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.
> 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
