Hi James,
grep '^\(ATOM\|HETATM\|CRYST1\)' protein.pdb lipid.pdb > merged.pdb
Oh, the joy one has from reading a sed/grep/awk tutorial :)
Cheers,
Tsjerk
On Thu, Sep 4, 2014 at 12:19 PM, James Starlight <jmsstarli...@gmail.com>
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,
>
> 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.
>>
>>
>
--
Tsjerk A. Wassenaar, Ph.D.
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