Dear Maintainer,

Loading a pdb manually or through the fetch command immediately results in a
segmentation fault and pymol closes.

tags 783653 +unreproducible
thanks

Hi,

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

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

"

Hi,

My bet would be that this is an issue with your graphics driver.  Can
you display any kind of graphics, e.g. the formaldehyde molecule I've
attaced in XYZ format? Just running "pymol h2co.xyz" works here.


Michael

Hello,
Same error:

" 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.
 ExecutiveLoad: "h2co.xyz" loaded as "h2co", through state 1.
Segmentation fault
"

I agree, looking at it now this could be due to running it in VMWare
fusion. Perhaps I should look elsewhere for a fix.

Sincerely,
Michael

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:


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

Hello,

seemingly the same bug is observed using pymol 1.8.4.0+dfsg-1build1 on
Ubuntu-18.04. The greeting message of pymol tells that my graphics
driver is blacklisted:

 Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 1.40.
 OpenGL graphics engine:
  GL_VENDOR:   nouveau
  GL_RENDERER: NV137
  GL_VERSION:  3.1 Mesa 18.2.8
 Detected blacklisted graphics driver.  Disabling shaders.
 Detected 24 CPU cores.  Enabled multithreaded rendering.

Best,
Andrius

Found the same problem both in 1.8.4.0+dfsg-1 and 2.2.0+dfsg-4 versions.

Andrius

Hi, this bug is still affecting us today.  Is there any known solution
or workaround?  We get it by doing

fetch 5zal

With version 2.5 from bookworm.

Thanks,
-ryan

There is a workaround, which is to use

set retain_order, 1

within pymol before opening the file.