James - you do the most sensible informative tests! Thank you.. Eleanor On Fri, 4 Oct 2019 at 16:39, James Holton <[email protected]> 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 > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > 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
