..and one question about grep (really didn't find it in the tutorial)
using
grep '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb |cat > merged.pdb
I've obtained good pdb BUT each line prior to the ATOM the name of the pdb
of the previous files have been added eg:
tarr_se.pdb:ATOM 1 N ASP X 1 35.722 8.306 92.256 0.00
0.00 N
tarr_se.pdb:ATOM 2 CA ASP X 1 35.252 8.836 93.529 0.00
0.00 C
tarr_se.pdb:ATOM 3 C ASP X 1 35.797 10.339 93.708 0.00
0.00 C
tarr_se.pdb:ATOM 4 O ASP X 1 34.979 11.297 93.674 0.00
0.00 O
tarr_se.pdb:ATOM 5 CB ASP X 1 35.593 7.984 94.698 0.00
0.00 C
tarr_se.pdb:ATOM 6 CG ASP X 1 34.692 8.171 95.960 0.00
0.00 C
tarr_se.pdb:ATOM 7 OD1 ASP X 1 33.481 8.453 95.823 0.00
0.00 O
tarr_se.pdb:ATOM 8 OD2 ASP X 1 35.257 8.362 97.046 0.00
0.00 O1-
tarr_se.pdb:ATOM 9 HA ASP X 1 34.180 9.033 93.580 0.00
0.00 H
tarr_se.pdb:ATOM 10 HB2 ASP X 1 35.496 6.916 94.504 0.00
0.00 H
tarr_se.pdb:ATOM 11 HB3 ASP X 1 36.648 7.969 94.970 0.00
0.00 H
such pattern are always produced by grep
so I'd like that tarr_se.pdb: have not been included (of course I can it
remove easily after merging but this step is not good for me :) )
Also i'll be very thankful for any useful grep awk sed tutorial in case of
the bioinformatics application
James
2014-09-04 16:03 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> 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:
>>>>>> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Tsjerk A. Wassenaar, Ph.D.
>>>>>
>>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
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>>>>
>>>
>>>
>>
>
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