Re: [PyMOL] how to call the align command without opening Pymol GUI window

[Li X. <me....@gm...>]

Thanks, Jason, it works. :)

Li

On Sun, Sep 12, 2010 at 5:40 PM, Jason Vertrees <
jas...@sc...> 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....@gm...> 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....@gm...
> >
> >
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>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (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....@gm...