Subject: CCL: Re[2]: software to convert XYZ format to PDB ?

From: Michael <shokhen(at)netvision.net.il>
Date: Fri, 02 Jul 2004 13:26:24 +0200

Hello Michael,

Obviously there are side residues also with hydrogens, and you know this
> from my replay that I send to you responding on your first remark.
I simply did not present the whole protein pdb in the three different
formats (XYZ, defected pdb, and correct pdb) in order to save place
in the email. I wrote in my original message presented for CCL
that it is a fragment from the whole protein.
I thought that to see the problem it is sufficient to present
only four lines from the whole protein.

Following your logic:

 Imagine that you are the programmer: how could you know from
 the atomic symbols and the X,Y,Z coordinates what could be
the residue ? The N,CA,C,O coordinates of all residues of
all known proteins in the PDB offer quite similar 3D patterns.

Sure... if you have the side chains ! (were not indicated in the example)
It needs other assumptions: true residues, no HETATM, lexicographical
ordering coherent with the PDB conventions...

why didn't you suggest that the protein was consisted from only four
atoms presented in my email?

Kind regards,
Michael

To: chemistry(at)ccl.net
Subject: CCL:software to convert  XYZ format to PDB ?

Konrad Hinsen <hinsen(at)cnrs-orleans.fr> wrote:
> On Jul 1, 2004, at 11:57, Michel Petitjean wrote:
> > Imagine that you are the programmer: how could you know from
> > the atomic symbols and the X,Y,Z coordinates what could be
> > the residue ? The N,CA,C,O coordinates of all residues of
> > all known proteins in the PDB offer quite similar 3D patterns.
>
> If I had to do this (fortunately I don't), I'd first identify the
> peptide planes as patterns of pairwise distances (they are quite
> rigid). I'd then identify the sidechains atom by atom starting from the
> C-alphas, again by distance criteria. Not a trivial task, but not an
> impossible one either.

Sure... if you have the side chains ! (were not indicated in the example)
It needs other assumptions: true residues, no HETATM, lexicographical
ordering coherent with the PDB conventions...

Michel Petitjean,                     Email: petitjean(at)itodys.jussieu.fr
ITODYS (CNRS, UMR 7086)                      ptitjean(at)ccr.jussieu.fr
1 rue Guy de la Brosse                Phone: +33 (0)1 44 27 48 57
75005 Paris, France.                  FAX  : +33 (0)1 44 27 68 14
http://petitjeanmichel.free.fr/itoweb.petitjean.html

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