Hi Bill,
This 0.91 OS X build is a new beast. I finally figured out how
to successfully fuse a unix commmand-line application with a MacOS X
application bundle, making life a whole lot easier. For one thing,
there are no longer any environmental variables to edit and set -- the
path is detected automatically.
To launch this new PyMOL from the command line with files or
options, just call the executable inside the bundle:
PyMOL.app/Contents/MacOS/PyMOL
or with arguments:
PyMOL.app/Contents/MacOS/PyMOL -q myfile.pdb -d count_atoms -d quit
One minor annoyance I've noticed is that a symlink to this file
doesn't work. So, it might be desirable to use a "pymol" script to
launch the executable, and to put this in your path Something like:
#!/bin/sh
/Applications/PyMOL.app/Contents/MacOS/PyMOL $*
# Might put this script in /usr/bin, /usr/local/bin, or $HOME/bin
By the way, this version of PyMOL can also work well on the mac as a PDB
helper application with Netscape or IE. (For IE, type=TEXT
creator=PyML)
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of William Scott
> Sent: Sunday, September 07, 2003 7:18 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] How do I auto-load my startup pymol script in the new
os
> x version?
>
> Hi folks:
>
> I just installed the new pymol 0.91 for os x.
>
> I used to start pymol this way:
>
> alias pymol "/Applications/PyMOL/Darwin/pymol.com -q
> /Users/wgscott/pymol/alias.pml"
>
> Now that option appears to be gone, so I tried
>
>
> alias pymol "open -a /Applications/PyMOL.app
> /Users/wgscott/pymol/alias.pml"
>
> open -a /Applications/PyMOL.app
>
> by itself works, as does
>
> open -a /Applications/PyMOL.app foo.pdb
>
> but open -a /Applications/PyMOL.app bar.pml
>
> doesn't seem to allow me to read in a pymol script.
>
>
> Is there some new argument flag I have to add or what?
>
> Thanks.
>
> Bill
>
>
> William G. Scott
>
> Associate Professor
> Department of Chemistry and Biochemistry
> and The Center for the Molecular Biology of RNA
> Sinsheimer Laboratories
> University of California at Santa Cruz
> Santa Cruz, California 95064
> USA
>
> phone: +1-831-459-5367 (office)
> +1-831-459-5292 (lab)
> fax: +1-831-4593139 (fax)
> url: http://chemistry.ucsc.edu/~wgscott/
>
>
>
>
>
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