[phenixbb] NCS restraints

Nathaniel Echols nechols at lbl.gov
Thu Jun 30 21:52:54 PDT 2011

On Thu, Jun 30, 2011 at 9:07 PM, Yuri <yuri.pompeu at ufl.edu> 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

> 2- Should one try to use it in lower res data (3 A and worse)?

Absolutely, the lower the resolution, the more helpful any additional
restraints will be.   I'm sure there are exceptions (mostly local
deformations, which we're working on), but always start out with NCS
restraints enabled.

> 3- Is the presence of NCS macromolecule specific, or crystal specific? In
> other words, if for the same enzyme one crystal goes to 3.1 and another 1.5
> A could one have significant NCS but not the other?

NCS is a phenomenon, not necessarily a refinement protocol; whether it
is present depends both on the native state of the protein (lots of
enzymes form symmetric multimers) and how it crystallizes.  Resolution
is a separate issue from crystal form - it only tells you how to treat
the related molecules.  At 3.1A you need to avoid overfitting; at 1.5A
the NCS-related chains may appear identical, but NCS restraints are
unnecessary.  (A relevant review - although somewhat dated - review
that discusses this is here:


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