[PyMOL] molecular sculpting

I would like to understand the molecular sculpting possibilities of pymol but haven't been able to figure it out yet. When using the wizard, the first request is to click and atom but how to proceed from there? I have used the bit of script provided on the web page and deformed the benzene ri

Re: [PyMOL] molecular sculpting

patricia.a.elk...@gsk.com wrote: > I would like to understand the molecular sculpting possibilities of pymol > but haven't been able to figure it out yet. When using the wizard, the > first request is to click and atom but how to proceed from there? > > I have used the bit of script provided on th

RE: [PyMOL] molecular sculpting

Molecular sculpting works like a real-time energy minimizer, except that it isn't minimizing the energy. Instead, its just trying to return local atomic geometries (bonds, angles, chirality, planarity) to the configuration the molecules possess when they were first loaded into PyMOL. To actu

Re: [PyMOL] pymol without GL

Oops! I forgot to mention that this is related to the GeForce4 Ti 4400 that we have in our lab. So I am guessing it also applies to the Ti4600. On the other hand, the Quadro4 700 XGL works fine, except for the annoying stereo-good mono-bad performance glitch. Zac DeLano, Warren wrote: Zac,

[PyMOL] fitting residues

Hello: I was wondering if there was anyway to make the cartoon backbone match the real backbone to a greater extent. Now I have residues displayed as sticks and a backbone displayed as loop and the loop doesn't really come near the residue so it looks like the residue is floating in space. I am

RE: [PyMOL] fitting residues

Jason, Try turning off "Smooth Loops" in the Cartoon menu. or set cartoon_smooth_loops=0 Also potentially useful is set cartoon_flat_sheets=0 Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S.

[PyMOL] trouble making movie on linux

HI, I am attempting to make a movie from a series of 50 pdb files. When I load the files individually they work fine, however when I load the files into a movie using a series of "load file.pdb,mov" commands only the first 2 frames are correct. In frames 3 and higher the connections between a