Re: [PyMOL] Shell utilities for structural bioinformatics

[James S. <jms...@gm...>]

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 <jms...@gm...>:

> Thanks you very much!
>
> James
>
> 2014-09-05 20:18 GMT+02:00 Folmer Fredslund <fo...@gm...>:
>
>> 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" <gia...@ib...>:
>>
>> 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
>>> >
>>> >
>>> >
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>>>
>>>
>>> --
>>> Gianluca Santoni,
>>> Dynamop Group
>>> Institut de Biologie Structurale
>>> 6 rue Jules Horowitz
>>> 38027 Grenoble Cedex 1
>>> France
>>> _________________________________________________________
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>>>
>>>
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