[PyMOL] Mysterious crash bug
Hi everyone, On a few structures (some partially-built) I have run into an odd barely-reproducible crash bug with PyMOL 0.99rc6 (once on windows and once on linux). When a "problem" molecule is loaded (sometimes this is a specific combination of molecules, and not a single molecule), mousing-over any file in the File->Open dialog causes pymol to instantly crash. Altering the problem molecule's coordinates (either by rotation/translation in PyMOL or with subsequent rounds of building into density) often causes this problem to go away for that molecule. This issue has bitten me on two occasions, but before I spend time trying to track down a reproducible case, I would like to find out if anyone else has noticed it, or if it's an isolated problem. Jacob -- Jacob Corn The Berger Lab UC Berkeley - Molecular and Cell Biology jc...@uclink.berkeley.edu phone: 510-643-8893 fax: 510-643-9290
Re: [PyMOL] loosen secondary structure
Hi, * O. J. Ganesh [2006-05-18 16:09] wrote: > > Hey PyMOL gurus: > > I have a 'perfect' helix. Is there some way to 'loosen' all of the > angles in the helix so instead of 3.6 residues per turn, I could > have, say, 8 residues per turn. My goal is to make the helix more > 'coil-like'. Is this possible? Well, if you know the phi/psi angles you like, then you could just build it and specify those angles with my build_seq.py script: http://adelie.biochem.queensu.ca/~rlc/work/pymol/build_seq.py You can specify the phi, psi angles on the command line. Alternatively, you can create a file of resname, phi, psi and build it with: http://adelie.biochem.queensu.ca/~rlc/work/pymol/build_seq_phi_psi.py if you don't want the phi/psi angles to be the same for every residue. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associatephone: 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
Re: [PyMOL] "unset" surface colors
Hi Natasja, That should be done with (IIRC) set surface_color,-1 Tsjerk On 5/24/06, Natasja Brooijmans wrote: I accidently used the "set surface_color, x" command, and then unset. Now the full surface is colored white. Rather, I want the surface to be colored by the color of the underlying residues, but it looks like I can't get it to do that after having used the set command. Any way of resetting the surface settings back to the default? I tried deleting the object I created for the surface and remaking it, but the settings are "stuck". Thanks, Natasja -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336
[PyMOL] "unset" surface colors
I accidently used the "set surface_color, x" command, and then unset. Now the full surface is colored white. Rather, I want the surface to be colored by the color of the underlying residues, but it looks like I can't get it to do that after having used the set command. Any way of resetting the surface settings back to the default? I tried deleting the object I created for the surface and remaking it, but the settings are "stuck". Thanks, Natasja
