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If you filled a whole resolution bin with zeroes, refmac divides by zero on calculating the R-value for that bin, doesn't it? -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Fri, 28 Apr 2006, James Holton wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > Okay, this discussion has gone beyond Rmerge, but it does inspire an old > question of mine that I have never been able to find a good answer to: > > Does zero-filling help crystallographic refinement? > [...] > I once tried filling the outer shells of a data set with zeroes and fed > it to refmac. This caused refmac (4.0) to crash, and I never did get > back to that project. > > Garib? > > -James Holton > MAD Scientist > > > Vaheh Oganesyan wrote: > > > The intensity of the reflection (hkl) being zero is a piece of > > information, provided there are other reflections in that resolution > > shell that are not zero (above sigma). If all of the reflections in > > the resolution shell are essentially zero (<< sigma), then the > > resolution cut-off is too optimistic. > > > > /_There are two somewhat separate questions here: (1) what data to > > use in refinement and (2) how to define a "nominal resolution" > > _/ > > How do you see those questions being separate? Let say you collected > > data to resolution A (edge or corner of detector), then refined to > > resolution B. You probably looked at the data and considered that the > > data beyond B are either compromised by experimental setup or just > > absent. Why would anyone consider calling the resolution of the > > refined model or resolution of the presented structure other than B? > > One may state in the main body of the paper that the crystal actually > > diffracted to much higher resolution A but for such and such reasons > > we were able to use the data only till resolution B. > > > > > > > >> that will give the outside world a good idea of how far out the data > >> extended, which needs some vague sort of uniform standard. I'd > >> suggest the answers are (1) any datum you believe you really did > >> measure should be thrown into the pot and (2) the reported nominal > >> resolution should be where I/sigI falls below 2, perhaps with the > >> output statistics from scalepack or whatever was used included as > >> supplementary material to show that the sigmas are not grossly > >> mis-estimated. Unfortunately this creates logistical problems with > >> deposting coordinates, etc. if you want to call the official > >> "resolution" something other than that of the farthest-out fly speck > >> you refined against. > >> > >> At 09:29 AM 4/28/2006, Bart Hazes wrote: > >> > >>> *** For details on how to be removed from this list visit the *** > >>> *** CCP4 home page http://www.ccp4.ac.uk *** > >>> > >>> > >>> This is an interesting conceptual question. A reflection with an > >>> intensity of virually zero does not contribute to your electron > >>> density map, so can it be data? If it is can I claim to have a 0.02 > >>> Angstrom structure although all intensities beyond 2 Angstrom are > >>> virtually zero? > >>> > >>> The answer to question 1 is YES it can be data > >>> The answer to question 2 is NO KEEP DREAMING > >>> > >>> A very weak reflection does not contribute to your map so leaving it > >>> out doesn't hurt since missing a reflection is equivalent to > >>> assuming it is zero, not a bad approximation. However, a lot of our > >>> maps are of the 2Fo-Fc and Fo-Fc types. Similarly refinement a > >>> depends on |Fobs-Fcalc|. Thus, if Fcalc is big and you measured it > >>> as being near zero then the discrepancy is large and the reflection > >>> has a large contribution to refinement and these kinds of maps. Had > >>> you not measured the reflection then its contribution would be > >>> ignored (equivalent to Fo-Fc being zero). > >>> > >>> The difference at the high resolution limit is that Fcalc starts to > >>> approach zero as well as Fobs. So now both Fobs and Fo-Fc are > >>> virtually zero and small relative to the errors in Fo and Fc. So > >>> this time there really is no information left to speak of. > >>> > >>> Bart > >>> > >>> [EMAIL PROTECTED] wrote: > >>> > >>>> *** For details on how to be removed from this list visit the *** > >>>> *** CCP4 home page http://www.ccp4.ac.uk *** > >>>> > >>>> What is "observable data"? If I observe a reflection by passing it > >>>> through > >>>> the Ewald sphere I can measure its intensity > >>>> Phil > >>>> > >>>>> Here's what Acta Cryst has to say about resolution- > >>>>> > >>>>> From the "Notes for authors 2006" from Acta Cryst D: > >>>>> http://journals.iucr.org/d/issues/2006/02/00/me0308/index.html > >>>>> > >>>>> "11.1. Resolution > >>>>> > >>>>> The effective resolution should be described clearly. Values of the > >>>>> internal > >>>>> agreement of the data, Rmerge, together with the multiplicity, the > >>>>> mean > >>>>> value > >>>>> of I/ and the percentage completeness of the data are required for > >>>>> the > >>>>> overall > >>>>> data set and the highest resolution shell together with the limits > >>>>> of that > >>>>> shell in Å. For high-quality data obtained with synchrotron > >>>>> radiation, > >>>>> values > >>>>> of Rmerge < 20%, completeness > 93% and observable data > > >>>>> 70% should > >>>>> be > >>>>> achievable for the highest resolution shell. A complete table > >>>>> listing the > >>>>> above > >>>>> criteria as a function of resolution should also be submitted, but > >>>>> will > >>>>> normally > >>>>> be included in the supplementary material..." > >>>> > >>>> > >> > >> --------------------------------------------------------------------------------------------------------------------------- > >> > >> 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 > >> >
