Hi Marko,
in my case
this (long ) is works fine
gleb@gpu2:~/Documents/script/docking/Complex/OR1A1_MULTI> cat receptor.pdb
xx001.pdb | grep -v '^ROOT'| grep -v '^ENDROOT' | grep -v '^TORSDOF 0' |
grep -v '^MODEL' | grep -v '^REMARK' | sed -e 's/^ENDMDL/TER/g' >
complex.pdb
but in the below case grep (in one command style) was not work
gleb@gpu2:~/Documents/script/docking/Complex/OR1A1_MULTI> cat receptor.pdb
xx001.pdb | grep -v "^ROOT\|^ENDROOT\|^TORSDOF 0\^MODEL\^REMARK"| sed -e
's/^ENDMDL/TER/g' > complex.pdb
2014-09-12 12:16 GMT+02:00 Marko Hyvonen <mh...@cam.ac.uk>:
> Hi James,
>
> How about
>
> egrep -v "MODEL 1|ROOT|ATOMS|ENDROOT|TORSDOF" myoriginalfile | sed
> 's/ENDMDL/TER/' > mynewfile
>
> -v in egrep is to reverse the selection so you get all lines except that
> ones in the expression. Without that you _only_ "grep" the lines with
> those expressions.
> (egrep might be grep, or something similar depending on OS or variant of
> it)
>
> And sed (stream editor) then s(ubstitutes) ENDMDL with TER.
>
> hth, Marko
>
>
> On 12/09/2014 11:00, James Starlight wrote:
> > 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
> > <mailto: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 <mailto: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 <mailto:jmsstarli...@gmail.com>>:
> >
> > Thanks you very much!
> >
> > James
> >
> > 2014-09-05 20:18 GMT+02:00 Folmer Fredslund
> > <folm...@gmail.com <mailto: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
> > <mailto: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
> > <mailto:PyMOL-users@lists.sourceforge.net>)
> > > Info Page:
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> > > Archives:
> >
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> > >
> >
> >
> > --
> > 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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> > Manually upgrade your production database.
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> >
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> > _______________________________________________
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> >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Want excitement?
> > Manually upgrade your production database.
> > When you want reliability, choose Perforce
> > Perforce version control. Predictably reliable.
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> >
> >
> > _______________________________________________
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> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
> --
>
> Marko Hyvonen
> Department of Biochemistry, University of Cambridge
> mh...@cam.ac.uk
> http://www-cryst.bioc.cam.ac.uk/groups/hyvonen
> tel: +44-(0)1223-766 044
>
>
>
>
> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
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>
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