Dear Melanie, To obtain a reasonable error estimate of R-free you could try to refine your structure against different sets of reflections. You can force the R-free set to be the reflections flagged with 1 or 2, etc. instead of 0 (at least in Refmac) and refine to convergence again. You should get similar (but not the same) R-free values. This will give you a good view of possible R-free values. I admit it is a lot of work (and probably totally over the top) but you can script this quite easily. I tried it a few times and the SD of R-free values is typically a few tenths of a percent(age point). Cheers, Robbie Joosten
---------------------------------------- > Date: Tue, 2 Mar 2010 08:44:18 -0800 > From: [email protected] > Subject: Re: [ccp4bb] Deposition of a BUSTER refined structure > To: [email protected] > > On Tuesday 02 March 2010 07:09:47 Melanie Vollmar wrote: >> Hi all >> >> I did my first deposition of a BUSTER refined structure and I was very >> surprised when I was asked for an "estimated error of free R value" and >> "estimated error of bin free R value" as well an "ESD based on Luzzati Plot" >> during the deposition process. > > These instructions are unfortunate, since the use of Luzzati plots > to estimate error is at this point a historical remnant. > > The same 'problem' occurs when depositing structures refined with refmac. > The error estimates output by the program are based either on the > maximum likelihood statistics or on Cruickshank's DPI indicator. > > Bottom line: Just ignore the request for Luzzati plot esds. > > Ethan > > >> I had a detailed look into the refinement log file and I tried the Buster >> documentation but I have absolutely no clue where I can find these values. >> >> Can someone give me a hint where I can find some information about this or >> where the values are in the log file? If they are not listed anywhere, in >> which way do they have to be estimated? And what is a Luzzati Plot? I have >> never heard of such a plot before... >> >> >> Thank you very much. >> >> Cheers >> >> Melanie >> > > > > -- > Ethan A Merritt > Biomolecular Structure Center > University of Washington, Seattle 98195-7742 > _________________________________________________________________ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop
