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----- Original Message -----
From: "Jan Abendroth" <Jan.Abendroth@uni-koeln.de> To: "ccp4" <ccp4bb@dl.ac.uk> Sent: Wednesday, December 20, 2000 7:21 PM Subject: [ccp4bb]: unmeasured data in map-calculations > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html *** > > Dear all, > with many apologizes (because it's mostly a a cns-related question) I > like to submit a question to the ccp4bb. But it's soon x-mass and you > might forgive this. > > My data set is quite incomplete in the highest resolution shell. When I > calculate maps with the cns script model_map the sigmaA-weighted > fofc-map (mFoDFc) has many "unreasonable" peaks at 3sigma-level. When I > make cns to take Fc for the unmeasured Fo's the sigmaA-weighted fofc-map > shows much fewer and much more reasonable peaks, simply this map becomes > significanly better. > > This seems to make sense, but what is the physical/mathematical reason > for this? > How treats cns unmeasured hkl's in the "normal" mode in difference maps? > Is there a related ccp4-option in refmac/fft? > > Thanks for any reply, kind regards and merry christmas > > Jan Hi Jan, the idea behind this is, as far as I have understood it, that the maximum likelihood formalism should be able to produce reasonable estimates for the "real" data (not necessarily the observed data). These (current) estimates are model structure factors weighted by a factor for incorrectness of the (partial) model, that is D*Fc. Unfortunately, only the amplitudes are downweighted by this procedure, whereas the phases come directly from the model and are still somewhat biased towards the model, depending on how far the incomplete/incorrect model is kept apart from the observed data. By substituting the missing Fo by D*Fc you have two opposite effects on the resulting 2mFo-DFc electron density map (the mFo-DFc is not affected): the positive effect is a much cleaner map, because any missing data in reciprocal space will generally lower the quality of the map in real space (especially when the missing data are not randomly distributed resulting in a certain "shape" for the observed data, which will give a folding of your real electron density map with the Fourier transform of that shape), the negative effect is a somewhat increased model bias in your map. Some time ago, I posted a related question on the CCP4BB, the feedback showed me, that most crystallographers are not sure which effect is the more important one. My suggestion would be (and this is what I will also do next time) to omit a few well defined and a few poorly defined parts of your model and inspect the electron density maps with and without Fo substitution for these "known" parts. This procedure was suggested quite a long time ago by Rice to give the user a feeling about model bias in maps calculated with combined phases including model phases. I wish all members of the CCP4BB a Merry Christmas and a Happy New Year! Dirk. *************************************************************** Dirk Kostrewa Paul Scherrer Institut e-mail: dirk.kostrewa@psi.ch Life Sciences phone: +41-56-310-4722 OSRA/007 fax: +41-56-310-4556 CH-5232 Villigen PSI WWW: www.sb.psi.ch Switzerland *************************************************************** |