[phenixbb] phenix and ncs

Pavel Afonine pafonine at lbl.gov
Sun Sep 23 13:33:56 PDT 2007

Hi Jan,

thanks for the questions.

> - How does phenix.refine use ncs restraints? 

It is harmonic restraints between NCS copies, applied to coordinates and 
individual isotropic ADPs; similar to CNS.

> - Can one define the tightness of the ncs restraints?

Yes, indeed, it is missing in the manual. I will add it asap.
Use :
to set up the NCS weights for all NCS groups.
Or you can do it for each individual NCS group by setting same 
parameters inside of restraint_group{} scope.

Note, you should be careful with changing NCS weights since NCS 
restraints added to all geometry restraints, so if you drastically 
change the NCS contribution you can easily distort the contributions 
from other restraints, like covalent bonds, angles ... For an extreme 
example, setting up huge NCS weight will result in perfect match of NCS 
groups (= small rmsd between them) with totally distorter stereochemistry.
> Can one put different restraints on mainchain and sidechain atoms?

Currently no. Unless you split out your NCS group selections into main 
chain and side chain.
The default for coordinate sigma is 0.05. If we do this split in the 
future what would be the default for main and side chain sigmas?


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