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.

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: http://www.ncbi.nlm.nih.gov/pubmed/8590014) -Nat

Hi Yuri,

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?

yes and no. Relevant methods are in active development and in general things change quickly. To get some very superficial impression, see pages 56-59 here: http://www.phenix-online.org/presentations/latest/pavel_refinement_general.p...

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

Definitely yes. In phenix.refine there are two types of NCS restraints, applied in Cartesian or torsion angles spaces (global/local). Torsion NCS supposed to be the best but the relevant code in phenix.refine is too fresh and requires more testing. You should try both to see which one works best for you.

3- Is the presence of NCS macromolecule specific, or crystal specific?

It's rather packing.. Say, if more than one copy packs in the asymmetric unit then you have NCS, roughly speaking..

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?

I'm not sure I understood this... May some one else did? Pavel.