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
like
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
James
2014-09-04 15:47 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> Thanks Guys!
> I'll check the tutorials.
>
> All the best,
>
> James
>
>
> 2014-09-04 13:15 GMT+02:00 David Hall <li...@cowsandmilk.net>:
>
> (sed '1d' protein.pdb; sed '1d' lipid.pdb) > merged.pdb
>>
>> --or--
>>
>> tail -q -n '+2' protein.pdb lipid.pdb > merged.pdb
>>
>> -David
>>
>>
>>
>>
>> On Thu, Sep 4, 2014 at 6:19 AM, 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
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Slashdot TV.
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>>>>> _______________________________________________
>>>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>> Archives:
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>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Tsjerk A. Wassenaar, Ph.D.
>>>>
>>>>
>>>
>>>
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>>
>>
>
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