Rotational near-crystallographic ncs is easy to handle this way, but
what about translational pseudo-symmetry (or should that be
pseudo-translational symmetry)? In such cases one whole set of spots
is systematically weaker than the other set. Then what is the
"theoretically correct" way to calculate Rfree? Write one's own code
to sort the spots into two piles?
Phoebe
At 01:05 PM 2/8/2008, Axel Brunger wrote:
In such cases, we always define the test set first in the high-symmetry
space group choice. Then, if it is warranted to lower the crystallographic
symmetry and replace with NCS symmetry, we expand the test set
to the lower symmetry space group. In other words, the test set itself
will be invariant upon applying any of the crystallographic or NCS operators,
so will be maximally "free" in these cases. It is then also possible to
directly compare the free R between the high and low crystallographic
space group choices.
Our recent Neuroligin structure is such an example (Arac et al.,
Neuron 56, 992-, 2007).
Axel
On Feb 8, 2008, at 10:48 AM, Ronald E Stenkamp wrote:
I've looked at about 10 cases where structures have been refined in lower
symmetry space groups. When you make the NCS operators into
crystallographic
operators, you don't change the refinement much, at least in terms of
structural changes. That's the case whether NCS restraints have
been applied
or not. In the cases I've re-done, changing the refinement program
and dealing
with test set choices makes some difference in the R and Rfree values. One
effect of changing the space group is whether you realize the copies of the
molecule in the lower symmetry asymmetric unit are "identical" or
not. (Where
"identical" means crystallographically identical, i.e., in the same packing
environments, subject to all the caveats about accuracy, precision, thermal
motion, etc). Another effect of going to higher symmetry space groups of
course has to do with explaining the experimental data with simpler
and smaller
mathematical models (Occam's razor or the Principle of Parsimony).
Ron
Axel T. Brunger
Investigator, Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University
Web: <http://atb.slac.stanford.edu>http://atb.slac.stanford.edu
Email: <mailto:[EMAIL PROTECTED]>[EMAIL PROTECTED]
Phone: +1 650-736-1031
Fax: +1 650-745-1463
---------------------------------------------------------------------------------------------------------------------------
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/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
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