On Mon, 25 Aug 2003 13:28:37 -0700 Modeller Care modeller-care@salilab.org forwarded : > From: Michael Grabe mgrabe@itsa.ucsf.edu > 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