Gentoo Forums
Gentoo Forums
Gentoo Forums
Quick Search: in
PyMol cannot load PDB files [Solved]
View unanswered posts
View posts from last 24 hours

 
Reply to topic    Gentoo Forums Forum Index Other Things Gentoo
View previous topic :: View next topic  
Author Message
jswails1
n00b
n00b


Joined: 19 Oct 2011
Posts: 19

PostPosted: Wed Sep 18, 2013 3:17 pm    Post subject: PyMol cannot load PDB files [Solved] Reply with quote

This is a relatively new problem (happened after a large upgrade --with-bdeps=y that had been waiting for well over a year). The error message I get when attempting to load any PDB file is this:

Code:

 PyMOL(TM) Molecular Graphics System, Version 1.6.0.0.
 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 1.20.
 OpenGL graphics engine:
  GL_VENDOR: VMware, Inc.
  GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.1, 128 bits)
  GL_VERSION: 2.1 Mesa 9.1.2
 Detected 6 CPU cores.  Enabled multithreaded rendering.
HEADER    HYDROLASE                               23-MAR-97   3LZT
TITLE     REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: LYSOZYME;
COMPND   3 CHAIN: A;
COMPND   4 EC: 3.2.1.17;
COMPND   5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 Symmetry: Found 1 symmetry operators.
 CmdLoad: "3lzt.pdb" loaded as "3lzt".
Floating-point arithmetic operators only work with floating-point types!
  %357 = fsub <4 x i32> zeroinitializer, %356
Broken module found, compilation aborted!
/usr/bin/pymol: line 3: 15036 Aborted                 "/usr/bin/python2.7" "/usr/lib64/python2.7/site-packages/pymol/__init__.py" "$@"


The only place I could find the "Floating-point arithmetic operators..." error message from Google was in some LLVM source file: https://llvm.org/svn/llvm-project/llvm/tags/cremebrulee/cremebrulee-56/lib/VMCore/Verifier.cpp

This may be relevant: I changed my default GCC version from 4.5 to 4.7 when I did the monster upgrade. Has anybody else seen this problem? Does anybody have any clues?

Thanks!
Jason

P.S. I originally had the latest stable version (1.5.0.3-r2), but upgraded to 1.6.0.0-r2 in an attempt to fix this problem. I also looked at the dependency graph (equery g pymol) of pymol and re-emerged all of its dependencies. I even unmerged and re-emerged all of those packages. Still no dice.


Last edited by jswails1 on Fri Sep 20, 2013 4:31 pm; edited 1 time in total
Back to top
View user's profile Send private message
jswails1
n00b
n00b


Joined: 19 Oct 2011
Posts: 19

PostPosted: Fri Sep 20, 2013 4:31 pm    Post subject: Solved Reply with quote

Turns out the error was coming from one of the OpenGL libraries that PyMol was using. I could trace this back to portage not correctly installing the Nvidia video driver.

When I downloaded the binary install file myself from the Nvidia website and installed it by hand, this problem was fixed (in addition to the poor performance I was seeing in my other OpenGL-based programs).
Back to top
View user's profile Send private message
lpablo
n00b
n00b


Joined: 27 Oct 2013
Posts: 1

PostPosted: Sun Oct 27, 2013 2:47 am    Post subject: Reply with quote

Hello,

Let me just say im practically new to Linux and i am currently using version 12.04 in an Oracle virtualbox. I encountered the same error, however i don´t have any NVidia files. Could you specify which OpenGL libraries PyMol was trying to use?

Thanks!

Pablo
Back to top
View user's profile Send private message
jswails1
n00b
n00b


Joined: 19 Oct 2011
Posts: 19

PostPosted: Mon Oct 28, 2013 3:00 am    Post subject: Reply with quote

I think you might be mistaking distros here. The 12.04 version suggests to me that you're using Ubuntu rather than Gentoo. That said, the problems I was having dealt with the OpenGL libraries (such as /usr/lib64/libGL.so, /usr/lib64/libGLU.so, etc.), I believe. In any case, when I installed the vendor-supplied graphics driver instead of the package manager supplied file, everything worked as I expected it to.

Using VirtualBox complicates matters, since the kernel modules you need to use for the graphics card may not be the ones you would use on a 'native' system (without emulation).

I would suggest trying to upgrade the Guest Additions (or install them if you haven't), and fiddle around with the video settings until you get something that 'works.'

An alternative would be to download PyMol on your host OS (Windows, I'm assuming) and just use it on there.

Good luck,
Jason
Back to top
View user's profile Send private message
Display posts from previous:   
Reply to topic    Gentoo Forums Forum Index Other Things Gentoo All times are GMT
Page 1 of 1

 
Jump to:  
You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot vote in polls in this forum