[PyMOL] Viewing cavities?

Discussion:

Marcus Collins

2005-11-01 15:31:00 UTC

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."
*****************************************************************************

Peter Adrian Meyer

2005-11-01 15:38:28 UTC

Permalink

Hi Marcus,

Post by Marcus Collins
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?

The easiest way I'm aware of is to select the residues involved on the
surface of your cavity, and then do show surface, [selection].

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Grégori Gerebtzoff

2005-11-02 04:46:02 UTC

Permalink

Have you tried to simply use your mouse wheel? This will change the clipping
view.

Eric Zollars

2005-11-02 17:41:49 UTC

Permalink

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

Post by Marcus Collins
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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Sebastien Moretti

2005-11-03 05:49:53 UTC

Permalink

Post by Peter Adrian Meyer
Marcus,
http://xray.bmc.uu.se/usf/voidoo.html
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"
RE m1 cavity_1.ezd NEWEZD
WR m1 cavity_1.ccp4 CCP4
QU
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.

Post by Peter Adrian Meyer

--
Sébastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

Bingding Huang

2005-11-07 09:38:08 UTC

Permalink

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.

Post by Peter Adrian Meyer
Hi Marcus,
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.

Andrea Spitaleri

2005-11-07 21:30:32 UTC

Permalink

what about Caver:
http://loschmidt.chemi.muni.cz/caver/concept.php
very nice and it works very well

andrea

Post by Bingding Huang
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
Dear Bingding,
CASTp cavities are pre-computed for most of PDB entries.
"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.

--
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
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Tame your development challenges with Apache's Geronimo App Server. Download
it for free - -and be entered to win a 42" plasma tv or your very own
Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php
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