antibodies-epitopes
cheers,
Doug
Quoting Andreas Warnecke <4ndreas.warne...@gmail.com> on Wed, 20 Jul
2016 00:57:39 +0200:
> I haven't used it before, but I there is a PyMOL plugin called KVfinder
> that detects cavities. Potentially this offers an approach for you.
> On Jul 20, 2016 12:05 AM, "Daniel James" wrote:
>
>> Hi all,
>>
>> I haven't used this list before but can't find an answer to my question
>> elsewhere. I am selecting the antibody binding site automatically to
>> calculate the surface area of the binding sites.
>>
>> However, some of the binding sites have holes/cavities in the surface - I
>> would like to be able to detect if a surface has a hole in it on PyMol (to
>> make a note that it needs to be looked at manually).
>>
>> I create an object of the antigen binding site, show surface and then use
>> get_area to get SASA.
>>
>> Any help will be appreciated.
>>
>> Thanks,
>> Daniel
>>
>>
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_
Dr. Douglas R. Houston
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Institute of Quantitative Biology, Biochemistry and Biotechnology
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What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
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consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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