Low tech but simple. Exclude both conformers from the refinement. (set occs to 0.00 so you still see the coordinates in COOT) Look at the difference map density and make a rough estimate of occupancy from peak heights for a "fixed" bit of the conformers..
The relative ratios for different states should show up... Eleanor On Wed, 6 Sept 2023 at 11:49, <a.perra...@nki.nl> wrote: > 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> 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> 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> 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 >> > > > -- > *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 > ######################################################################## 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/
