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Re: [ccp4bb] an over refined structure |
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CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 07 February 2008Subject: Re: an over refined structure From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL Date: 2008-02-07 > present, choosing the free set randomly is *never* a better choice, > and almost always significantly worse. hmmm ... I wonder if that is true. For low order NCS (two- three- fold, even five-fold) I don't believe that thin shells are better, since they are a systematic omission of data (whcih can affect maps) and in my experience they do not add much. I have only limited experience on this but I somehow tried both and I seem to have settled with random Rfree. With an NCS axis parallel to a crystallographic one (or when translation NCS is there) that might be a whole different ball game though ... not sure. A. > Together with multicopy refinement, randomly chosen test sets were > almost certainly a major contributor to the spuriously good Rfree > values associated with the retracted MsbA and EmrE structures. ehm ... I think 16 models systematically displaced along a direction parallel to helix axes contributed much more to that ... as the authors basically said in the original publication if my recollection is not bad. A. CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 07 February 2008 |
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