Re: [phenixbb] NCS restraints

Hi Nat,

On Thu, Jun 30, 2011 at 9:07 PM, Yuri wrote:

...

I have some fundamental questions about NCS: 1- I think its somewhat of a consensus that at higher res. it should not be used to avoid missing out "real" detailed discrepancy. Is this true? Usually, yes. There is some risk in the use of NCS restraints, because (depending on how the NCS relates to crystallographic symmetry) it can bias R-free due to symmetry inherent in the data. At moderate resolution (maybe 2.0A) some people will start with NCS restraints at the early stages of refinement, and release them later. As always, it's difficult to give an exact rule of thumb, but I think Pavel has cited 2.0A as the cutoff before, and that's pretty reasonable.

this is based on my ~4 or 5 years old tests, when I re-refined all structures in PDB that have NCS with and without applying NCS restraints, and very roughly at resolution about 2A or higher I saw more cases where using NCS was doing more harms than good (judged by Rfree, and Rfree-Rwork only). However, with improved NCS restrains (applied in torsion angle space) this limit may be pushed farther towards higher resolution. We need to re-run these tests over the whole PDB again to see what's the current state of the art... Pavel.