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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:[log in to unmask]] Sent: Thu 1/24/2008 7:35 PM To: Van Den Berg, Bert Cc: [log in to unmask] 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: [log in to unmask] Phone: +1 650-736-1031 Fax: +1 650-745-1463