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: 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 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
