Ubuntu

Segmentation Fault (core dumped)

Asked by HARESH AJANI

Please help me for solving this error

ajanihar@haresh:~$ pymol
 PyMOL(TM) Incentive Product - PyMOL Executable Build
 Copyright (C) Schrodinger, LLC

 This PyMOL Executable Build is available only to PyMOL Power, Casual, and
 Developer Users who have a valid license to use this software product. Any
 other usage is specifically prohibited and may constitute a violation of
 United States and international copyright laws.

 This Executable Build integrates and extends Open-Source PyMOL 1.5.0.4.
 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 3.4, 256 bits)
  GL_VERSION: 2.1 Mesa 10.1.3
 Detected 4 CPU cores. Enabled multithreaded rendering.
HEADER TRANSFERASE/TRANSFERASE INHIBITOR 25-OCT-10 3PE1
TITLE CRYSTAL STRUCTURE OF HUMAN PROTEIN KINASE CK2 ALPHA SUBUNIT IN COMPLEX
TITLE 2 WITH THE INHIBITOR CX-4945
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CASEIN KINASE II SUBUNIT ALPHA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 1-337;
COMPND 5 SYNONYM: CK II ALPHA;
COMPND 6 EC: 2.7.11.1;
COMPND 7 ENGINEERED: YES
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 Symmetry: Found 2 symmetry operators.
 CmdLoad: "/home/ajanihar/Desktop/3PE1.pdb" loaded as "3PE1".
Segmentation fault (core dumped)

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Revision history for this message
Manfred Hampl (m-hampl) said : 		#1

What release of Ubuntu and what version of pymol are you running?

Please provide the output of the following terminal commands

lsb_relase -a
uname -a
dpkg -l | grep pymol

Revision history for this message
HARESH AJANI (ajaniharesh) said : 		#2

lsb_release -a

No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu Utopic Unicorn (development branch)
Release: 14.10
Codename: utopic

uname -a

Linux haresh 3.13.0-26-generic #48-Ubuntu SMP Wed May 7 23:31:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

ajanihar@haresh:~/Programs$ dpkg -l | grep pymol
rc pymol 1.7.0.0-1 amd64 Molecular Graphics System

Regards,

HARESH

Revision history for this message
Thomas Krüger (thkrueger) said : 		#3

I guess this is also related to https://answers.launchpad.net/ubuntu/+question/248706

Revision history for this message
Manfred Hampl (m-hampl) said : 		#4

Besides the fact that you are running the utopic release of Ubuntu which is only in its early stages of development (to be published in October this year), you seem also to be running pymol from some non-Ubuntu source.

There is not much support possible in such situation. I can only recommend that you install a supported release of Ubuntu (e.g. 14.04 LTS), and install the pymol version from the standard Ubuntu repositories.

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