Re: [PyMOL] Ray Tracing A Protein Gallery

Dear All, Thanks for all your suggestions on ray tracing the protein gallery. In the end, I used several of the techniques suggested, and everything worked out really well! To summarize: 1. Use the grid_mode option (only available in the compiled from source pymols) 2. Make a fake .pdb th

[PyMOL] Mutating an Ion in Pymol and Displaying van der waals Radii

Dear All, I'd like to mutate an ion in pymol from a potassium to a sodium. Is there an easy way to do this from the command line without having to edit the pdb file of the structure? Also, when one displays an atom (for instance a K atom) using the spheres representation, is the radius of

[PyMOL] surface properties

Hi All I have searched thru the archive and couldn't find an answer, to this. I would like to make pymol surface(s) colored by (1) hydrophobicity and (2) concavity/convexity. These are easily produced in grasp, so one possibility maybe to import some type of grasp file. Thanks in advance for sugg

[PyMOL] weird visualization of a peptide structure

Hi all, I have a little problem with the visualization of a peptide conformation: as you can see from the picture I enclose, the structure appears as if every atom is bound to every neighbour atom. What (and how) can I set in PyMOL, to visualize a correct structure? Thank you very much for your he