Re: [PyMOL] Viewing cavities?

[Eric Z. <zo...@ca...>]

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

Marcus Collins wrote:
> 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."
> ***************************************************************************** 
> 
> 
> 
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