Hi James,
These are the sort of questions that'll be answered elsewhere. Most notably
on stackoverflow:
http://stackoverflow.com/questions/18364411/using-regex-to-tell-csplit-where-to-split-the-file
csplit -b "%04d.pdb" file.pdb /^MODEL/ {*}
Cheers,
Tsjerk
On Fri, Sep 12, 2014 at 11:25 AM, James Starlight <jmsstarli...@gmail.com>
wrote:
> Hi,
>
> some new question.
>
> I need to some combination of shell utilities to split multi_model.pdb on
> several pdbs as well as separate command to seek multi_model.pdb and to
> save only this model as the separare model1.pdb. I've tried to do it using
> grep
> grep '^MODEL 1' my_docking.pdb > model1.pdb
>
> but results were empty.
>
> James
>
> 2014-09-08 15:48 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
>
>> Thanks you very much!
>>
>> James
>>
>> 2014-09-05 20:18 GMT+02:00 Folmer Fredslund <folm...@gmail.com>:
>>
>>> Hi
>>>
>>> Small correction to Gianlucas suggestion
>>>
>>> ">" will direct the output to a file, overwriting the contents
>>> ">>" will direct the output to a file, appending the contents
>>>
>>> Venlig hilsen
>>> Folmer Fredslund
>>> Den 05/09/2014 19.16 skrev "Gianluca Santoni" <gianluca.sant...@ibs.fr>:
>>>
>>> Don't even need cat
>>>> simply do
>>>>
>>>> grep PPC ref.pdb > tar_i.pdb
>>>>
>>>> redirecting std out with > appends it directly to the file (after the
>>>> last line)
>>>>
>>>> Cheers
>>>>
>>>> On 9/5/14 6:48 PM, James Starlight wrote:
>>>> > Dear Pymol users!
>>>> >
>>>> > I've decided to open new topic focused on the implementation of the
>>>> > common shell utilities like grep awk and sed for the structural
>>>> > bioinformatics tasks like processing and editing of the large sets of
>>>> pdbs.
>>>> >
>>>> > In my current task I need to copy all lipids from one pdb (called it
>>>> > ref) to another call it tar_i.pdb (both files have the same 3D shape
>>>> and
>>>> > have been superimposed before that): so in that case I guess lipids
>>>> > could be recognized by residue name in pdb file (PPC) as well as by
>>>> its
>>>> > #4 column number (what is actually do grep). So the algorithm might
>>>> be:
>>>> > select from the ref.pdb all strings where #4 column is PPC and merge
>>>> it
>>>> > (by means of CAT I guess) with the tar_i.pdb. Please show me some
>>>> > example of the one-line method of this realization.
>>>> >
>>>> > Thanks,
>>>> >
>>>> > 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
>>>> >
>>>>
>>>>
>>>> --
>>>> Gianluca Santoni,
>>>> Dynamop Group
>>>> Institut de Biologie Structurale
>>>> 6 rue Jules Horowitz
>>>> 38027 Grenoble Cedex 1
>>>> France
>>>> _________________________________________________________
>>>> Please avoid sending me Word or PowerPoint attachments.
>>>> See http://www.gnu.org/philosophy/no-word-attachments.html
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
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>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
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>>>
>>
>>
>
>
> ------------------------------------------------------------------------------
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--
Tsjerk A. Wassenaar, Ph.D.
------------------------------------------------------------------------------
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