Anders, * Anders Madsen <mad...@ccs.ki.ku.dk> [2005-06-21 16:33] wrote: > Dear PyMol users, > I would like to colour the beautiful > PyMol molecular surfaces according to > properties of the atoms involved. > Has anyone experimented with this? > > E.g. by accessing the coordinates that define > the surface and assign a colour to each triangle > involved in the surface mesh?
If you only need to colour it at the resolution of the atoms (as opposed to individual surface vertices), then you can do so by altering the B-factor or occupancy values and colouring the structure on those. I have a script for reading a file of data and applying it to the B-factor or occupancy. Then you just need to colour using the built-in spectrum method or using my color_b.py script. See the data2bfactor.py script in: http://adelie.biochem.queensu.ca/~rlc/work/pymol Within that script, four functions are defined: data2b_atom data2b_res data2q_atom data2q_res The "2b" functions alter the B-factor and the "2q" functions alter the occupancy. The "_atom" functions are used to apply a value to individual atoms, while the "_res" functions are used to apply a single value to the whole residue. You just need to create a data file that looks like: A 1 ALA N data A 1 ALA CA data A 1 ALA C data A 1 ALA O data A 1 ALA CB data etc. (or omit the chain if not defined in your structure) or A 1 ALA data A 2 SER data A 3 PRO data etc. (again omit the chain if not defined). Cheers, Rob -- Robert L. Campbell, Ph.D. <r...@post.queensu.ca> Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
