Hi Dirk and Kay, Excellent, many thanks for the refresher!
jbb Jeffrey B. Bonanno, Ph.D. Department of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Avenue Bronx, NY 10461 off. 718-430-2452 fax. 718-430-8565 email [email protected] -----Original Message----- From: CCP4 bulletin board <[email protected]> On Behalf Of Dirk Kostrewa Sent: Friday, August 27, 2021 12:06 PM To: [email protected] Subject: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis? CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the "Phish Alert" button on the top right of the Outlook dashboard to report any suspicious emails. Dear Jeffrey, just using thin shells of reflections for the test set might not be enough to eliminate any correlation to working set reflections. The distance of the test set reflections in reciprocal space, after applying the NCS rotations in reciprocal space, to any reflections of the working set should be large enough to be uncorrelated. A typical maximum distance for correlation in reciprocal space is the first zero (root) of the Fourier transform of the approximated spherical shape of the protein molecule, the so-called G-function (see [1) and [2]). However, this means, that shells should be thicker than 2 times this distance to blindly exclude any potential correlation between test set and working set reflection in reciprocal space. This would be way too expensive! An better way to select uncorrelated reflections is described in [3] (same reference that Kay has given), where for each test set reflection, after applying the NCS rotations in reciprocal space, the distances to the working set reflections are taken into account, and test and working set reflections are chosen such that their distances are large enough to be uncorrelated. Best regards, Dirk. [1] Rossmann & Blow, Acta Cryst, 15, 24 -31 (1962) [2] Main & Rossmann, Acta Cryst, 21, 67-72 (1966) [3] Fabiola, Korostelev & Chapman, Acta Cryst, D62, 227-238 (2006) On 8/27/21 4:47 PM, Kay Diederichs wrote: > Hi Jeffrey, > > good question. Both twinning and NCS may couple reflections across free and > working sets, and this should be avoided by proper selection - otherwise > Rfree is biased towards Rwork. Selecting thin shells should be a good option, > and can be done in SFTOOLS (or DATAMAN, or SHELXPRO). > > How much does it matter? Actually I started to search the literature after > reading your question, and expected that one of Z. Dauter's papers would > enlighten me, but until a minute ago couldn't find the one(s) that I thought > existed. But I found Fabiola et al., Acta Cryst. (2006). D62, 227-238 which > is relevant for the coupling by NCS. Ah I just found Smietanska et al., Acta > Cryst. (2020). D76, 653-667 where they indeed selected thin shells. > > Best wishes, > Kay > > On Fri, 27 Aug 2021 13:24:05 +0000, Jeffrey B Bonanno > <[email protected]> wrote: > >> Hi Kay, >> >> Can you also comment on Rfree set selection? It seems thin shell might be >> preferred in these cases? >> >> jbb >> >> Jeffrey B. 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