Re: [PyMOL] segmentation fault pymol 1.4 rev 3938

[Tsjerk W. <ts...@gm...>]

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.

Cheers,

Tsjerk


On Mon, Apr 11, 2011 at 12:06 PM, Abhinav Verma <abh...@gm...> 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 <ts...@gm...> 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 (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
>



-- 
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