Hi Cedric,
Check out the "Launching PyMOL from Python programs" section from here:
http://www.pymolwiki.org/index.php/Python_Integration
HTH,
Matt
On 10/24/2014 02:02 PM, Cedric wrote:
> Hi,
>
> I know how to write small scripts in pymol and then call them within pymol.
>
> But I am not sure how to use one of pymol commands in a python script that I
> can run in the terminal.
>
> Example, I want to align a series of files in a folder but for test
> purposes, let's say 1.pdb and 2.pdb… I tried the following (from the
> terminal).
> Any suggestions?
>
> from pymol import cmd
>
> cmd.align('1.pdb','2.pdb',cycles=0)
>
> Thank you,
> cedric
>
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