Re: [PyMOL] BEWARE: recent nVidia drivers
Yes, I've also downgraded from the 7174 driver to the 6629 driver because of huge performance problems with another open source density fitting program. We are using Scientific Linux, another RedHat Enterprise Clone, as operating system. Cheers, Dirk. Warren DeLano wrote: Folks, You may have seen some related messages go by on the PyMOL and/or VMD mailing lists, but just to reiterate: If you have nVidia graphics hardware, PLEASE avoid updating your nVidia graphics drivers for the time being. The 7-series (e.g. 71.74) simply do not work with PyMOL, VMD, and other tools on many (but not all) system configurations. We are working to understand just what the problem is... Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com --- This SF.Net email is sponsored by: New Crystal Reports XI. Version 11 adds new functionality designed to reduce time involved in creating, integrating, and deploying reporting solutions. Free runtime info, new features, or free trial, at: http://www.businessobjects.com/devxi/728 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch
[PyMOL] orient the molecule
Hi, When I try orient command to orient the molecule, the camera changes but the coodinates don't change. I wonder whether it is possible that when I orient the molecule the coodinates also change. Thanks Bingding
Re: [PyMOL] orient the molecule
Thanks! But translate[x,y,z] only translate the molecule. What I want is to put longest length of molecule in the X axes, the second Y axes, the third z axes. Just like what orient command does which change the view of camera but not the coordinates. Now I want the coordinates also change after orient it. Regards Bingding Hi, I think that you should use translate[x,y,z] to change the coordinates of your molecule bye andrea 2005/4/21, Bingding Huang bhu...@biotec.tu-dresden.de: Hi, When I try orient command to orient the molecule, the camera changes but the coodinates don't change. I wonder whether it is possible that when I orient the molecule the coodinates also change. Thanks Bingding --- This SF.Net email is sponsored by: New Crystal Reports XI. Version 11 adds new functionality designed to reduce time involved in creating, integrating, and deploying reporting solutions. Free runtime info, new features, or free trial, at: http://www.businessobjects.com/devxi/728 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- This SF.Net email is sponsored by: New Crystal Reports XI. Version 11 adds new functionality designed to reduce time involved in creating, integrating, and deploying reporting solutions. Free runtime info, new features, or free trial, at: http://www.businessobjects.com/devxi/728 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Bingding Huang PhD student Bioinformatics group Biotec Department of Computing Tazberg 47, 01307 TU Dresden, Germany Tel:0049 351 46340064 (Office) Tel:0049 351 4403368 (Home) Fax:0049 351 46340061 Mobile: 01772981375 E-mail: bhu...@biotec.tu-dresden.de
RE: [PyMOL] orient the molecule
This is tricky because the view matrix isn't quite the same format as the coordinates translation matrix. Here's some code that will do what you want: # transform selection coordinates by the camera view cv=list(cmd.get_view()) cmd.transform_selection(all, \ cv[0:3]+[0.0]+ \ cv[3:6]+[0.0]+ \ cv[6:9]+[0.0]+ \ cv[12:15]+[1.0]) cmd.reset() Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Bingding Huang Sent: Thursday, April 21, 2005 1:36 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] orient the molecule Hi, When I try orient command to orient the molecule, the camera changes but the coodinates don't change. I wonder whether it is possible that when I orient the molecule the coodinates also change. Thanks Bingding --- This SF.Net email is sponsored by: New Crystal Reports XI. Version 11 adds new functionality designed to reduce time involved in creating, integrating, and deploying reporting solutions. Free runtime info, new features, or free trial, at: http://www.businessobjects.com/devxi/728 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Connectivity Problem for Visualizing Pseudo-structure
I am using Pymol to visualize a pseudo polymer generated by some brownian dynamics code. We take the coordinate files generated by our simulation and convert them into a PDB file using the hetatm representation and having explicit connections defined with conect. For example: HETATM1P UNK A 2.637 1.188 0.470 HETATM2C UNK A 2.883 0.865 0.178 HETATM3N UNK A 3.176 0.740 0.564 . . . . CONECT12 CONECT2134 CONECT32 I also have the associated HETNAM and FORMUL header lines, but this doesn't seem to make any difference. Pymol displays the individual files in the trajectory fine, but when we go to load in a trajectory of structures to view as a movie, the connectivity gets weird after only a couple of frames. Random atoms are attached to each other. Another strange behavior is that after 72 frames of the movie it regains the correct bonding for one frame and then dies again. For long trajectories, in other word, frames 1,2,74, 146, 218, etc are ok. However there are only 61 atoms in each file, so I don't see an obvious reason for this cycle. If anyone wants a zipped archive of some of the pdb files to play around with, please email me. Any suggestions would be most appreciated. Joshua Adelman -- Joshua L. Adelman Biophysics Graduate Group Lab: 510.643.2159 218 Wellman HallFax: 510.642.7428 University of California, Berkeley http://www.ocf.berkeley.edu/~jadelman Berkeley, CA 94720 USA jadel...@ocf.berkeley.edu --
[PyMOL] Fedora 3 problem
I recently upgraded to Fedora Core 3 and have been having some strange problems with PyMOL. Molecules look fine when rendered as lines, sticks or mesh, but spheres, surfaces, and sometimes cartoons only appear for half the molecule. See the following page for examples of this. I've also posted various diagnostic information in the hope that some Linux guru out there may be able to help. The graphics card is an Intel 82865G. This is (in theory) supported out-of-the box by FC3; I have not installed anything except the distribution. The Intel homepage has some drivers for this card, but they are the same as the ones bundled with FC3. When I tried installing them after the OS, I got exactly the same problem. http://www.ebi.ac.uk/~gareth/pymol/fc3_problem Gareth -- Gareth Stockwell gar...@ebi.ac.uk European Bioinformatics Institute
