[PyMOL] freeglut (pymol): Unable to create direct context rendering for window 'PyMOL Viewer'
Hi Thomas and all, I branched the thread from the original: http://sourceforge.net/mailarchive/message.php?msg_id=28507590 After PyMOL running, console says: freeglut (pymol): Unable to create direct context rendering for window 'PyMOL Viewer' but I will try to check and contact here as another issue if not succeeded. KB-order .mol2 can be opened, but some large (MB-order) .pdb cannot and shutdown with 'abrupt termination.' glxinfo | grep direct direct rendering: No do you have a graphics driver with direct rendering support installed? No. I think firmly caused by lack of graphic driver. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05060.html OpenGL graphics engine: GL_VENDOR: Intel GL_RENDERER: Intel 945G GL_VERSION: 1.2 (1.4.0 - Build 4.14.10.4543) Have anyone experienced some workaround for above driver? (Might be fit the following, but I cannot find how to install appropriate one) http://intellinuxgraphics.org/download.html Regards, Masataka -- 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 (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
[PyMOL] Context sensitive mutation wizard
Dear PyMOL List I'm frequently using the PyMOL mutagenesis wizard. Consider the mutation of tryptophan to phenylalanin. If the sidechain is mutated from W to F, its reasonable to assume that the plane of the phenyl moiety of F would/should/could/might lie in the same plane as the indol part of the W if there was such a protein. Would it be possible to scriptically adjust the F side chain, after mutation, such that it lies in the W plane? Of course, this becomes ambiguous when, say, a A is mutated to a D, because what would then be the reference for the D side chain? However, N to D would be another case, where it would be desired to have the D end group be in as much overlay with the former N end group as possible. Any ideas on how this might be afforded? Probably not a one-liner though. Kind regards Martin -- 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 (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
Re: [PyMOL] Context sensitive mutation wizard
Can this plugin solve it: http://www.pymolwiki.org/index.php/Rotamer_Toggle Note, that you have to collect the script yourself, and replace the original pymol menu.py file. Not a easy solution to problem. Note, it the script: http://www.pymolwiki.org/index.php/Rotkit You can mutate through a command line, and selecting which rotamer to use. But that would not solve your problem of specifying which plane to select. In http://www.pymolwiki.org/index.php/Propka#Mutagenesis_analysis are some more examples of mutating in PyMOL and get the pKa for the mutations. Best Troels 2011/12/8 Martin Hediger ma@bluewin.ch Dear PyMOL List I'm frequently using the PyMOL mutagenesis wizard. Consider the mutation of tryptophan to phenylalanin. If the sidechain is mutated from W to F, its reasonable to assume that the plane of the phenyl moiety of F would/should/could/might lie in the same plane as the indol part of the W if there was such a protein. Would it be possible to scriptically adjust the F side chain, after mutation, such that it lies in the W plane? Of course, this becomes ambiguous when, say, a A is mutated to a D, because what would then be the reference for the D side chain? However, N to D would be another case, where it would be desired to have the D end group be in as much overlay with the former N end group as possible. Any ideas on how this might be afforded? Probably not a one-liner though. Kind regards Martin -- 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 (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 -- 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 (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
[PyMOL] Intel Video Drivers for Windows
Greetings, I learned a little more about Intel video drivers for Windows yesterday and wanted to share the news with the community. First, there is a difference between Intel Graphics and Intel HD Graphics and their other mobile chipsets. It is important that you choose the correct driver for your device. Yesterday, a user downloaded the wrong driver (he downloaded the non-HD version) and PyMOL had some issues. A few minutes later, when he installed the correct HD version of his driver, all issues went away. Second, always try to use the latest driver. PyMOL v1.4 and later need a driver that can render GLSL 1.2 or later. The old Intel drivers had GLSL 1.10 capabilities. The new drivers were updated to GLSL 1.3. Next, try to stay away from these Intel mobile video cards if you can. First, they're notoriously problematic. Second, they don't even have their own video memory--they use system RAM. Third, Intel is extremely unsupportive when it comes to driver feedback and community involvement. Last, the latest Intel Mobile drivers were updated a few months ago (Sept--Nov) so if you haven't you might consider upgrading. Hope this helps. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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 (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
[PyMOL] Creating Temporary Atoms
Hi PyMol users, I'm new to pymol and was wondering if there was a way of creating temporary atoms that can be used to create distance objects? Or if there was a way of creating distance objects between two positions in space without creating a temporary atom? I'm writing a function file and this file is measuring distances between groups or sets of atoms and a distance object would make it much easier for a user to see where the group distances are measured from. Since I'm writing the function in python a command written way of producing this distance object is necessary and is much appreciated. -George Kvaratskhelia -- 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 (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
[PyMOL] Graphical Problems
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 (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
Re: [PyMOL] Creating Temporary Atoms
Hi George, Check out http://www.pymolwiki.org/index.php/Pseudoatom. Please Google or search the PyMOLWiki for common things like this. Cheers, -- Jason On Thu, Dec 8, 2011 at 3:59 PM, George Kvaratskhelia kvaratskhel...@gmail.com wrote: Hi PyMol users, I'm new to pymol and was wondering if there was a way of creating temporary atoms that can be used to create distance objects? Or if there was a way of creating distance objects between two positions in space without creating a temporary atom? I'm writing a function file and this file is measuring distances between groups or sets of atoms and a distance object would make it much easier for a user to see where the group distances are measured from. Since I'm writing the function in python a command written way of producing this distance object is necessary and is much appreciated. -George Kvaratskhelia -- 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 (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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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 (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
Re: [PyMOL] Graphical Problems
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 frankjulian.zachm...@uab.cat 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 (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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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 (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
Re: [PyMOL] Graphical Problems
I have this problem when I run pymol using the Intel driver on my Ubuntu 11.10 64bit machine. However, if I fire it up using the nvidia driver, I have no issues and it's very smooth. As someone else mentioned, this is likely due to the poor quality of Intel Sandy Bridge graphics chips. Here are my cards: Intel mobile - i915 driver Nvidia geforce gt 520m - nvidia-280.13-0ubuntu6 driver I use ironhide to run the nvidia card for graphics intensive programs Ian - Ian Berke, PhD Associate Research Scientist, Modis Lab Department of Molecular Biophysics and Biochemistry Yale University 266 Whitney Ave, Bass 431 New Haven, CT 06520 (203) 432-4414 Message: 6 Date: Wed, 7 Dec 2011 19:15:28 +0100 From: Julian Zachmann frankjulian.zachm...@uab.cat Subject: [PyMOL] Graphical Problems To: pymol-users@lists.sourceforge.net Message-ID: cahctmqsod9mu4mnum+pdzy_t1q2mxv2bwjuwf9ggv2xqn2d...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 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 -- next part -- An HTML attachment was scrubbed... -- 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 (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
