thanks!
and do I need to pipe the below command to smth
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb > merged.pdb
if I need to change 'END' to 'TER' in the merged.pdb ?
2014-09-04 16:54 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> thanks!
>
> and do I need to pipe the below command to smth
> grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb > merged.pdb
>
> if I need to change 'END' to 'TER' in the merged.pdb ?
>
>
> 2014-09-04 16:41 GMT+02:00 Matthew Baumgartner <mp...@pitt.edu>:
>
> Use the -h flag with grep to suppress the filename.
>> Also, you don't need to pipe to cat, you can write directly to the file.
>>
>> grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb > merged.pdb
>>
>>
>>
>> On 09/04/2014 10:38 AM, James Starlight wrote:
>>
>> ..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.
>>>>>>>> Video for Nerds. Stuff that matters.
>>>>>>>> http://tv.slashdot.org/
>>>>>>>> _______________________________________________
>>>>>>>> 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.
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Slashdot TV.
>>>>>> Video for Nerds. Stuff that matters.
>>>>>> http://tv.slashdot.org/
>>>>>> _______________________________________________
>>>>>> 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
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Slashdot TV.
>> Video for Nerds. Stuff that matters.http://tv.slashdot.org/
>>
>>
>>
>> _______________________________________________
>> 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
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Slashdot TV.
>> Video for Nerds. Stuff that matters.
>> http://tv.slashdot.org/
>> _______________________________________________
>> 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
>>
>
>
------------------------------------------------------------------------------
Slashdot TV.
Video for Nerds. Stuff that matters.
http://tv.slashdot.org/
_______________________________________________
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
