Dear Miha, On beamline I23 at Diamond, we can collect above and below the absorption edges of both Tb and Ca. It would be quite an easy experiment to collect data above and below the Ca edge, generate anomalous difference Fourier maps from each and look at the difference between them. This would allow you to determine how much of your anomalous signal is coming from Ca vs Tb, which could help in revealing the occupancy.
Feel free to contact me off list if you'd like to discuss further. Best, Chris Christian Orr Beamline Scientist - I23 Diamond Light Source Harwell Research and Innovation Campus Fermi Avenue Didcot, OX11 0DE 01235 56(7435) ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Miha Pavšič <miha.pav...@fkkt.uni-lj.si> Sent: Thursday, March 6, 2025 14:50 To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Alternative ion occupancy refinement (anomalous) [You don't often get email from miha.pav...@fkkt.uni-lj.si. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Dear Eleanor and John, Thanks for suggestions! Unfortunately the resolution is not 1.3 Å, this was the wavelength used (and where Tb gives a quite good anomalous signal), resolution is approx. 2.4 Å. It seems that the group refinement did the trick (each group composed of one Tb and one Ca at the same site), plus distance restraint to keep the alternative ions at the same spot. The anomalous map was used to estimate occupancy of Tb, indeed. Still some other work to be done on the model, though. The anomalous map (yellow on the attached screenshot) of course nicely reveals different Tb occupancy for the two sites. Kind regards, Miha On 2025-03-05 16:05, John R Helliwell wrote: > Dear Miha, > This paper, weblink just below, I imagine will be of interest to you for such > a case of occupancy estimation involving shared metals, in this case zinc and > gallium:- > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjournals.iucr.org%2Fpaper%3Fhw5009&data=05%7C02%7Cchristian.orr%40DIAMOND.AC.UK%7C0b3920231ecd49c913c008dd5cbe50f6%7C9d27ba7401004d0d81ff1d728dae8df6%7C0%7C0%7C638768694704557708%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=yHx0oq82re3uqe5oUJyUla6G65RviFtfFN%2BwS6Y90Ws%3D&reserved=0<https://journals.iucr.org/paper?hw5009> > > <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjournals.iucr.org%2Fpaper%3Fhw5009&data=05%7C02%7Cchristian.orr%40DIAMOND.AC.UK%7C0b3920231ecd49c913c008dd5cbe50f6%7C9d27ba7401004d0d81ff1d728dae8df6%7C0%7C0%7C638768694704575717%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=olun3BS0GLUVT8npjeKCrPXzsfxUxnppnq4GLMkTkGA%3D&reserved=0<https://journals.iucr.org/paper?hw5009>> > If you want uncertainty estimates too then JANA software gave them. > Best wishes, > John > > Emeritus Professor John R Helliwell DSc > > > > >> On 5 Mar 2025, at 13:07, Miha Pavšič <miha.pav...@fkkt.uni-lj.si> wrote: >> >> Dear all, >> >> I have a question regarding alternative ion occupancy refinement (anomalous). >> >> We are working with a dataset from a metal ion binding protein with two ion >> binding sites, one predominantly occupied by Tb(III), the other by Ca(II). >> Dataset contains anomalous signal, collected at 1.3 Å wavelength. The >> expected occupancy (Tb+Ca) at each of the sites is believed to be 1 or very >> close to 1. I am wondering if it is possible to somehow refine >> (phenix.refine) using anomalous data a model with two alternative ions at >> each site (i.e. Tb and Ca), or just place the predominant one at each of the >> two sites and call it a day? >> >> Any hints much appreciated! >> >> Best regards, >> Miha >> >> -- >> Assoc. 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