PDB amino acid positions

reece at whoville.wustl.edu reece at whoville.wustl.edu
Thu Feb 5 18:48:34 EST 1998


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>>>>> IF == Iddo Friedberg <idoerg at cc.huji.ac.il> wrote 
>>>>> In bionet.software
>>>>> On Thu, 05 Feb 1998 11:53:21 +0200
>>>>> Re PDB amino acid positions

IF> Does anybody know of a good, robust  program which will accept a PDB
IF> file as input, and for the output deliver for each amino acid it's PDB
IF> position number.

If I understand correctly, you want the ordinal position of each amino
acid.

perl -ne 'if (/ATOM.{13}(...)...(....)/ and not $seen{$2}++) \
  {printf("%3d $1\n",++$o)}' file.pdb

(don't type the '\')

The above worked on a test with perl 5.004_03 (type perl -v), 1hvr (2
chains) and 3ptb (discontinuous numbering).  Whether it's 'good' or
'robust' depends on your needs, but I hope this helps.

perl is freely available from www.perl.com.

- -- 
Reece Hart, http://dasher.wustl.edu/~reece/
Do not send unsolicited bulk email.  Boycott companies which do so.

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