Bert,
That explains it. We observed similar behavior to what you described
with the previous
version of CNS (1.1). Version 1.2 should hopefully fix your problem.
See my paper in Nature Protocols *(* /Nature Protocols/ *2*, 2728-2733
(2007)), for details.
Axel
Van Den Berg, Bert wrote:
No, we have been using version 1.1 so far. Thanks for the suggestion,
we'll use version 1.2 from now on and try Phenix as well.
Bert
-----Original Message-----
From: Axel Brunger [mailto:[EMAIL PROTECTED]
Sent: Thu 1/24/2008 7:35 PM
To: Van Den Berg, Bert
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] low-res cutoff in refinement
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: [EMAIL PROTECTED]
Phone: +1 650-736-1031
Fax: +1 650-745-1463
--
Axel T. Brunger
Investigator, Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University
Web: http://atb.slac.stanford.edu
Email: [EMAIL PROTECTED]
Phone: +1 650-736-1031
Fax: +1 650-745-1463
