Re: [PyMOL] MSMS Cavity Visualization in Pymol

[Robert C. <rob...@qu...>]

Hi Buz,

On Wed, 30 Jan 2008 14:41:00 -0500, Buz Barstow <bu...@ma...> 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:

  PyMOL>msms_cgo ?
  Usage: msms_cgo file_name [, obj_name [, surfcolor ]]

or

  PyMOL>help 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: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc