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Re: [ccp4bb] Model ensemble for x-ray crystallography
 

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CCP4bb <-- 2008 <-- March 2008 <-- 28 March 2008
Previous message:
Subject: Abstract submission deadline
From: "Sanishvili, Ruslan" rsanishvili {- at -} ANL {- dot -} GOV
Date: 2008-03-28 		Next message:
Subject: Re: Model ensemble for x-ray crystallography
From: Pavel Afonine pafonine {- at -} LBL {- dot -} GOV
Date: 2008-03-28


Subject: Re: Model ensemble for x-ray crystallography
From: "Das, Debanu" debanu {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2008-03-28
Something to think about in using ensembles for refinement:
Even in ultra high resolution crystal structures, usually only a single conformation for MC (maybe dual in some places) is seen and maybe 2-3 conformations for many SCs. Occupancies of these SCs can be adjusted during refinement with even the lowest occupany ones ending up with something like 0.1-0.2 occ. In that case, what extra knowledge is gained by modeling 5 or more ensembles other that possibly some lowering of R/Rf (which in itself may be justifiable since lower R/Rf ==> higher model accuracy).
-Debanu.

-----Original Message-----
From: CCP4 bulletin board on behalf of Bryan W. Lepore
Sent: Fri 3/28/2008 8:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Model ensemble for x-ray crystallography

> At 10:13 AM 3/28/2008, Lucas Bleicher wrote :
>> Some time ago I've heard about the idea of proposing an ensemble of
>> models (as in NMR), instead of a single model for x-ray crystallography
>> structures. If I remember correctly, this idea has been published
>> somewhere. Can anyone tell me what article is that?

jmb 301 1237-1256, 2000 analyzes the disorder in calmodulin that considers
such a treatment along with other models of disorder.

http://www.ncbi.nlm.nih.gov/pubmed/10966818

-bryan

CCP4bb navigation

CCP4bb <-- 2008 <-- March 2008 <-- 28 March 2008
Previous message:
Subject: Abstract submission deadline
From: "Sanishvili, Ruslan" rsanishvili {- at -} ANL {- dot -} GOV
Date: 2008-03-28 		Next message:
Subject: Re: Model ensemble for x-ray crystallography
From: Pavel Afonine pafonine {- at -} LBL {- dot -} GOV
Date: 2008-03-28


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