I am assuming a new viewport is added to the main window when the
sequence viewer is displayed. This brings up the question, how possible
would it be to create a plugin that creates yet another viewport in the
main window? Where would I look in the code to do this, or would this
require
Dear PyMol users,
I'm looking for a program that can calculate and write out cavities in a
format that can be converted such that I can display it with PyMol (I'm not
satisfied with the results from VOIDOO). Could you please send me any pointer
to a program that you found useful? BTW, this
I was looking for such a program couple of days ago, and I found pass.
http://www.ccl.net/cca/software/UNIX/pass/overview.shtml
I saw the cavities in couple of minutes in pymol :) I'm not familiar with
voidoo, so I don't know if you will find this usefull or not...
My current problem is related
One program which can do this is SURFNET:
http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html
There are two ways in which cavities can be displayed:
i) SURFNET can write out PDB format files containing the atoms/residues
lining each cleft, which you can view directly
ii) If linked with
Related the issue of inside-surface coloring, a useful feature to add to pymol
would be the ability to flip surface normals for selected surfaces.
Just a thought.
JP Cartailler
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
Okay, it seems that set auto_zoom, off does work for PDB files, but not
for SDF files. I have a python script that gives these three commands:
set auto_zoom, off
load gsk_77553_l.sdf
show sticks, gsk_77553_l
But when you call the script, this is what happens in pymol
PyMOLset auto_zoom, off
