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Re: [ccp4bb] Highest shell standards |
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CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 27 March 2007Subject: Re: Highest shell standards From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2007-03-27 I have always been a bit sceptical about this, since if nothing is measured because of the anisotropy no sharpening will generate a term .. The "free lunch" algorithm is certainly useful. We used this with ACORN to correct phases at high resolution, setting all missing data to the mean normalised value - ie All missing Es = 1, and that does help. You can understand why. And the same idea must help with any form of phasing - estimate of the amplitude than F=0 and if there is some useful phase info from density modification or density averaging then the maps will improve. But just sharpening unmeasured data - hmmmmm eleanor F.Xavier Gomis-Rüth wrote: > I think it is important to differentiate between two stages: first, > when you want to solve the structure, and second, when you produce a > final model > you're going to deposit with the PDB. In the first case, it has proven > useful for us lately in two cases to apply anisotropic scaling, be it > through the > Sawaya&Dickerson server or through XPREP, for getting useful electron > density maps. In the latter case the difference between isotropic and > anisotropic scaling was as simple as a completely messy density vs. > clear regular secondary structure elements that are currently enabling > to (manually) > build a model. Once a complete model is obtained, (final) refinement > should be performed against the anisotropic, unmodified data as > refinement > programs such as refmac and cns properly account for data anisotropy > through appropriate anistropic scaling. > > If you have concerns regarding fabricated data: Even more astonishing > is the "free-lunch" approach: you completely fabricate data up to 1.0A > resolution > and this apparently makes the difference between solving a structure > or not ! > Maybe Isabel or George could comment on this. > > Xavier > > > price@UCHICAGO.EDU wrote: >> Isn't automatically included fabricated data for missing reflections >> 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 <-- 27 March 2007 |
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