Re: [PyMOL] problem with .pml file

[Tsjerk W. <ts...@gm...>]

Hi Hally,

It's worthwhile getting on terms with Linux. You mention you start a
"blank program" suggesting to me you're starting pymol without
anything to be loaded ("pymol"). It's not true that this can only be
done in the pymol directory. You can do it anywhere, as long as you've
got pymol in your PATH or you explicitly include the directory where
the pymol executable is. If you do it in the directory where you're
foo.pml file is, you can just do 'pymol foo.pml'. Otherwise you could
still do 'pymol /home/hally/somedirectory/foo.pml'.
The same goes if you've just started pymol. If you've started it in
the correct directory, you can just do @foo.pml. In any case you can
do @/home/hally/somedirectory/foo.pml. You could also, within pymol,
change directories to go to the place where you have the script, as
Lieven suggests. The thing is, you need to tell the computer where the
programs/scripts are. It can't know it by itself. It only 'knows'
which directory it was called from.

Cheers,

Tsjerk


On 1/23/08, Hally Shaffer <gt...@ma...> wrote:
> I installed pymol onto a linux system.  I can open the program, open the pdb
> file, and open a .pse file, but I cannot open the .pml file which contains the
> manipulations that I've already made. Any suggestions?
>
> --
> Hally Shaffer
> <>< Graduate Student
> Georgia Institute of Technology
> School of Chemistry and Biochemistry
> gt...@ma...
>
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623