Re: [ccp4bb] Post facto fix to R-free selection

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CCP4bb <-- 2007 <-- April 2007 <-- 10 April 2007

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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

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Subject: Stretching Modelled B-DNA
From: Balvinder Dhaliwal balvinder {- dot -} dhaliwal {- at -} GMAIL {- dot -} COM
Date: 2007-04-10

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

Probably easiest to start again with the correct FreeR
You can perturnb the strucures
pdbset xyzin MR.pdb xyzout- MRshaken.pdb
NOISE 0.3

That moves everything a bit.

Or if you do enough cyles the FreeR should increase steadily to a
sensible value then level off

Easiest to use the GUI and click the button - add FreeR from existing
mtz file!

Eleanor

Harry M. Greenblatt wrote:
> 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
>
>
>

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CCP4bb <-- 2007 <-- April 2007 <-- 10 April 2007

Previous message:
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

Next message:
Subject: Stretching Modelled B-DNA
From: Balvinder Dhaliwal balvinder {- dot -} dhaliwal {- at -} GMAIL {- dot -} COM
Date: 2007-04-10