[Bio-software] Inconsistent PDB file formats

Jyothish NT via bio-soft%40net.bio.net (by joyjoy.nt from gmail.com)
Sat Apr 26 05:38:53 EST 2008


Hi,

PDB files are not Perfect.  Infact, using an automated program, retrieving
information
from a PDB file is hard as its format is not consistent.
For example, the missing coordinate informarion is usually given in REMARK
465 and 470.
But if we check for protein 2FL8 there  is no REMARK 465 or 470, instead
this missing
information is written on REMARK 3 (as there are more number of missing
coordinates).

Also, there is an unusual numbering given for each residue  (ATOM).
For example, First few resudues in the sequence are given 380 to 399.
then for the rest, 12 - 200. (eg : 1K4J)

I would like to know if there is any program or s/w for making the PDB files
perfect?




Thanks,
Jyothish N.T.
Research Assistant
116, Dept. of Mathematics,
Indian Institute of Technology Bombay,
Powai, Mumbai-400076.

Email : jyothish from iitb.ac.in
Ph : +91-9920980148


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