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incomplete model

D.L.D.Caspar caspar at pro.sb.fsu.edu
Thu Dec 9 09:39:11 EST 1999

Just wanted to make sure.


Yu Wai Chen wrote:

> > I have a model which is incomplete at the ends (N and C terminals)
> > In CNS I know I can put a break in the MIDDLE of
> > a chain and also that the C-terminal needs the OT1/OT2 oxygens which CNS
> > automatically generates from the pdb file.
> >
> > How can I set it up so that the program learns that there are no N and
> > C-terminal
> > ends due to an incomplete model and that the total length of the
> > molecule is
> > longer than what it has to work with. As it is if I give a BREAK at the
> > end of the
> > chain it still generates OT's and I am wondering if that is what it is
> > considering as the terminal?
> We all work with proteins with disordered N and C termini most of the
> time.  You don't really need to tell CNS about it, just leave your
> incomplete model as if it is an intact chain.  It doesn't make any
> difference to CNS (if your model is complete) as far as refinement is
> concerned.  If you don't like it, you can remove one of the C-terminal
> OT1/OT2 atom to make it realistic at the end of refinement.  You need to
> do nothing to the N-terminal, and you don't need to put a break.
> --
> ===================================================================
> Yu Wai CHEN, Ph.D. ..................   email:ywc at mrc-lmb.cam.ac.uk
>  Centre for Protein Engineering,             tel:+44-(0)1223-402148
>  MRC Centre, Hills Rd, Cambridge CB2 2QH, UK fax:+44-(0)1223-402140
>  WWW homepage: http://www.mrc-cpe.cam.ac.uk/~ywc

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