Hi all,
I’ve spent some time going through different flags for free
reflections for (somewhat stupid) reason to get lower Rfree. I made
sure all different flags were used only for each of sets of
refinement. I wanted to satisfy my inner belief that it doesn’t
matter which flag is used (between 0 and 19). To be short: I failed.
Free reflections have been chosen “randomly”, no suspicion there.
However, there was clear difference at the end. The difference was
about 2-3% difference in Rfree value. This tells me that the
randomness has some sort of rule, which makes “random” choice not so
random. Having found this I also tried to see “a rule” that breaks
this randomness, like even numbers, odds, etc. I did not. Because
this was only on few cases I won’t even try to connect it to # of
molecules per AU, or SG. For each structure (I tried this for 2-3
structures about 10 years ago) it was a different flag. I’m not sure
if DCC also is looking through different flags, but at the end it
finds the best, making these exercises unnecessary. Sorry, cannot
present a case. Was too long ago.
Vaheh Oganesyan, Ph.D.
[cid:[email protected]]
R&D | Biologics Engineering
One Medimmune Way, Gaithersburg, MD 20878
T: 301-398-5851
[email protected]<mailto:[email protected]>
From: CCP4 bulletin board <[email protected]> On Behalf Of Randy
John Read Sent: Monday, June 23, 2025 10:29 AM
To: [email protected]
Subject: Re: [ccp4bb] free R in shells
Hi Ben,
I would be very interested if you have a case where it makes a
difference to do this. At one point I was convinced that it had been
important when we were working on the structure of a Shiga-like toxin
bound to trisaccharide (1bos), with four pentamers in the asymmetric
unit. However, Pavel Afonine challenged me to show that the free set
was less biased when chosen in shells than when chosen randomly, and
even in that relatively extreme case I couldn’t see evidence of it.
So it’s probably not worth the bother. Also, if you select the free
set randomly, it’s distributed over the same resolutions as the
working data, which arguably is important when you’re using it to
calibrate the sigma(A) estimates for likelihood targets.
Best wishes,
Randy
[...]
-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building
Hills Road E-mail: [email protected]<mailto:[email protected]>
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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