Marcus,
Here is one way (courtesy Kyle Lassila):
Check out VOIDOO:
http://xray.bmc.uu.se/usf/voidoo.html
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 (also
found as Uppsala Software Factory) to
convert to .ccp4 so that pymol can read it.
Load the map with "load filename.ccp4".
View the map with "isomesh msh1,filename,1.0"
mapman input file:
RE m1 cavity_1.ezd NEWEZD
WR m1 cavity_1.ccp4 CCP4
QU
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
Eric
Hi Marcus,
You can install the CASTp plugin for PyMOL :
http://cast.engr.uic.edu/cast/?mode=CASTpyMOL
CASTp (http://cast.engr.uic.edu/cast/) is "Computed Atlas of Surface
Topography of proteins" and analyzes the "Anatomy of Protein Pockets and
Cavities".
So, with the plugin, you can get every cavities (pockets), CASTp has
predicted, automatically.
I hope this will help you.
Hello all,
The surface rendering in PyMOL is quite nice, but I cannot separate
the "branches" of the surface. That is, I would like to view a large
cavity inside of a protein independently from the outer, solvent
accessible surface. Is anyone aware of a means to do this?
Marcus Collins
*****************************************************************************
Marcus D. Collins
Gruner Biophysics Group, Cornell University Dept. of Physics, LASSP
(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."
*****************************************************************************
--
Sébastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex
