[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 :
refinement.ncs
{
coordinate_sigma=None
b_factor_weight=None
}
}
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?
Pavel.
More information about the phenixbb
mailing list