Re: [ccp4bb] Figure of merit in refinement

Dear Eleanor, Yes, difference maps are weighted by FOM, with the coefficient being m*Fo-D*Fc, phased by the model. If Fc is small, then m will be small because, even if Fo is large, you have no idea what phase to assign to the difference. If Fc is large because you haven't treated bulk

Re: [ccp4bb] Figure of merit in refinement

This is hunch speak - not proper analysis, but it is possible to get huge Fcalc, and hence large difference map terms, at low resolution by assuming the solvent volume is a vacuum, not full of partially ordered water molecules. The Babinet scaling can do something to correct this but it is a very

Re: [ccp4bb] Figure of merit in refinement

>>And as we often end our beer-discussions - may be all protein space groups >>are actually true P1, just close enough to satisfy the high symmetry rules .. >>but this is getting a bit philosophical I know .. Could we add that all crystals are twinned, just some are in such a way as to be a

Re: [ccp4bb] Figure of merit in refinement

Dear all, regarding the "remaining strong differences" between measured data and calculated SFs from a a finished (high res structure) I once investigated a bit into this going back to images and looking up some extreme outliers. I found the same - those were clear strong diffraction spots, not

Re: [ccp4bb] Figure of merit in refinement

James, Where we diverge is with your interpretation that big differences lead to small FOMs. The size of the FOM depends on the product of Fo and Fc, not their difference. The FOM for a reflection where Fo=1000 and Fc=10 is very different from the FOM for a reflection with Fo=5000 and

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Figure of merit in refinement

esting map. Best, Herman Von: CCP4 bulletin board Im Auftrag von James Holton Gesendet: Mittwoch, 16. Oktober 2019 17:02 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] Figure of merit in refinement EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@j

Re: [ccp4bb] Figure of merit in refinement

All very true Randy, But nevertheless every hkl has an FOM assigned to it, and that is used to calculate the map.  Statistical distribution or not, the trend is that hkls with big amplitude differences get smaller FOMs, so that means large model-to-data discrepancies are down-weighted. I

Re: [ccp4bb] Figure of merit in refinement

Hi Fellows, I have tried to summarize these issues James raised, in consistent notation in Chapter 12 of BMC of which you can download an excerpt here: https://www.dropbox.com/s/crzwoa5lb8bk3x5/Pages_611-619_from%20BMC_rupp_ch12.pdf?dl=0 > if your R factor is 55% then your phases probably

Re: [ccp4bb] Figure of merit in refinement

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

Re: [ccp4bb] Figure of merit in refinement

James - you do the most sensible informative tests! Thank you.. Eleanor On Fri, 4 Oct 2019 at 16:39, James Holton 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

Re: [ccp4bb] Figure of merit in refinement

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

Re: [ccp4bb] Figure of merit in refinement

Thank you, Eleanor, for an important reminder : obviously, one more recent and relevant paper is that by Read and McCoy (Acta Cryst, D, 2016) [ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784668/ | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784668/ ] With best wishes, Sacha -

Re: [ccp4bb] Figure of merit in refinement

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

Re: [ccp4bb] Figure of merit in refinement

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 | https://scripts.iucr.org/cgi-bin/paper?vs0124 ] The authors remind a very important point that

Re: [ccp4bb] Figure of merit in refinement

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 wrote: > This is a very good place to start: > > https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html > > Also recommend this one: >

Re: [ccp4bb] Figure of merit in refinement

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

[ccp4bb] Figure of merit in refinement

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.