Doug, I can't be sure, but this looks like a problem with MacOS X binding PyMOL to the wrong shared object, quite possibly due to some change in the resolution order...your analysis is on track. To fix this, try to figure out what entry in PATH, LD_LIBRARY_PATH, (or whatever mechanism MacOS uses for shared object resolution) is causing the problem.
You may then be able to simply change the order of the entries in order to get things to work correctly. Alternatively, you could reset the environment variable within your macpymol shell script... 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 > Douglas Kojetin > Sent: Friday, June 10, 2005 10:16 AM > To: 'pymol' > Subject: [PyMOL] OSX: fink image libs, pymol and the command line > > Hi All- > > I've been using a shell script called 'macpymol' to start > PyMOL from the command line under OS X (pre-Tiger): > > > > #!/bin/sh > /Applications/PyMOLX11Hybrid.app/Contents/MacOS/PyMOL $* > > usage: macpymol file.pdb > > > > I noticed if I use Fink to install an application under OS X > (Tiger) that requires image libraries to be complied and > installed (e.g. /sw/ lib/libJPEG.dylib), PyMOL fails to start > using the above command and gives the following error output > (from the terminal): > > > File "/Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/ > __init__.py", line 90, in ? > import pymol > File "/Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/ > __init__.py", line 306, in ? > import _cmd > ImportError: Failure linking new module: /Applications/ > PyMOLX11Hybrid.app/pymol/modules/pymol/_cmd.so: Symbol not found: > __cg_jpeg_resync_to_restart > Referenced from: /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ > Versions/A/ImageIO > Expected in: /sw/lib/libJPEG.dylib > > > > If I uninstall all Fink installed image libraries (jpeg, png, > etc.), PyMOL starts w/ no problems. If I click directly on > the PyMOLX11Hybrid.app icon, PyMOL starts w/ no problems. > > Any idea of how to resolve this so that I can start PyMOL > from the command line? I think it could have something to do > with Fink's /sw/ bin/init.csh adding some /sw info near the > beginning of my $PATH. > > Many thanks, > Doug > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: NEC IT Guy Games. How far > can you shotput a projector? How fast can you ride your desk > chair down the office luge track? > If you want to score the big prize, get to know the little guy. > Play to win an NEC 61" plasma display: > http://www.necitguy.com/?r=20 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
