Hi Thomas,
PyMOL can detect cavities and voids on its own. From the upper
control window, select
Settings > Surface > Cavities and Pockets
and then show your object or selection as surface, which will show the
cavities as surface, not the outer molecular surface.
If you need a properly vetted
I find HOLLOW (http://hollow.sourceforge.net/) to be quite good.
On Fri, Dec 3, 2010 at 12:15 PM, Thomas Evangelidis wrote:
> Dear Pymol users,
>
> I want to display clearly the volume of a buried cavity inside my protein.
> Does anybody know how to do this? I've tried CastP and Caver plugins
> a
Hi, Tom,
have a look at MSPocket:
http://appserver.biotec.tu-dresden.de/MSPocket/
It uses MSMS to generate protein solvent excluded surface (SES) and then
detects pockets on the SES. It also calculates the volume for cavities
(internal pockets buried in proteins) based on the SES.
cheers,
hongbo
Dear Pymol users,
I want to display clearly the volume of a buried cavity inside my protein.
Does anybody know how to do this? I've tried CastP and Caver plugins
already, but they do not produce exactly the volume I want to display. I
would greatly appreciate any advice.
thanks,
Tom
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