I would be tempted to try phenix.ensemble_refinement instead. Look at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949522/ or https://phenix-online.org/phenixwebsite_static/mainsite/files/presentations/ensemble_refinement_burnley_at_al_10DEC2012.pdf or https://elifesciences.org/articles/00311
Tassos On 6 Sep 2023, at 12:37, Matt Mcleod <mjmcleo...@gmail.com<mailto:mjmcleo...@gmail.com>> wrote: Hi, I should be a bit more specific. We have many crystal structures to indicate that a loop adopts conformation A and conformation B, or - the loop can be disordered where the electron density is washed out. These states are dependent on how we perturb the system. We have a series of data, as a function of osmolyte concentration, that adjusts this equilibrium and we want to put a numerical value onto it. Resolution is between 1.7 - 2.0 A. This is non-anomalous data but certainly would be helpful in the future to include if possible some anomalous scatters. Have been using phenix.refine. So what we have done is modeled both conformation A and B and are refining the data in order to get the occupancies (fixing B-factors) regardless of if there is electron density present for one of the two conformations since in some cases (likely all) there will be a population of both A, B, and disordered and the relative true occupancies will move. I am trying to sort out how accurate these occupancy values are as opposed to showing the electron density for each conformation fit at some common threshold. My general sense is that if it is modeled but no electron density, there will be a non-zero value and vice versa if it is the only conformation present it will be less than unity. I will take a look at the references! Very much appreciated. Matt On Wed, 6 Sept 2023 at 02:08, Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>> wrote: 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<mailto: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<mailto: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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://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 -- Matthew Jordan McLeod, PhD Post-Doctoral Fellow - Cornell University ________________________________ 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/
