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.li...@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.li...@gmail.com
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing
http://p.sf.net/sfu/novell-sfdev2dev
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