[ccp4bb] R-sleep

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

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From: Jim Naismith naismith {- at -} ST-ANDREWS {- dot -} AC {- dot -} UK
Date: 2007-10-01

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Subject: Re: R-sleep
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-10-01

Subject: R-sleep
From: "Mark J {- dot -} van Raaij" vanraaij {- at -} USC {- dot -} ES
Date: 2007-10-01

Dear All,

the short paper by Gerard Kleywegt (ActaD 63, 939-940) treats an
interesting subject (at least I think so...). I agree that what we
are now doing in many cases is effectively refining against Rfree.
For example, the standard CNS torsion angle refinement does n
refinement trials with randomised starting points. If you then take
the one with lowest Rfree (or let a script do this for you), you are
biasing Rfree!
Therefore, his proposal to put an extra set of reflections in a
dormant "vault" (R-sleep) sounds like a good idea to me. However, how
would the "vault" be implemented to be effective? If left to the
experimenter, it would be very tempting to check R-sleep once in a
while (or often) during refinement, rendering it useless as an
unbiased validator.

or am I being paranoid and too pessimistic?

Mark J. van Raaij
Unidad de Bioquímica Estructural
Dpto de Bioquímica, Facultad de Farmacia
and
Unidad de Rayos X, Edificio CACTUS
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/

CCP4bb navigation

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

Previous message:
Subject:
From: Jim Naismith naismith {- at -} ST-ANDREWS {- dot -} AC {- dot -} UK
Date: 2007-10-01

Next message:
Subject: Re: R-sleep
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-10-01