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
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
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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
>> >
>>
>>
>> --
>> 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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