[phenixbb] Picking Rfree in thin resolution shells using command line

Nathaniel Echols nechols at lbl.gov
Tue Jan 31 11:22:20 PST 2012

On Tue, Jan 31, 2012 at 11:01 AM, Pavel Afonine <pafonine at lbl.gov> wrote:
> NCS: given state-of-the-art NCS restraints there is (probably) no clear-cut
> answer, but there are three ones: "definitely yes", "definitely no", and
> "try to find out". Obviously, at low enough resolution NCS should be always
> used (say ~2A and lower), simply because this provides a luxury of
> additional a priori information to alleviate the poor data-to-parameters
> ratio problem. Obviously, at high enough resolution (~1.5-1.7A or so) NCS
> should not be used since the amount of data may be enough to see actual
> differences between NCS copies, and using NCS would probably wipe out these
> difference (or at least there is such a risk). In the grey area, ~1.7-2.0A,
> one should try using vs not using NCS to know for sure.

A more quantitative answer: using the last six months' worth of PDB
releases, for structures in the range 1.75 - 2.0 the best choice of
NCS restraint (judged by R-free) was:

none: 27%
cartesian/global NCS: 11% (average improvement: 0.0073)
torsion NCS: 62% (average improvement: 0.0036)

However, some random checks (across a wider resolution range) indicate
that a significant fraction of the structures where Cartesian NCS
works best have under-assigned symmetry.

Jeff is working on much more thorough tests, so a more definitive
answer will eventually be available - but Pavel's recommendation will
probably remain true.


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