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Re: [ccp4bb] an over refined structure |
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CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 08 February 2008Subject: Re: an over refined structure From: price {- at -} UCHICAGO {- dot -} EDU price {- at -} UCHICAGO {- dot -} EDU Date: 2008-02-08 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: >Email: >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 http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 08 February 2008 |
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