FYI: Note that in MacPyMOL 0.99, if you "cd" into the application bundle "cd MacPyMOL.app" and run ./setup.sh, it will create a PyMOL startup script for you in the outer directory that you can then relocate to /usr/bin or wherever.
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 > andr...@biochem.utah.edu > Sent: Wednesday, February 08, 2006 12:26 AM > To: Andrew Wollacott > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] paths in MacPyMol > > Hey Andrew, > > On my system, open launches Graphic Converter. In any case, > I have an alias defined in ~/.bashrc to start pymol: > > alias pymol='/Applications/PyMOLX11Hybrid.app/Contents/MacOS/PyMOL' > > > This way, pymol test.pdb opens the pdb file in pymol, and the > path is set correctly. > > > Andreas > > > > > I recently switched to MacPyMol 0.99. I frequently open a pdbfile > > using the command line in OsX using the "open" command. > This opens up > > the pdbfile in macpymol. The problem is that the present working > > directory is not set up properly. > > > > For instance: > > % cd pdbfiles > > % open test.pdb > > PyMol > pwd > > > > I get "/" as the path > > > > if I open the pdb in the following way: > > % cd pdbfiles > > % /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL > test.pdb PyMol > > > pwd > > > > I get "/Users/andrew/pdbfiles" as the path. > > > > Does anyone know how to get around this problem? Incidently I have > > the same issue when clicking on pdbfiles using the finder. > > > > > > Andrew Wollacott, PhD > > Baker Research Lab > > University of Washington > > -- > --> Andreas Förster <-- > 8 rue Doudart de Lagrée, 38000 Grenoble > ++33.(0)438.866201 and ++33.(0)456.452000 > b5foan at skype and yahoo messenger > docandreas.blogspot.com > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep > through log files for problems? Stop! Download the new AJAX > search engine that makes searching your log files as easy as > surfing the web. DOWNLOAD SPLUNK! > http://sel.as-us.falkag.net/sel?cmd=k&kid3432&bid#0486&dat1642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
