Dear all,
I download CASTpyMOL.pyc and put it in the right folder.
Now I want to use it for detecting cavity for 50 proteins. I don't want
to do that one after one by hand.
Is it possible to write a python (pymol) script to do that automatically?
Thanks a lot!
Regards
Bingding
Sebastien Moretti wrote:
Dear Bingding,
CASTp cavities are pre-computed for most of PDB entries.
So, you could create a PyMOL script (.pml) which could look like that:
"call the CASTp plugin for xxxx" ?
save xxxx.pdb
reinitialize
"call the CASTp plugin for yyyy" ?
...
With this kind of script you could be able to get the cavities for your
50 proteins with only one PyMOL execution.
Nevertheless, I don't know how to call the CASTp plugin from a PyMOL
script. And how to save all cavities as distinct pdb files.
But I know that that is possible.
Only the PyMOL mailing list or Wiki are able to help you now.
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."
*****************************************************************************
--
Bingding Huang
PhD student
Bioinformatics group
Biotec & Department of Computing
Tazberg 47, 01307
TU Dresden, Germany
Tel: 0049 351 46340064 (Office)
Tel: 0049 351 4403368 (Home)
Fax: 0049 351 46340061
Web: http://www.biotec.tu-dresden.de/~bhuang
E-mail: bhu...@biotec.tu-dresden.de
