Thank you for your responses guys.
CAVER is another possible PyMOL plugin http://www.caver.cz
Thanks Emilio. I have installed CAVER and I'm looking into it now - will
let you know if this works well for me.
Also thank you to Andreas and Doug. I'll be sure to check your suggestions
out! It doesn't necessarily need to be in PyMol, but more important that it
can iteratively check multiple pdbs and output all the results together. I
think at least one of your suggestions will allow this.
Daniel
On Wed, Jul 20, 2016 at 3:22 PM, Emilio Xavier Esposito <
emilio.espos...@gmail.com> wrote:
> Hi Daniel
> CAVER is another possible PyMOL plugin http://www.caver.cz
>
> From the CAVER website, "CAVER provides rapid, accurate and fully
> automated calculation of tunnels and channels in static and dynamic
> structures. The molecules amendable to analysis of CAVER include
> proteins, nucleic acids, or inorganic materials."
>
> Emilio
>
> On Tue, Jul 19, 2016 at 6:57 PM, Andreas Warnecke
> <4ndreas.warne...@gmail.com> wrote:
> > 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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> >> planning
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> >
> >
> --
> > 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
> > ___
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--
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___
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