Re: [ccp4bb] low-res cutoff in refinement

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CCP4bb <-- 2008 <-- January 2008 <-- 24 January 2008

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Subject: low-res cutoff in refinement
From: "Van Den Berg, Bert" Lambertus {- dot -} VandenBerg {- at -} UMASSMED {- dot -} EDU
Date: 2008-01-24

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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

Subject: Re: low-res cutoff in refinement
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2008-01-24

Hi Bert,

try phenix.refine: it uses very efficient and robust bulk solvent
correction and anisotropic scaling protocol (Acta Cryst. (2005). D61,
850-855) as well as it automatically detects and removes
reflections-outliers before the refinement starts. I think the
combination of these things may help.

More information:
http://phenix-online.org/
http://phenix-online.org/documentation/
http://phenix-online.org/documentation/refinement.htm

or replay me with your questions.

Cheers,
Pavel.

On 1/24/2008 3:21 PM, 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
>
>

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CCP4bb <-- 2008 <-- January 2008 <-- 24 January 2008

Previous message:
Subject: low-res cutoff in refinement
From: "Van Den Berg, Bert" Lambertus {- dot -} VandenBerg {- at -} UMASSMED {- dot -} EDU
Date: 2008-01-24

Next message:
Subject: Re: low-res cutoff in refinement
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-01-24