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incomplete model

Yu Wai Chen ywc at mrc-lmb.cam.ac.uk
Wed Dec 8 18:21:14 EST 1999

> 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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