Hi James, I'm sure you realise this, but it's important for other readers to remember that the FOM is a statistical quantity: we have a probability distribution for the true phase, we pick one phase (the "centroid" phase that should minimise the RMS error in the density map), and then the FOM is the expected value of the phase error, obtained by taking the cosines of all possible phase differences and weighting by the probability of that phase difference. Because it's a statistical quantity from a random distribution, you really can't expect this to agree reflection by reflection! It's a good start to see that the overall values are good, but if you want to look more closely you have to look a groups of reflections, e.g. bins of resolution, bins of observed amplitude, bins of calculated amplitude. However, each bin has to have enough members that the average will generally be close to the expected value.
Best wishes, Randy Read > On 4 Oct 2019, at 16:38, James Holton <jmhol...@lbl.gov> wrote: > > I've done a few little experiments over the years using simulated data where > I know the "correct" phase, trying to see just how accurate FOMs are. What I > have found in general is that overall FOM values are fairly well correlated > to overall phase error, but if you go reflection-by-reflection they are > terrible. I suppose this is because FOM estimates are rooted in amplitudes. > Good agreement in amplitude gives you more confidence in the model (and > therefore the phases), but if your R factor is 55% then your phases probably > aren't very good either. However, if you look at any given h,k,l those > assumptions become less and less applicable. Still, it's the only thing > we've got. > > 2qwAt the end of the day, the phase you get out of a refinement program is > the phase of the model. All those fancy "FWT" coefficients with "m" and "D" > or "FOM" weights are modifications to the amplitudes, not the phases. The > phases in your 2mFo-DFc map are identical to those of just an Fc map. > Seriously, have a look! Sometimes you will get a 180 flip to keep the sign > of the amplitude positive, but that's it. Nevertheless, the electron density > of a 2mFo-DFc map is closer to the "correct" electron density than any other > map. This is quite remarkable considering that the "phase error" is the same. > > This realization is what led my colleagues and I to forget about "phase > error" and start looking at the error in the electron density itself > (10.1073/pnas.1302823110). We did this rather pedagogically. Basically, > pretend you did the whole experiment again, but "change up" the source of > error of interest. For example if you want to see the effect of sigma(F) > then you add random noise with the same magnitude as sigma(F) to the Fs, and > then re-refine the structure. This gives you your new phases, and a new map. > Do this 50 or so times and you get a pretty good idea of how any source of > error of interest propagates into your map. There is even a little feature > in coot for animating these maps, which gives a much more intuitive view of > the "noise". You can also look at variation of model parameters like the > refined occupancy of a ligand, which is a good way to put an "error bar" on > it. The trick is finding the right source of error to propagate. > > -James Holton > MAD Scientist > > > On 10/2/2019 2:47 PM, Andre LB Ambrosio wrote: >> Dear all, >> >> How is the phase error estimated for any given reflection, specifically in >> the context of model refinement? In terms of math I mean. >> >> How useful is FOM in assessing the phase quality, when not for initial >> experimental phases? >> >> Many thank in advance, >> >> Andre. >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 The Keith Peters Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
