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Re: [ccp4bb] low-res cutoff in refinement
 

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CCP4bb <-- 2008 <-- January 2008 <-- 24 January 2008
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Subject: Re: low-res cutoff in refinement
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-01-24 		Next message:
Subject: Re: Real space rotation translation
From: Charlie Bond Charles {- dot -} Bond {- at -} UWA {- dot -} EDU {- dot -} AU
Date: 2008-01-24


Subject: Re: low-res cutoff in refinement
From: Axel Brunger brunger {- at -} STANFORD {- dot -} EDU
Date: 2008-01-24
Are you using CNS 1.2? This version has a robust bulk solvent model and
anisotropic correction
that is much improved compared to CNS 1.1. It is similarly robust as
that of Phenix (although
different in detail).

Axel Brunger



Van Den Berg, Bert wrote:
>
> Hi all,
>
> during refinement of our (membrane protein) structures, basically in
> all cases the R/Rfree values depend a lot on the low resolution
> cutoff. Putting the cutoff at lower res (20-50 A) results in
> substantially higher R/Rfree values (sometimes few percent). For this
> reason we mostly refine the data from the high-res limit down to 10A
> or so. I have noticed that this occurs fairly often in the literature,
> but I don't know if this is a membrane protein related issue or not.
>
> Could it be that the bulk solvent model used in CNS (we refine
> exclusively with CNS) does not model the situation with membrane
> proteins, due to the presence of detergents? Or is it related to data
> collection issues (low-res spots overloaded etc)? Anything else? What
> could be done to overcome the problem, and to use all the data in
> refinement?
>
> Thanks, Bert
>
> Bert van den Berg
> University of Massachusetts Medical School
> Program in Molecular Medicine
> Biotech II, 373 Plantation Street, Suite 115
>
>

--
Axel T. Brunger
Investigator, Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University

Web: http://atb.slac.stanford.edu
Email: brunger@stanford.edu
Phone: +1 650-736-1031
Fax: +1 650-745-1463

CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 24 January 2008
Previous message:
Subject: Re: low-res cutoff in refinement
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-01-24 		Next message:
Subject: Re: Real space rotation translation
From: Charlie Bond Charles {- dot -} Bond {- at -} UWA {- dot -} EDU {- dot -} AU
Date: 2008-01-24


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