[ccp4bb] Post facto fix to R-free selection

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Summary - Valid to stop Refmac after TLS refinement?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-04-10

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Subject: Re: Post facto fix to R-free selection
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-04-10

Subject: Post facto fix to R-free selection
From: "Harry M {- dot -} Greenblatt" harry {- dot -} greenblatt {- at -} WEIZMANN {- dot -} AC {- dot -} IL
Date: 2007-04-10

BS"D

Dear All,

Someone has come to ask my opinion about some inhibitor-protein
complexes they have refined, isomorphous with a known native
structure (P21212). After a short look at the statistics, I became
suspicious about the R-free selection for the new complexes. Indeed,
the person was not careful about taking the the same R-free set as
the native. Each complex had a new R-free set, and Refmac was used
(i.e., they did not benefit from simulated annealing, which according
to some would have saved the situation). So the difference between R
and Rfree is about 2-3% for each structure, since the structures are
biased to a large fraction of the new Rfree set. Technically, the
process was incorrect, but how can they remedy the situation (short
of starting from scratch with the proper Rfree set)? Run simulated
annealing now, and then a round of Refmac?

Thanks,

Harry
------------------------------------------------------------------------
-
Harry M. Greenblatt
Staff Scientist
Dept of Structural Biology harry.greenblatt@weizmann.ac.il
Weizmann Institute of Science Phone: 972-8-934-3625
Rehovot, 76100 Facsimile: 972-8-934-4159
Israel

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Summary - Valid to stop Refmac after TLS refinement?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-04-10

Next message:
Subject: Re: Post facto fix to R-free selection
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-04-10