Hello Santiago, have you tried using the graphics drivers from the xorg-edgers project?
That helped me with the stick coloring problem: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09210.html and may also help with your problem. Bernhard -----Original Message----- From: Santi Rios <srios...@gmail.com> To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Pymol 1.4.1 problem coloring cartoons. They turn to black. Date: Thu, 28 Jul 2011 11:37:56 +0200 Dear Pymol Users, I've found a problem with Pymol version 1.4.1. I am using Ubuntu 10.10 in a laptop with Intel Mobile 4 graphics controller. The problem comes when I load any PDB file, then try to show it as a cartoon. It displays the cartoon but in black color, so I cannot see it unless I turn the background to white. With "lines" it's correctly displayed but "cartoon" or "sticks" show the same behaviour (colored black). This only happens if I use the "set use_shaders, 1". If I don't use this command, the "cartoon" and "stick" are displayed in the right colour, but then I have problems coloring the sticks (it's a known bug : http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09181.html). I don't know if this is related but immediately after loading the pdb I get this message in the pymol console : PyMOL>load FILE.pdb ObjectMoleculeGuessValences( 1,1): Unreasonable connectivity in heteroatom, unsuccessful in guessing valences. Is this a known bug ? Does anybody know what to do ? Thanks Regards, Santiago By the way, this is a relevant piece of output of my glxinfo command on linux : OpenGL vendor string: Tungsten Graphics, Inc OpenGL renderer string: Mesa DRI Mobile Intel® GM45 Express Chipset GEM 20100330 DEVELOPMENT x86/MMX/SSE2 OpenGL version string: 2.1 Mesa 7.9-devel ------------------------------------------------------------------------------ Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
