[Debichem-devel] Bug#783653: pymol: Segmentation fault immediately after loading pdb

[Michael Beck]

It still crashes for me. The output is below:
"
PyMOL(TM) Molecular Graphics System, Version 1.7.2.1.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.

    Created by Warren L. DeLano, Ph.D.

    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.

    If PyMOL is helpful in your work or study, then please volunteer
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at "http://www.pymol.org".

    Enter "help" for a list of commands.
    Enter "help <command-name>" for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 1.30.
 OpenGL graphics engine:
  GL_VENDOR:   VMware, Inc.
  GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.5, 256 bits)
  GL_VERSION:  3.0 Mesa 10.3.2
 Detected 2 CPU cores.  Enabled multithreaded rendering.
PyMOL>fetch 3iol
 please wait ...
HEADER    SIGNALING PROTEIN/SIGNALING PROTEIN     14-AUG-09   3IOL
TITLE     CRYSTAL STRUCTURE OF GLUCAGON-LIKE PEPTIDE-1 IN COMPLEX WITH THE
TITLE    2 EXTRACELLULAR DOMAIN OF THE GLUCAGON-LIKE PEPTIDE-1 RECEPTOR
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: GLUCAGON-LIKE PEPTIDE 1 RECEPTOR;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: N-TERMINAL EXTRACELLULAR DOMAIN, UNP RESIDUES 24-145;
COMPND   5 SYNONYM: GLP-1 RECEPTOR, GLP-1-R, GLP-1R;
COMPND   6 ENGINEERED: YES;
COMPND   7 MOL_ID: 2;
COMPND   8 MOLECULE: GLUCAGON;
COMPND   9 CHAIN: B;
COMPND  10 FRAGMENT: UNP RESIDUES 98-128;
COMPND  11 SYNONYM: GLP-1, GLUCAGON-LIKE PEPTIDE 1, GLICENTIN,
GLICENTIN-RELATED
COMPND  12 POLYPEPTIDE;
COMPND  13 ENGINEERED: YES
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 Symmetry: Found 4 symmetry operators.
 CmdLoad: "./3iol.pdb" loaded as "3iol".
Segmentation fault

"



On Thu, Apr 30, 2015 at 4:40 AM, Michael Banck <mbanck at debian.org> wrote:

> tags 783653 +unreproducible
> thanks
>
> Hi,
>
> On Tue, Apr 28, 2015 at 02:57:55PM -0400, nbx909 wrote:
> > Package: pymol
> > Version: 1.7.2.1-1
> > Severity: important
> >
> > Dear Maintainer,
> >
> > Loading a pdb manually or through the fetch command immediately results
> in a
> > segmentation fault and pymol closes.
>
> I tried to fetch the molecule of the month ("fetch 3iol"), and had no
> issues.
>
> Can you attach a .pdb file with crashed for you? Also, please add the
> output you get when you start pymol from a terminal.
>
>
> Cheers,
>
> Michael
>
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