One pure PyMOL-based approach is to use the surface_carve settings as
follows:
load $TUT/1hpv.pdb, tmp
extract lig, organic
extract prot, polymer
delete tmp
set surface_carve_cutoff, 4.5
set surface_carve_selection, lig
set surface_carve_normal_cutoff, -0.1
show surface, prot within 8 of lig
set
Warren,
Thanks very much for your suggestions. Turning on Millions of
Colors seems to have solved the problem.
David
DeLano Scientific wrote:
David,
Are the misclicks plausible or absurd? For example, if you click on the
left side of the screen are unrelated atoms being selected on the
David,
Are the misclicks plausible or absurd? For example, if you click on the
left side of the screen are unrelated atoms being selected on the right
side?
If so, then the problem can probably be corrected by running under Millions
of Colors instead of Thousands (see Display under System Prefer
Hi,
I am using MacPyMol under OS X 10.4 on a G5 PowerMac, and I
frequently have problems select atoms by clicking on them. Very often,
no matter how carefully I aim with the mouse, the atoms selected are far
from the ones I wanted. It seems that this should be simple! Is there
something
I'm not sure it's exactly what you're looking for, but this seems similar:
http://hollow.sourceforge.net/
On Tue, May 27, 2008 at 4:53 PM, Thomas S. Leyh, Ph. D.
wrote:
> From time to time I find it valuable to view the suface of a
> ligand-binding pocket looking out from the surface's in
Hi Tom,
I'm not sure this (http://lmc.uab.cat/~xavi/) is what you're looking
for.
If it is, you can build the surface in the CASTp server (or using the
PyMOL plugin) and then display the surface of the pocket (the .poc
object) of the residues forming the binding pocket (e.g. 5 Ang. around
