[PyMOL] MSMS Cavity Visualization in Pymol

2008-01-30 Thread Buz Barstow 

Hi All,

Does anyone know of a script that is capable of displaying the  
surfaces identified by msms in pymol?


It would be nice to have a program that could read in existing .vert   
and .face files. I've included small starting sections of these .face  
and .vert files as examples:


# MSMS solvent excluded surface vertices for protein.xyzr
#vertex #sphere density probe_r
2821296  1.00  1.20
   26.022 6.472 7.936-0.226 0.027-0.974
0 607  2
   24.564 6.680 6.807 0.989-0.147-0.033
0 655  2
   25.071 7.472 6.969 0.567-0.807-0.168
0 657  2
   24.499 6.386 6.838 0.956-0.293-0.018
0 655  2
   25.956 6.178 7.966-0.259-0.120-0.958
0 607  2
   25.398 5.470 7.845 0.206 0.471-0.858
0 608  2
   25.738 5.204 7.835 0.376 0.338-0.863
0 608  2



# MSMS solvent excluded surface faces for protein.xyzr
#faces  #sphere density probe_r
5601296  1.00  1.20
 1  5195  3  3
   195  5196  3  3
   195196  2  3  3
 2196  4  3  3
 5  8  6  3  5
 6  8  7  3  5
 8 11  9  3  7
 9 11 10  3  7


Thanks! and all the best,

--Buz

Re: [PyMOL] MSMS Cavity Visualization in Pymol

2008-01-30 Thread Robert Campbell 
Hi Buz,

On Wed, 30 Jan 2008 14:41:00 -0500, Buz Barstow b...@mac.com wrote:

 Does anyone know of a script that is capable of displaying the  
 surfaces identified by msms in pymol?

I have a script called msms_cgo.py that you can download from:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Download it and run it. You can get some usage information by doing:

  PyMOLmsms_cgo ?
  Usage: msms_cgo file_name [, obj_name [, surfcolor ]]

or

  PyMOLhelp msms_cgo
  msms_cgo file_name, [obj_name ] , surfcolor
default surfcolor is white (1.,1.,1.) 
 
So only a file name is required (and you can omit the .face or
.vert).  You can just give it a file name (e.g. your surfaces are in
my_mol.vert and my_mol.face:

  msms_cgo my_mol

It will create an object called my_mol_msms and colour it white.  If you
want a different colour and object name, then do:

  msms_cgo my_mol, my_surf, surfcolor=(.5,.5,.5)

to make it gray.

Unfortunately it can only do one colour at the moment.  I haven't tried to
modify it to colour the surface according to the atom, although that
shouldn't be too hard to do.

Remember that if the cavities are enclosed, interior surfaces, then they
likely have inward pointing normals and the outside of the cavity will not
be lit unless you select Two Sided Lighting from the Display menu.

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc