Went through and cleaned out everything I could find with pymol then reinstalled the v0.98 rc3 release (since that is what was working fine before) and pymol is back to normal. It looks like the FC4 update really screwed around with python and that in turn messed with pymol. Cleaning out both and reinstalling from scratch seems to have fixed everything.
Thanks for the mixed install suggestion, it looks like the RPM install got messed up and parts of it stayed around even after I hit with an rpm -e as root (probably the python associated stuff that the update messed up), and when I tried to install from the tarball afterwards I got the mixed install. Cleaning out everything got rid of the conflict (apparently) and allowed a successful reinstall. Stuart On Monday 03 October 2005 13:50, you wrote: > 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 -- ____________________________________ Stuart Endo-Streeter Structural Biology and Biophysics Dept. Biochemistry LSRC C266 Duke University 919-681-1668 stuart.endostree...@duke.edu
