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