AMBER Archive (2005)

Subject: Re: AMBER: Question about PDB format

From: FyD (fyd_at_u-picardie.fr)
Date: Sun Nov 20 2005 - 08:21:22 CST

Quoting Ross Walker <ross_at_rosswalker.co.uk>:
Quoting "David A. Case" <case_at_scripps.edu>:
Quoting Andy Purkiss <a.purkiss_at_mail.cryst.bbk.ac.uk>:

> The pdb format is based on the old fortran card format 8F3 starting with the
> x-coordinate in column 31 and then the y in 39 and the z in 47. This means
> that
> the length of each coordinate entry is 8 characters with 3 digits after the
> decimal place. So the maximum number allowed is 9999.999 and the minimum
> -999.999.
>
> Coordinate <- x -><- y -><- z ->
> Column 333333333444444444455555
> Number 123456789012345678901234

Thank you very much: I was not aware of that...

This means the PDB format generated by R.E.D.-I/II/III is wrong. I am going to
change the PDB format in R.E.D. & provide corrections @
http://www.u-picardie.fr/labo/lbpd/RED/bugs-II for R.E.D.-II

Best regards, Francois

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