[PyMOL] Bugs squashed in my scripts
Dear PyMOLers, It was brought to my attention yesterday that 2 of my scripts had problems with their selection routines, so I've put repaired versions up on my web site. They are: color_by_attype.py seq_select.py The problems arose if you had more than one object up with multiple chains and tried to colour just one object. I'm not sure how I managed to miss this bug before! :( Cheers, Rob -- Robert L. Campbell, Ph.D. r...@post.queensu.ca 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] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
On Thu, Feb 19, 2004 at 12:24:53PM +0100, Michael Banck wrote: On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote: For me PyMol on SuSE 8.2 crashed always when raytracing a line element. That seems to be identical to Debian Bug #229080 (http://bugs.debian.org/229080) The stock compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I got the same crash with gcc 3.3.1, but not with gcc 2.95. I have not tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only) solved the problem for me. See PyMol bugreport 806361. Thanks for the information, I will see whether that helps on Debian, too. For the record, the current gcc-3.3 in Debian testing/unstable seems to work fine again for rendering sticks and lines, so I uploaded 0.95-1 using the standard gcc on all architectures again. Michael
RE: [PyMOL] color
Yes, it's called spectrum...but it looks like the docs don't exist yet. PyMOLspectrum ? Usage: spectrum [ expression [, palette [, selection [, minimum [, maximum [, byres [, quiet ]]] eg: spectrum b spectrum q spectrum b, selection=my_obj spectrum b, minimum=5, maximum=60 spectrum count, selection spectrum b, TAB will show you the list of spectra names currently available spectrum count, red_green etc. Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of s...@bu.edu Sent: Thursday, April 08, 2004 8:12 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] color Hi, I have a naïve question here. Is there any command line equivalent to using the menu color the by spectrum (rainbows and etc)? Thanks! -shuhsien
[PyMOL] Pymol and Matlab
Hello to all, I have created a GUI for a particular application I am developing in Matlab. I would love to be able to call Pymol and operate it from within this GUI. My GUI does certain calculations on protein based structures and I do need to visualize the results; in particular, I would be interested in residue selection and their display over a cartoon of the protein. Has anyone interfaced Matlab and Pymol and can give me a push in the right direction to do this? I know I could create a script and load it from PyMol but this would not be the best solution. Is PyMol for Win DDE capable? Thanks a lot for your help! Zach Fernandez
[PyMOL] spectrum, util.rainbow
Hi folks: Why is spectrum and the internal gui (which I assume invokes spectrum) so much faster than util.rainbow ? I like the util.rainbow default color scheme a bit better, but it takes forever for large complexes. Is there a simple way to get spectrum to mimic the rainbow color scheme? Thanks. Bill
