Re: [PyMOL] Viewing cavities?

[Sebastien M. <seb...@ig...>]

> Marcus,
>     Here is one way (courtesy Kyle Lassila):
> Check out VOIDOO:
> http://xray.bmc.uu.se/usf/voidoo.html
>=20
> Then:
> Use VOIDOO to make a map of the cavity.  That gives a
> map in one of the electron density formats, .ezd.  Then use MAPMAN (als=
o=20
> found as Uppsala Software Factory) to
> convert to .ccp4 so that pymol can read it.
>=20
> Load the map with "load filename.ccp4".
> View the map with "isomesh msh1,filename,1.0"
>=20
> mapman input file:
> RE m1 cavity_1.ezd NEWEZD
> WR m1 cavity_1.ccp4 CCP4
> QU
>=20
> sample voidoo input file:
> c
> n
> voidoo_etc/cavity.lib
> design.pdb
> 0.75
> 1.2
> 20
> 1.05
> 1
> y
> 49.1 32.7 46.5
> n
> cavity.log
> y
> 10
> o
> 0.90
> 15
> 0.05
> 0.05
> n
> y
> cavity
> 0.2
> n
>=20
> Eric

Hi Marcus,
You can install the CASTp plugin for PyMOL :
http://cast.engr.uic.edu/cast/?mode=3DCASTpyMOL

CASTp (http://cast.engr.uic.edu/cast/) is "Computed Atlas of Surface=20
Topography of proteins" and analyzes the "Anatomy of Protein Pockets and=20
Cavities".
So, with the plugin, you can get every cavities (pockets), CASTp has=20
predicted, automatically.

I hope this will help you.

>> Hello all,
>>
>> The surface rendering in PyMOL is quite nice, but I cannot separate=20
>> the "branches" of the surface.  That is, I would like to view a large=20
>> cavity inside of a protein independently from the outer, solvent=20
>> accessible surface.  Is anyone aware of a means to do this?
>>
>> Marcus Collins
>>
>> **********************************************************************=
*******=20
>>
>>                               Marcus D. Collins
>>      Gruner Biophysics Group, Cornell University Dept. of Physics, LAS=
SP
>>              (h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650
>>        "You have opened a new door, and I share this with you,
>>             for I have been where you are now."
>> **********************************************************************=
*******=20

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex