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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 along c. We were also skeptic, but ... it worked. Eleanor Dodson wrote: > What resolution do you have? > > 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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