Hello Engin, we discussed this a year or two ago in relation to NCS when Ian Tickle convinced me that since overfitting is due errors in the data, there is no reason to expect these errors to be correlated by NCS and picking the R-free set uniformally or in shells doesn't matter. No doubt my incompetence, but I can't see why twinning would be different.
Cheers, Jon.C. Sent from ProtonMail mobile -------- Original Message -------- On 29 Aug 2021, 05:32, Engin Özkan wrote: > Hi, > > I believe this is taken care of automatically if you use phenix to pick > your free reflections. > > From http://www.phenix-online.org/documentation/tutorials/twinning.html > > "When a test set is designed, care must be taken that free and work > reflections are not related by a twin law. The R-free set assignment in > phenix.refine and phenix.reflection_file_converter is designed with this > in mind: the free reflections are chosen to obey the highest possible > symmetry of the lattice." > > I believe this applies to all datasets, just in case there may be twinning. > > Engin > > On 8/27/21 11:12 AM, Jeffrey B Bonanno wrote: >> 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 jeffrey.bona...@einsteinmed.org >> >> >> -----Original Message----- >> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Dirk Kostrewa >> Sent: Friday, August 27, 2021 12:06 PM >> To: CCP4BB@JISCMAIL.AC.UK >> 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 >>> <jeffrey.bona...@einsteinmed.org> wrote: >>> >>>> Hi Kay, >>>> >>>> Can you also comment on Rfree set selection? It seems thin shell might be >>>> preferred in these cases? >>>> >>>> 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 jeffrey.bona...@einsteinmed.org >>> ###################################################################### >>> ## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww. >>> jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&d >>> ata=04%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C34839cf0455841166ca2 >>> 08d96974a30a%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637656772499 >>> 344795%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJ >>> BTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=XIDw7gK4YhuU02YwVY4F3DyeH >>> LvPfvamkOvqOnREXWM%3D&reserved=0 >>> >>> This message was issued to members of >>> https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.j >>> 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