Stuart, It looks to me like you've got a mixed install with potentially old/incompatible files hanging around.
For starters, see if the latest linux standalone build works http://delsci.com/beta pymol-0_99beta14-bin-linux-x86-glibc23.tgz That should help enable you to separate general PyMOL compability issues from specific configuration issues on your machine. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Stuart Endo-Streeter > Sent: Thursday, September 29, 2005 10:24 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] pymol problems with python after FC4 update > > After running a routine update on my FC4 box that included > updates to X11, launching Pymol causes one of two things: > > 1. X completely crashes and must be killed from a remote > login to regain system control. > > 2. Pymol manages to launch with the following messages: > > > [stu...@localhost installs]$ pymol > /usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py:326: > RuntimeWarning: Python C API version mismatch for module > _cmd: This Python has API version 1012, module _cmd has version 1011. > import _cmd > > This PyMOL(TM) Incentive Product is Copyright (C) 2005 > DeLano Scientific LLC. > > A current PyMOL Maintenance and/or Support Subscription may > be required for legal usage of this Build beyond a finite > honor-system evaluation period. > Please visit http://www.pymol.org/funding.html for more information. > > This PyMOL Executable Build is based on Open-Source PyMOL > version 0.98. > /usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py:323: > RuntimeWarning: Python C API version mismatch for module > pcatch: This Python has API version 1012, module pcatch has > version 1011. > _cmd.runpymol() # only returns if we are running pretend GLUT > /usr/lib/python2.2/site-packages/pymol/modules/pymol/xray.py:16: > RuntimeWarning: Python C API version mismatch for module > sglite: This Python has API version 1012, module sglite has > version 1011. > import sglite > /usr/lib/python2.2/site-packages/pymol/modules/pymol/xray.py:16: > RuntimeWarning: Python C API version mismatch for module > ExtensionClass: This Python has API version 1012, module > ExtensionClass has version 1011. > import sglite > OpenGL-based graphics engine: > GL_VENDOR: NVIDIA Corporation > GL_RENDERER: GeForce FX 5700LE/AGP/SSE2/3DNOW! > GL_VERSION: 1.2 (2.0.0 NVIDIA 76.67) > Adapting to GeForce hardware... > > > > I uninstalled/reinstalled pymol, both from the RH9.0 RPM and > tarballs, updated to the latest stable python release and > installed Pymol again, but no change in messages. There was > a similar listing back in 2003 on the mailing list, but no > response was posted. The messages suggest Pymol is looking > for information in /usr/lib/python2.2, which is empty of > pretty much anything at all now, I think the update cleaned > it out when it updated to 2.4, but I can't figure out if I > need to transfer files from the 2.4 directory to the 2.2, or > install 2.2 manually. > > Any ideas anyone? > > Thanks, > Stuart Endo-Streeter > > > > > > > > ____________________________________ > Stuart Endo-Streeter > Structural Biology and Biophysics > Dept. Biochemistry > LSRC C266 > Duke University > 919-681-1668 > stuart.endostree...@duke.edu > > > ------------------------------------------------------- > This SF.Net email is sponsored by: > Power Architecture Resource Center: Free content, downloads, > discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
