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

[Alois Schloegl]

I confirm that this bug occurs under some specific conditions.
For testing I used this file
  http://www.pdb.org/pdb/files/1bl8.pdb
which works fine on a local installation of pymol (Debian/Stretch).

It works also when connecting to OSX (through xquartz 2.7.12 with "ssh
-Y " to a Debian/Jessie server with Pymol installed.

However, when I try to connect from my Debian/Stretch Laptop through
"ssh -X  " to the same Debian/Jessie server, and I try to open the same
file on the server, pymol crashes with the following error message:


>  PyMOL(TM) Molecular Graphics System, Version 1.8.4.0.
>  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 3.8, 256 bits)
>   GL_VERSION:  3.0 Mesa 13.0.6
>  Detected 32 CPU cores.  Enabled multithreaded rendering.
> HEADER    MEMBRANE PROTEIN                        23-JUL-98   1BL8
> TITLE     POTASSIUM CHANNEL (KCSA) FROM STREPTOMYCES LIVIDANS
> COMPND    MOL_ID: 1;
> COMPND   2 MOLECULE: PROTEIN (POTASSIUM CHANNEL PROTEIN);
> COMPND   3 CHAIN: A, B, C, D;
> COMPND   4 ENGINEERED: YES;
> COMPND   5 MUTATION: YES
>  ObjectMolecule: Read secondary structure assignments.
>  ObjectMolecule: Read crystal symmetry information.
>  CmdLoad: "1bl8.pdb" loaded as "1bl8".
> Segmentation fault


I tried also with some other Debian machines, and it seems a
contributing factor is whether the GL_RENDERER is 128 or 256 bits.

>   GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.8, 256 bits)


It crashes in case of 256 bits, but does not crash when 128 bit renderer
is reported.

Maybe someone else can make use of this information ?



Cheers,
   Alois