Re: [ccp4bb]: Re: Ramachandran Idealization

["Lesa J. Beamer" <lesa@bluebird.biochem.missouri.edu>]

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Paul,

The answer to your question below is found in a paper by Sali (guru
of homology modeling) et al - Proteins, Str. Func. Genetics 23:318-326 
(1995) - Evaluation of Comparative Protein Modeling...

where it was shown that:
"most ways of relaxing the template coordinates to improve the stereo
chemistry of the model increase the rms differences from the correct
target structure"

-Lesa	

>>>>>>
However, why build a model at all if it violates standard geometry of
proteins. Thats like making a model of a house which doesn't have a front
door or any windows (bad analogy - but you get the point!). Why not
introduce beta phi/psi angles to a region which is predicted to be a
beta-strand?