Well - occupancy refinement is particularly imprecise, and highly correlated with temperature factors. Also the population for a surface ARG or LYS may well have more than two conformations, whereas some internal residue is better defined. There is also the Q of solvent - dual occupancies will generate dual solvent networks..
..You dont say what resolution your data are. Again at 0.8A you can be confident - at 3A it is at best a guess. So I for one do not take the numbers very seriously - they are a flag only. Presumably you didnt model the second conformation unless there was some feature in an earlier map to suggest it existed? Good luck Eleanor On Wed, 6 Sept 2023 at 03:18, Pavel Afonine <pafon...@gmail.com> wrote: > Hi Matt, > I believe figure 3 here: > https://www.nature.com/articles/s41467-018-06957-w > is relevant to your question. > Pavel > > > On Tue, Sep 5, 2023 at 11:32 AM Matt McLeod <mjmcleo...@gmail.com> wrote: > >> Hi all, >> >> I am trying to get some insight in the accuracy/precision of occupancy >> refinements. I have done some 2-state occupancy refinements and have >> observed the refinement achieving ~0.25-0.3 occupancy for the minor >> population. This population, when observing the electron density maps, had >> essentially no evidence for it being present. I was wondering: >> >> What are the errors in the reported occupancies? >> >> Is there a lower and upper limit to occupancy refinements? As in, if you >> occupancy refine two states and one is imaginary will it refine to >> approximately 1 and 0? Or does the background noise always given a >> positive number to the imaginary set? This would, to me at least, be the >> lower and upper limits to the occupancy refinements and could be used as a >> normalization factor for other atoms. Maybe my logic is off... >> >> Any insight or literature would be appreciated! >> Matt >> >> ######################################################################## >> >> 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/ >> > > ------------------------------ > > 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/
