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" <daniel.jjam...@gmail.com> 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
>
>
> ------------------------------------------------------------------------------
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and protocols
> are
> 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
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
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
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
