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?
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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
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