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Re: [ccp4bb] low-res cutoff in refinement |
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CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 25 January 2008Subject: Re: low-res cutoff in refinement From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2008-01-25 Your R factor is a function of your scaling algorithm as well as your model, and as you point out the apparent R factor increases when you include the low resolution data. This doesnt mean your model is worse - it is still the same model! All refinement programs now have a fudge correction to try to account for the missing solvent model. This usually assumes that the low resolution data distribution is OK, ie the data is a) measured and b) measured correctly.. Unfortunately this is often not so - all strong low resolution reflections may be overloads and therefore missing altogether giving a very distorted distribution. (Look at any of the plot from CCP4 data processing or refinement which show And if the scaling algorithm gets itself in a twist it can force up the R factors across all the resolution ranges - again you can check a REFMAC plot of if the scaling is poor they may not.. Eleanor Dale Tronrud wrote: > Dear Bert, > > I think is it important here to remember that R and R free are tools > to help judge the quality of the model, not the data. You cannot reject > data because it disagrees with your model. Lowering your free R by > changing your resolution limit is no different than finding all the > individual reflections that disagree most with your model and rejecting > them. Neither procedure increasing the quality of your model, it > simply lowers the R value. > > If you suspect you have a problem with overloads, you have to go > to your data reduction log files and see if you have this problem. If > you suspect your bulk solvent model is poor you need to find out what > model you are using and decide if it is correct for your crystal. It > is certainly a good idea, as Pavel suggests in another response, to > try other programs that have different approaches. > > Membrane protein crystals have a particular problem with bulk solvent > because there is the lipid part of the bulk solvent and the water part > and most bulk solvent models assume a single kind of bulk solvent. > Hopefully someone else will reply with some references to such > two-component bulk solvent models. > > If you can't figure out how to lower your R's by improving your > model, I'm afraid you just have to live with it. Your R values will > be higher because they reflect the inability of your model to fit > your data. > > Dale Tronrud > > > 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 >> >> > > CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 25 January 2008 |
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