Bug#783653: pymol: Segmentation fault immediately after loading pdb
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 " 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. > HEADERMEMBRANE PROTEIN23-JUL-98 1BL8 > TITLE POTASSIUM CHANNEL (KCSA) FROM STREPTOMYCES LIVIDANS > COMPNDMOL_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
Bug#783653: pymol: Segmentation fault immediately after loading pdb
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 " 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 On Thu, Apr 30, 2015 at 2:21 PM, Michael Banck wrote: > Hi, > > On Thu, Apr 30, 2015 at 01:22:28PM -0400, Michael Beck wrote: > > 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 > > 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 >
Bug#783653: pymol: Segmentation fault immediately after loading pdb
Hi, On Thu, Apr 30, 2015 at 01:22:28PM -0400, Michael Beck wrote: > 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 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 h2co.xyz Description: Xmol XYZ data
Bug#783653: pymol: Segmentation fault immediately after loading pdb
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 " 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 ...
HEADERSIGNALING PROTEIN/SIGNALING PROTEIN 14-AUG-09 3IOL
TITLE CRYSTAL STRUCTURE OF GLUCAGON-LIKE PEPTIDE-1 IN COMPLEX WITH THE
TITLE2 EXTRACELLULAR DOMAIN OF THE GLUCAGON-LIKE PEPTIDE-1 RECEPTOR
COMPNDMOL_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 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
>
Bug#783653: pymol: Segmentation fault immediately after loading pdb
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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Bug#783653: pymol: Segmentation fault immediately after loading pdb
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. -- System Information: Debian Release: 8.0 APT prefers stable APT policy: (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 3.16.0-4-amd64 (SMP w/2 CPU cores) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages pymol depends on: ii freeglut3 2.8.1-2 ii libc6 2.19-18 ii libfreetype6 2.5.2-3 ii libgcc1 1:4.9.2-10 ii libgl1-mesa-glx [libgl1] 10.3.2-1 ii libglew1.10 1.10.0-3 ii libglu1-mesa [libglu1]9.0.0-2 ii libpng12-01.2.50-2+b2 ii libstdc++64.9.2-10 ii python2.7.9-1 ii python-numpy [python-numpy-abi9] 1:1.8.2-2 ii python-pmw1.3.2-6 ii python-tk 2.7.8-2+b1 pn python2.7:any Versions of packages pymol recommends: ii apbs 1.4-1 pymol suggests no packages. -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
