Thanks so much for the suggestion!
For me it works great !
1) but below case (where I'm choosing to select ATOMS or HETATMS from CYX)
is not worked.
grep "ATOM|HETATM" ${pdb} | grep CA | awk 'BEGIN{n=0}{n++; if
($4=="CYX"){print n}}' >> results.txt
2) also I tried to change | grep CA to | grep SG - which is more case
sensetive to CYX but also produced wrong positions.
What's wrong here with the syntax in those two cases?
James
2014-09-24 14:18 GMT+02:00 Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>:
> Ouch.
>
> Just a few problems I spotted with this:
> 1) grep ATOM: will return _any_ line with the string 'ATOM' occuring
> _anywhere_ on a line; some codes may also decide to use 'HETATM'
> instead because CYX is non-standard
> 2) grep CA: same as above, could be calcium atom, part of a residue
> name, segment name or possibly some other abuse of the format or simply
> any occurence on a non ATOM/HETATM record
> 3) awk: the ancient PDB format is a _fixed-column_ format which also
> implies that columns can "run" into each other while awk splits (by
> default) on whitespace which may not be there; also, the residue
> name is not the 4th datum in a ATOM/HETATM record.
>
> The two lines code doubles this but why would one need parse the input
> twice anyway?
>
> Cheers,
> Hannes.
>
>
> On Wed, 24 Sep 2014 12:43:17 +0200
> Anselm Horn <Anselm.Horn.biochem.uni-erlangen.de> wrote:
>
> > Hi James,
> >
> > to obtain a list of all CYX residues in your pdb file in consecutive
> > numbering, you could do something like the following:
> >
> > grep ATOM XXXX.pdb | grep CA | awk 'BEGIN{n=0}{n++; if
> > ($4=="CYX"){print n}}'
> >
> > When you are sure, that only two CYX entries exist in your file, you
> > could simply used the 'head' and 'tail' command to extract the two
> > numbers:
> >
> > cyx1=`grep ATOM XXXX.pdb | grep CA | awk 'BEGIN{n=0}{n++; if
> > ($4=="CYX"){print n}}' | head -n 1`
> > cyx2=`grep ATOM XXXX.pdb | grep CA | awk 'BEGIN{n=0}{n++; if
> > ($4=="CYX"){print n}}' | tail -n 1`
> --
> Scanned by iCritical.
>
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Received on Wed Sep 24 2014 - 06:00:03 PDT
