Hi Doug,

Please see the batch mode option:
http://www.pymolwiki.org/index.php/Command_Line_Options
I ran into some issues under Win
(http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg12855.html),
but it works fine on my Ubuntu.

Vitaly

On Tue, Nov 11, 2014 at 1:56 PM, Douglas Houston
<douglasr.hous...@ed.ac.uk> wrote:
> Hi all,
>
> Does anyone know if there's a way of accessing Pymol's API without the
> GUI? There are some useful functions in there and my loops would
> iterate a lot faster if the GUI didn't fire up every time.
>
> cheers,
> Doug
> _____________________________________________________
> Dr. Douglas R. Houston
> Lecturer
> Institute of Structural and Molecular Biology
> Room 3.23, Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
> http://tinyurl.com/douglasrhouston
>
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> Scotland, with registration number SC005336.
>
>
>
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