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In principle, it's true that NCS needn't always bias Rfree. However, at
3A resolution with 100A unit-cell lengths, even a 2 degree divergence
between the NCS 2-fold and the nearly parallel crystallographic axis
could lead to a full index offset between the NCS and
crystallographically related reflections. Also, in the case of the
retracted structures, even a small amount of cross-talk might have
obscured the errors, given the potential for overfitting associated with
the use of up to 16 semi-independent models at low resolution. Since
there's a decent work-around, I'd rather not take the chance of any
unnecessary cross-talk between the working and test sets.
Dean
[EMAIL PROTECTED] wrote:
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Not all cases of NCS undermine Rfree: There are many where the NCS axis
is roughly parallel to an xtal symmetry axis - e.g. P61 with a non-xtal
twofold running nearly parallel to the xtal 6fold screw, so that
NCS-related reflections are already xtal-symmetry - related. I don't
see how the NCS can affect Rfree in such cases?
Phoebe
At 02:49 PM 12/29/2006, Jan Abendroth wrote:
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A way to avoid biasing Rfree values is to choose the test set in thin
resolution shells whenever NCS is present. Currently, this precaution
is often ignored. It should become a de facto standard for
publication of structures containing NCS.
Hi all,
btw - it would be fantastic and certainly would encourage us to use it
more often if the assignment of free reflections in resolution shells
was incorporated in a ccp4 program. Yes, one can for instance go
through shelxpro, however if one wants to go back to ccp4 this route
is a bit painful.
Cheers
Jan
--
Jan Abendroth
University of Washington
Institute of Biochemistry
1959 NE Pacific Street, K-426
Box 357742
Seattle, WA-98195
phone: +1-206-616-4510
fax: +1-206-685-7002
---------------------------------------------------------------------------------------------------------------------------
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://bmb.bsd.uchicago.edu/index.html
http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
--
Dean R. Madden, Ph.D.
Department of Biochemistry
Dartmouth Medical School
7200 Vail Building
Hanover, NH 03755-3844 USA
tel: +1 (603) 650-1164
fax: +1 (603) 650-1128
e-mail: [EMAIL PROTECTED]
