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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: "F {- dot -} Xavier_Gomis-Rüth" xgrcri {- at -} IBMB {- dot -} CSIC {- dot -} ES Date: 2007-03-27 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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