Hey Jason, Intel GMA 950 card, 945GSE chipset, check :(
So this is a known problem, and is there a workaround? Do you need additional information from my side? Cheers, Tsjerk On Mon, Apr 11, 2011 at 6:06 PM, Jason Vertrees <jason.vertr...@schrodinger.com> wrote: > Hi, > >> The problem did not occur on another machine (Intel Core i7, 64bit), >> running Ubuntu 10.10. >> On my EeePC loading a python CGO file worked fine, while loading an >> empty PDB file segfaulted. So it seems to be related to loading the >> coordinates, not to the displaying. > > Is anyone else having this problem? We found and fixed a similar > HETATM-related issue a few weeks ago. PyMOL's HETATM bonding > determination needs improvement. > > Tsjerk, can you please send me a stack trace. Have you done a clean > build? Also, are your drivers up to date? (Is this an Intel GMA 9x5 > video card?) > > Cheers, > > -- Jason > >> Cheers, >> >> Tsjerk >> >> >> On Mon, Apr 11, 2011 at 12:06 PM, Abhinav Verma <abhinav1...@gmail.com> >> wrote: >>> Hi Jason & Tsjerk ... >>> Just for the info that I just downloaded, compiled and tried it on >>> OpenSuse 11.4 and it ran without any problems: >>> >>> PyMOL>load ../../3lzt.pdb >>> HEADER HYDROLASE 23-MAR-97 3LZT >>> TITLE REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION >>> COMPND MOL_ID: 1; >>> COMPND 2 MOLECULE: LYSOZYME; >>> COMPND 3 CHAIN: A; >>> COMPND 4 EC: 3.2.1.17; >>> COMPND 5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT >>> ObjectMolecule: Read secondary structure assignments. >>> ObjectMolecule: Read crystal symmetry information. >>> Symmetry: Found 1 symmetry operators. >>> ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in heteroatom, >>> unsuccessful in guessing valences. >>> CmdLoad: "../../3lzt.pdb" loaded as "3lzt". >>> >>> hth, >>> abhi >>> >>> >>> On Mon, Apr 11, 2011 at 9:43 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >>>> >>>> Hi Jason, >>>> >>>> I run into a segfault with Pymol 1.4 rev 3938 on my EEE PC, running >>>> Ubuntu 9.04. The segfault occurs when loading the PDB file. It happens >>>> regardless of the contents of the PDB file, but loading something with >>>> hetatms gives some insight in how far it goes: >>>> >>>> PyMOL>load ../../../3lzt.pdb >>>> HEADER HYDROLASE 23-MAR-97 3LZT >>>> TITLE REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION >>>> COMPND MOL_ID: 1; >>>> COMPND 2 MOLECULE: LYSOZYME; >>>> COMPND 3 CHAIN: A; >>>> COMPND 4 EC: 3.2.1.17; >>>> COMPND 5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT >>>> ObjectMolecule: Read secondary structure assignments. >>>> ObjectMolecule: Read crystal symmetry information. >>>> Symmetry: Found 1 symmetry operators. >>>> ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in >>>> heteroatom, >>>> unsuccessful in guessing valences. >>>> Segmentation fault >>>> >>>> If you need any information on libraries or such, let me know. >>>> >>>> Best, >>>> >>>> Tsjerk >>>> >>>> -- >>>> Tsjerk A. Wassenaar, Ph.D. >>>> >>>> post-doctoral researcher >>>> Molecular Dynamics Group >>>> * Groningen Institute for Biomolecular Research and Biotechnology >>>> * Zernike Institute for Advanced Materials >>>> University of Groningen >>>> The Netherlands >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Xperia(TM) PLAY >>>> It's a major breakthrough. An authentic gaming >>>> smartphone on the nation's most reliable network. >>>> And it wants your games. >>>> http://p.sf.net/sfu/verizon-sfdev >>>> _______________________________________________ >>>> 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 >>> >>> >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Molecular Dynamics Group >> * Groningen Institute for Biomolecular Research and Biotechnology >> * Zernike Institute for Advanced Materials >> University of Groningen >> The Netherlands >> >> ------------------------------------------------------------------------------ >> Xperia(TM) PLAY >> It's a major breakthrough. An authentic gaming >> smartphone on the nation's most reliable network. >> And it wants your games. >> http://p.sf.net/sfu/verizon-sfdev >> _______________________________________________ >> 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ------------------------------------------------------------------------------ Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev _______________________________________________ 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
