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 ------------------------------------------------------------------------------ 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
