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Re: [ccp4bb] Highest shell standards |
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CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 26 March 2007Subject: Re: Highest shell standards From: price {- at -} UCHICAGO {- dot -} EDU price {- at -} UCHICAGO {- dot -} EDU Date: 2007-03-26 a really bad idea for anisotropic data where most reflections are "missing" at high resolution? Shouldn't there be a big flashing red flag alerting the user to what's been done? Phoebe At 01:22 PM 3/26/2007, Edward A. Berry wrote: >Actually I was thinking of a somewhat earlier paper: > >Rayment,I. Molecular relacement method at low resolution: >optimum strategy and intrinsic limitations as determined >by calculations on icosahedral virus models. >Acta Crystallogr. A 39, 102 116 (1983). > >But thanks for bringing the Caliandro et al. paper to my attention. >Thanks also to Fred. Vellieux for his comments, and to Pete Dunton >for explaining to me that while fft doesn't do fillin by default, >the 2MFo-DFc map coefficients from refmac5 do have fillin values >for the missing reflection, making model bias a problem when >many missing residues are included. > >Now I understand Petrus's question. > >Ed > >Michel Fodje wrote: >>You are probably referring to the following works: >>Caliandro et al, Acta Cryst. D61 (2005) 556-565 >>and Caliandro et al, Acta Cryst. D61 (2005) 1080-1087 >>in which they used density modification to calculate phases for >>unmeasured reflections, and used the phases to extend the resolution by >>calculating rough estimates unmeasured amplitudes. Using this technique >>they actually could improve the electron density. >>If I'm not mistaken, George Sheldrick has implemented this "Free Lunch" >>algorithm in SHELXE. >>/Michel >>On Fri, 2007-03-23 at 08:05 -0800, Edward Berry wrote: >> >>>If instead you allow the missing F's >>>to "float", calculating them on each cycle from the previous map >>>using the fillin option, someone has shown (don't have the >>>reference handy at the moment) that the F's tend toward the true F's >>>(in the case that they weren't really missing but omitted as part >>>of the test). >>> >>>Ed --------------------------------------------------------------------------------------------------------------------------- Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 fax 773 702 0439 http://bmb.bsd.uchicago.edu/index.html http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 26 March 2007 |
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