On Mon, 25 Aug 2003 13:28:37 -0700
Modeller Care <> forwarded :
> From: Michael Grabe <>
> I take a small alpha helix (25 amino acids) and I copy it and
> translate it.
> <snip>
>
> I then start to work with this pdb file without any alignment file.
>
Ok. With missing backbone atoms, you are really asking for trouble with
modeller! The optimization step really wants reasonable backbone
geometry, since that is what comes out of the distance geometry
functions.
>
> Any hints about how to make this better?
Add the extra oxygens! Either find some plausible coordinates, use
something like the maxsprout server, do an approximate bond calculation,
or even use a viewer that can 'edit' pdb files (swisspdb will do this,
for instance).
The alternative is to wait for a bug-fix :-)
j.
_______________________________________________________________________
Dr JB Procter:Biomolecular Modelling at ZBH - Center for Bioinformatics
Hamburg http://www.zbh.uni-hamburg.de/mitarbeiter/procter