Hi James,
You can use pymol -cd "pymolcommands". See
http://www.pymolwiki.org/index.php/Command_Line_Options
However, the first part is much easier with grep or sed. To remove all
solvent molecules:
grep -v "^ATOM.*SOL" in.pdb > out.pdb
To remove NA+/CL- too
grep -v "ATOM.*\(SOL\|NA+\|CL-\)" in.pdb > out.pdb
The fitting is a bit more cumbersome :)
Hope it helps,
Tsjerk
On Thu, Sep 4, 2014 at 10:19 AM, James Starlight <jmsstarli...@gmail.com>
wrote:
> Dear PyMol users!
>
> I'd like to find possibilities for running of some pymol commands from the
> terminal. For instance in my case I' d like perform 2 simple steps (both in
> terminal not in the pymol GUI)
> to remove water and ions from my target input pdb (typical I do it via
> gromacs editconf)
> superimpose target.pdb against reference.pdb ( i do it by means of tmalign
> utility)
>
> Thanks for help,
>
> James
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
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