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,
James
2014-09-04 12:48 GMT+04:00 Tsjerk Wassenaar <tsje...@gmail.com>:
> 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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