Hi Matt, I guess that the datasets have the same spacegroup and very similar cell parameters?
And that you have two similar models that you obtained by refining against the datasets? What you can do is to find out which dataset gives the better model, and is therefore better (i.e. generally more useful - but maybe not in every place of the e.d. map). To arrive at this conclusion, use the two models for a paired-refinement-type of comparison, i.e. a) note Rwork_AA,Rfree_AA of model A (obtained by refinement against dataset A) b) note Rwork_BB,Rfree_BB of model B (obtained by refinement against dataset B) c) rigid-body-and-overall-B refine model A against dataset B to obtain Rwork_AB,Rfree_AB d) rigid-body-and-overall-B refine model B against dataset A to obtain Rwork_BA,Rfree_BA e) if Rfree_AB < Rfree_BB then dataset A is better than dataset B (and conversely) f) check the result of e): if Rfree_BA > Rfree_AA (and conversely) then this confirms the result from e) Hope that this at least is a step towards the insights you're after! Best, Kay On Fri, 14 Jun 2024 15:58:41 -0400, Matt Mcleod <mjmcleo...@gmail.com> wrote: >I should clarify. I am mostly concerned about the electron density map. > >I want to make sure that I can most closely compare the maps from two >different quality structures, rather than the datasets themselves via CC1/2 >or other metrics. This is more so for interpreting structural changes. > >For example, if there is sparse density for some particular thing >indicating partial occupancy, how can I compare those two maps. So for >low-resolution datasets, maybe there is less density but is that because of >data quality or because in that dataset there is a lower occupancy through >some meaningful structural change (compared to higher resolution/better >data)? > >On Fri, 14 Jun 2024 at 14:16, Matt McLeod <mjmcleo...@gmail.com> wrote: > >> Hi all, >> >> I am wondering what the best practice is to compare datasets that are of >> the same protein but different quality, for instance 2 vs. 3 A. >> >> I know that truncating the structures to the same resolution bin is >> alright, but the data quality in the lower resolution bins are also not the >> same. Is there a way to "inject" noise into the data such that the bins >> are more similar? >> >> These datasets cannot be recollected at higher resolution since they are >> collected at increasingly high pressure, and the resolution change is >> anticorrelated with the pressure; no way to get around crystal stability. >> >> Any suggestions are 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/ >> > > >-- >*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 > >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 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/
