Hi Tsjerk,
thank you very much for help.
this is a little bioinformatics question so probably it's better to ask it
here some expert of this topic like you :)
because in my case I need to further proceed each split model model (e,g
delete some lines or make changing) piping with some commands
e,g in my case each model after spliting consist of
MODEL 1
ROOT
ATOMS
ENDROOT
TORSDOF 0
ENDMDL
i'd like to remove lines consisted of ROOT ENDROOT TORSDOF 0 and change
ENDMDL to TER
i've tried to do it
csplit -b "%04d.pdb" my_docking.pdb /^MODEL/ {*} | grep -v '^ENDROOT' |
grep -v '^TORSDOF 0' | sed -e 's/^ENDMDL/TER/g'
but the resulted files still consist of unused lines
BTW might the csplit be used to extract only ONE (e,g first) model from the
multi-pdb file?
James
2014-09-12 11:39 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>:
> 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
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Slashdot TV.
>>>>> Video for Nerds. Stuff that matters.
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>>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Slashdot TV.
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>>>>
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
------------------------------------------------------------------------------
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