Hi all, Thanks for the useful advice. Clemens, I was indeed reminded of the <I/sig(I)> vs <I>/<sig(I)> discussion when I started this thread. The reason I brought it up here is because the ratio-of-means form is the way it is described in "Estimation of anomalous signal in diffraction data <https://journals.iucr.org/d/issues/2006/08/00/dz5079/#SEC2>" (Dauter 2006), and similarly in "Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing <https://journals.iucr.org/d/issues/2016/03/00/ba5234/index.html#SEC1>" (Terwilliger et al. 2015), where it appears as <|Δano|>/<σano>. Therefore, I'm not sure it is true that everyone really means <|ΔF|/σ(ΔF)> when discussing the anomalous signal to noise, but I am happy to adopt this version. The problem is, we have different formulations and different suggested cut offs, and given that we don't really have independent and identically distributed random variables, these criteria surely produce (slightly?) different results depending on which form is adopted.
There is a practical motive here: we want to report this metric in DIALS and we want to provide some indicative guiding lines on a plot to help the user make an interpretive judgement. It sounds like a plot of <|ΔF|/σ(ΔF)> with guidelines at 0.8 and 1.2 would be a good start, but it does seem there is scope for confusion, not immediately resolved by the literature. At least we will write the formula out on the plot explicitly, rather than hiding it behind an ambiguous name. Bernhard, unfortunately the copy of BMC I use for reference is currently locked up at the office. One of the side effects of working from home is that the group library of hardcopy textbooks is sat gathering dust. Cheers -- David On Fri, 18 Dec 2020 at 22:41, Petr Kolenko <petr.kole...@fjfi.cvut.cz> wrote: > Dear David, > > Although this is not exactly a topic of your question, an alternative > approach is to use the resolution screening and compare the results. I have > implemented this approach to my program SHELIXIR (because it uses SHELX > C/D/E), which can be found here: > > http://kmlinux.fjfi.cvut.cz/~kolenpe1/shelixir/ > > It also has its GUI here: > > http://kmlinux.fjfi.cvut.cz/~kolenpe1/shelixir/gui/ > > Once you have enough computational power, you can easily perform such > testing (and no longer need to understand everything that is written in the > manuscript :-) ). > > I hope that the program will soon be published and I would welcome if you > (or someone else) used it and potentially gave me some feedback or > suggestion. The program has other functions like parallelized solvent > content screening, etc. ;-) Feel free to ask for more. > > Best regards, > > Petr > > > > PS: Although tested on a number of cases, the command line is more stable > than the GUI. > > > > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *On Behalf Of *David > Waterman > *Sent:* Friday, December 18, 2020 12:53 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Anomalous signal to noise details > > > > Hi folks > > > > The paper "Substructure solution with SHELXD > <https://journals.iucr.org/d/issues/2002/10/02/gr2280/index.html>" > (Schneider & Sheldrick, 2002) describes how > > > > data can be truncated at the resolution at which [ΔF to its estimated > standard deviation as a function of the resolution] drops to below about 1.3 > > > > Is this referring to the quantity <|ΔF|>/<σ(ΔF)> calculated in resolution > shells, or the quantity <|ΔF|/σ(ΔF)> ? > > > > This entry > <https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php?title=SHELX_C/D/E#Resolution_cutoff_.28SHEL.29> > on the ccp4wiki gives a cutoff > > > > where the mean value of |ΔF|/σ(ΔF) falls below about 1.2 (a value of 0.8 > would indicate pure noise) > > > > this version sounds to me like <|ΔF|/σ(ΔF)> > > > > which is the "better" metric, and what do people mean when they say > DANO/SIGDANO? What is the justification for the 1.3 (or 1.2) value? > > > > Thanks! > > -- David > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
