one question :)

could someone explain me the ussage the pymol commands from the shell on the example
e.g i need to load 2 pdbs in pymol make its superimposition and than save one of the superimposed pdb
load ref.pdb tar.pdb
super tar, ref
save tar > tar_superimposed.pdb

I've tried to do part of this using
pymol ref.pdb tarr.pdb -cd "super tarr ref"

but eventually obtained error


2014-09-04 15:47 GMT+02:00 James Starlight <>:
Thanks Guys!
I'll check the tutorials.

All the best,


2014-09-04 13:15 GMT+02:00 David Hall <>:

(sed '1d' protein.pdb; sed '1d' lipid.pdb) > merged.pdb


tail -q -n '+2' protein.pdb lipid.pdb > merged.pdb


On Thu, Sep 4, 2014 at 6:19 AM, James Starlight <> wrote:
Hi Tsjerk,

Thanks alot!
Also I have the task to merge protein.pdb and lipids.pdb with some 1 line shell command ( like CAT) to obtain protein inserted in the lipids (the seccond file is consist of the whole which can locate the protein). My problem is that both protein.pdb and lipids.pdb consisted of the unusuall first line which should be deleated before it merging (in my case it's the HEADER lala.pdb). could you suggest me the combination of grep sed command which should be used to deleate the first line from both pdbs and than merge it in one-command method?

Many thanks,


2014-09-04 12:48 GMT+04:00 Tsjerk Wassenaar <>:

Hi James,

You can use pymol -cd "pymolcommands". See

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,


On Thu, Sep 4, 2014 at 10:19 AM, James Starlight <> 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,


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Tsjerk A. Wassenaar, Ph.D.

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