[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [ccp4bb]: low res dataset, need help with NCS constraints

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

On Wed, 23 Feb 2000, Susan Heffron wrote:

> If I do use NCS constraints, I have the complication that my protein is
> a multi-domain molecule that has flexibility in the orientations of the
> domains to each other. So, it would have to be constrained
> domain-by-domain.  Which programs can handle this?

restraints should be easier to deal with, just increase the weight for
stricter compliance.  I think all the major programs (CNS, X-plor, SHELX,
REFMAC) can handle this. i think the way SHELX handles NCS restraints is
more intelligent, but that program is generally not used for lower
resolution like yours. SHELX restrains NCS by weighting the 1-4 distance
(torsional bonds). CNS, X-Plor and i believe REFMAC (but someone will
correct me if i'm wrong) restrain the POSITION of the atoms by the NCS
operator. this does not work as well for hinge regions, and you should do
some rigid body refinement on your domains as well.

for REFMAC, see the NONX keyword of PROTIN to set up NCS.

BTW, if you want to do phase refinement, both DM and
magicsquash are set up for easy multiple domain averaging. your starting
phases would be model-biased if they come from the MR solution, but the
refinement itself will be influenced by solvent flattening, NCS symmetry,
histogram matching etc. but not model geometry.

It is characteristic of thoughtful people that they don't understand some
things that to others are as plain as a pikestaff.  -  A. G. Cairns-Smith
                        David J. Schuller
                        modern man in a post-modern world
                        University of California-Irvine