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Re: [ccp4bb] Highest shell standards |
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CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 23 March 2007Subject: Re: Highest shell standards From: Bart Hazes bart {- dot -} hazes {- at -} UALBERTA {- dot -} CA Date: 2007-03-23 > > As for the 2Fo-Fc (2mFo-DFc, or something like that) electron density map, > it again assumes that the phases are in good shape, and you essentially > lose any new information you could gain from the addition of new Fobs > terms, but the map isn't distorted since the terms are zero. Fc is certainly not zero. D will go towards zero as the correlation between Fobs and Fcalc decreases but may still be substantial for the higher resolution shells. I expect that data sets that still have a relatively high I/SigI in the outer shell will also have quite high D values in the outer shell whereas datasets that push the limits of the true resolution will start seeing D decrease towards zero (haven't actually checked this though). The most significant problem are data sets collected on square detectors with relatively strong reflections still visible in the corners. In these cases high resolution completeness is low and many missing reflections will be replaced by DFc, with both D and Fc not being close to zero. I must admit that I've never understood the rationale for including dFc for missing terms, although it has been discussed "lively" on a few occassions. Yes, dFc is a better estimate for the true structure factor than leaving out the term (equivalent to setting the amplitude to zero). But dFc does not provide any information on how reliable the model is or where the model may need to be changed. Since the latter is the main function of electron density maps in my opinion I'm not confinced that substituting dFc is a good idea at any time. Bart > > On Fri, March 23, 2007 4:02 am, Eleanor Dodson wrote: > >>This is a good point - I had thought that D would be very low for an >>incomplete shell, but that doesnt seem to be true.. >> >>Garib - what do you think? >>Eleanor >> >> >>Petrus H Zwart wrote: >> >>>>I typically process my data to a maximum I/sig near 1, and >>>>completeness in >>>>the highest resolution shell to 50% or greater. It >>>> >>> >>>What about maps computed of very incomplete datasets at high resolution? >>>Don't you get a false sense of details when the missing reflections are >>>filled in with DFc when computing a 2MFo-DFc map? >>> >>>P >>> >>> >>> >> > > -- ============================================================================== Bart Hazes (Assistant Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax: 1-780-492-7521 ============================================================================== CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 23 March 2007 |
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