The maths for estimating the FOM during refinement in REFMAC is given in some detail in the original paper.
However the assessment uses estimates of the observation standard uncertainly, and SigmaA - the estimate of the resolution dependent error due to coordinate errors and missing atoms - and both these terms can be inaccurate. Randy Read et al has suggested ways of improving the SigmaA estimates, and better data processing SHOULD help with the measurement errors.. So - beware but that is amn outline of the teheory Eleanor Refinement of macromolecular structures by the Maximum likelihood method. G.N.Murshudov, A.A.Vagin, E.J.Dodson,(1997) Acta crystallogr. D53, 240-255 On Thu, 3 Oct 2019 at 08:45, Alexandre Ourjoumtsev < alexander.ourjoumt...@univ-lorraine.fr> wrote: > Dear Andre, > > > I would strongly advice you to look at the article by Lunin and Skovoroda > (Acta Cryst, A, 1995) that addresses exactly your question: > > https://scripts.iucr.org/cgi-bin/paper?vs0124 > > The authors remind a very important point that after model refinement ML > phase errors are strongly underestimated if using all reflections, as that > was done in the original works (see references in the article). While the > same ML estimates work perfectly for unrefined models, that's not the case > for refined ones, as was observed yet in the beginning of 80ths. > These authors show then that using the test-set of reflections (the > same as for R-free) is crucial to get the correct phase error estimates and > respective FOMs for all cases, as this is implemented now in modern > refinement programs. See also the article by Pannu & Read (Acta Cryst, A, > 1996) > > https://onlinelibrary.wiley.com/doi/pdf/10.1107/S0108767396004370 > > > A more recent important article on this topic is that by Praznikar and > Turk (Acta Cryst, D, 2009) > > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257616/ > > who discuss what can be done if a statistically significant test set of > reflections is not available. > > I hope this helps you. > > > With best wishes, > > Sacha Urzhumtsev > > > > ----- Le 3 Oct 19, à 2:17, Andre LB Ambrosio <an...@ifsc.usp.br> a écrit : > > Dear Jonathan, many thanks for this. I will have a look at it right away. > With best wishes, > Andre. > > On Wed, Oct 2, 2019, 7:51 PM Jonathan Cooper <bogba...@yahoo.co.uk> wrote: > >> This is a very good place to start: >> >> https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html >> >> Also recommend this one: >> >> https://doi.org/10.1107/S0108767386099622 >> >> and Main, P. (1979) Acta Cryst. A35, 779-85 - the maths in this one are a >> bit easier! >> >> >> >> On Wednesday, 2 October 2019, 22:47:56 BST, Andre LB Ambrosio < >> an...@ifsc.usp.br> 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
