From: Julian Z. <Fra...@ua...> - 2011-12-07 18:15:34
|
Dear Pymol-Users, I have a rather strange error. I can open pymol without having any problems or warnings. But when I'm looking at a protein then - especially when it is in cartoon mode, and even more when i move it around a lot - it is getting more and more blurry and it seems as if there are many small black spots on my protein. When I have more proteins aligned in different colors then I also see spots in the different colors on the protein. Has this problem occured to anyone else before? Does anyone know a solution to this problem? My pymol version is PyMOL 1.4.1, I'm running it on Ubuntu 11.10 64bit, and my graphical card is Intel Corporation 2nd Generation Core Processor Family. Best Regards, Julian |
From: Jason V. <jas...@sc...> - 2011-12-08 21:41:28
|
Julian, Can you please send me a screenshot of what you see? Also, does: unset use_shaders help? It sounds like your video driver needs to be updated. Cheers, -- Jason On Wed, Dec 7, 2011 at 1:15 PM, Julian Zachmann <Fra...@ua...> wrote: > Dear Pymol-Users, > > I have a rather strange error. I can open pymol without having any problems > or warnings. > But when I'm looking at a protein then - especially when it is in cartoon > mode, and even more when i move it around a lot - it is getting more and > more blurry and it seems as if there are many small black spots on my > protein. When I have more proteins aligned in different colors then I also > see spots in the different colors on the protein. Has this problem occured > to anyone else before? Does anyone know a solution to this problem? > > My pymol version is PyMOL 1.4.1, I'm running it on Ubuntu 11.10 64bit, and > my graphical card is Intel Corporation 2nd Generation Core Processor Family. > > Best Regards, Julian > > ------------------------------------------------------------------------------ > Cloud Services Checklist: Pricing and Packaging Optimization > This white paper is intended to serve as a reference, checklist and point of > discussion for anyone considering optimizing the pricing and packaging model > of a cloud services business. Read Now! > http://www.accelacomm.com/jaw/sfnl/114/51491232/ > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Jason V. <jas...@sc...> - 2011-12-12 20:16:19
|
Julian, Glad it works. I'll add a note to the PyMOLWiki about that. Cheers, -- Jason On Mon, Dec 12, 2011 at 2:57 PM, Julian Zachmann <Fra...@ua...> wrote: > Hi Jason, > > finally I managed to solve the problem myself. > It was not a problem of pymol but of the drivers. > > If anybody has similar problems with Intel graphical cards and Ubuntu I > recommend this page: > https://launchpad.net/~glasen/+archive/intel-driver > > But thank you very much for your attention and your will to help me. > > Best regards, > Julian > > > 2011/12/12 Jason Vertrees <jas...@sc...> >> >> Hi Julian, >> >> > you were right, there was a problem with my graphical card. I updated >> > the >> > drivers but still I'm having the same problem. >> > Also unsetting the shaders didn't bring any improvement. >> >> Wow--that's cool enough to be a feature, not a bug. Just kidding, >> we're looking into it. >> >> Can you please answer a few questions: >> * how many objects were loaded in PyMOL? This image looks like there >> are three objects fighting for the depth buffer. >> * does this happen for all representations or just cartoon? >> * what did you do to replicate this in PyMOL? What should I type to >> try to recreate it? >> >> Cheers, >> >> -- Jason >> >> >> Julian, >> >> >> >> Can you please send me a screenshot of what you see? >> >> >> >> Also, does: >> >> >> >> unset use_shaders >> >> >> >> help? It sounds like your video driver needs to be updated. >> >> >> >> Cheers, >> >> >> >> -- Jason >> >> >> >> On Wed, Dec 7, 2011 at 1:15 PM, Julian Zachmann >> >> <Fra...@ua...> wrote: >> >> > Dear Pymol-Users, >> >> > >> >> > I have a rather strange error. I can open pymol without having any >> >> > problems >> >> > or warnings. >> >> > But when I'm looking at a protein then - especially when it is in >> >> > cartoon >> >> > mode, and even more when i move it around a lot - it is getting more >> >> > and >> >> > more blurry and it seems as if there are many small black spots on my >> >> > protein. When I have more proteins aligned in different colors then I >> >> > also >> >> > see spots in the different colors on the protein. Has this problem >> >> > occured >> >> > to anyone else before? Does anyone know a solution to this problem? >> >> > >> >> > My pymol version is PyMOL 1.4.1, I'm running it on Ubuntu 11.10 >> >> > 64bit, >> >> > and >> >> > my graphical card is Intel Corporation 2nd Generation Core Processor >> >> > Family. >> >> > >> >> > Best Regards, Julian >> >> > >> >> > >> >> > >> >> > ------------------------------------------------------------------------------ >> >> > Cloud Services Checklist: Pricing and Packaging Optimization >> >> > This white paper is intended to serve as a reference, checklist and >> >> > point of >> >> > discussion for anyone considering optimizing the pricing and >> >> > packaging >> >> > model >> >> > of a cloud services business. Read Now! >> >> > http://www.accelacomm.com/jaw/sfnl/114/51491232/ >> >> > _______________________________________________ >> >> > PyMOL-users mailing list (PyM...@li...) >> >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> > Archives: >> >> > http://www.mail-archive.com/pym...@li... >> >> >> >> >> >> >> >> -- >> >> Jason Vertrees, PhD >> >> PyMOL Product Manager >> >> Schrodinger, LLC >> >> >> >> (e) Jas...@sc... >> >> (o) +1 (603) 374-7120 >> > >> > >> > >> > >> > -- >> > Julian Zachmann >> > Laboratori de Medicina Computacional >> > Unitat de Bioestadistica. Facultat de Medicina >> > Universitat Autonoma de Barcelona >> > 08193 Bellaterra (Barcelona). Spain >> > Phone: (3493) 581 2797 >> > Fax: (3493) 581 2344 >> > E-mail: Fra...@ua... >> > http://lmc.uab.es >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) Jas...@sc... >> (o) +1 (603) 374-7120 > > > > > -- > Julian Zachmann > Laboratori de Medicina Computacional > Unitat de Bioestadistica. Facultat de Medicina > Universitat Autonoma de Barcelona > 08193 Bellaterra (Barcelona). Spain > Phone: (3493) 581 2797 > Fax: (3493) 581 2344 > E-mail: Fra...@ua... > http://lmc.uab.es -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |