Thanks, Jason, it works. :)

Li

On Sun, Sep 12, 2010 at 5:40 PM, Jason Vertrees <jason.vertrees@schrodinger.com> wrote:
Hi Li,

I created a small python script "testAlign.py" with the following 3
lines as its content:

cmd.fetch("1cll 1ggz", async=0)
rmsd = cmd.align("1cll", "1ggz")[0]
print "RSMD for aligning 1cll to 1ggz is: ", rmsd


This fetches two PDBs, aligns them and reports their RMSD.  Now, just
run "pymol -cq testAlign.py" and you should see

RSMD for aligning 1cll to 1ggz is:  3.85577607155

as the last line of output.

Cheers,

-- Jason


On Sun, Sep 12, 2010 at 6:09 PM, Li Xue <me.lixue@gmail.com> wrote:
> Hello all,
>
> Does someone happen to know how call the pymol commands (for example,
> align)  without opening Pymol GUI window?
>
> Thanks.
>
> --
> Xue, Li
> Bioinformatics and Computational Biology program
> Computer Science
> Iowa State University
> Ames, IA 50010 - USA
> Tel: 1-515-450-7183
> Email: me.lixue@gmail.com
>
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120



--
Xue, Li
Bioinformatics and Computational Biology program
Computer Science
Iowa State University
Ames, IA 50010 - USA
Tel: 1-515-450-7183
Email: me.lixue@gmail.com