I Am thinking about this problem re a set of four carbohydrate binding proteins - all isomorphous but with different Ligands and weird solvent features.. first task was to get all sets with same indexing convention! (SoacegroupP65) That can be done at the data processing stage by giving one as the reference set. Then I wanted all the models to be on the same origin and symmetry to make comparisons easier. You can do molecular replacement fir each then use the task “match model to reference” but it is easier to just start refinement with the basic first model then correct and refine the new one as the maps indicate.. maybe it is enough then to just look at all naps in COOT together but I want to do an Fobs1 - Fobs2 difference map.. There is a ccp4i2 task to compare datasets using scaleit to match them. That gives useful analysis of differences and then If you have calculated phases for your best model then you can do such a difference nap. It certainly shows up features which I expect to be different However there seems to be a bug in the cmapcoeff version for this.. The old *fft* script in ccp4i works OK with that input. Eleanor
On Sat, 15 Jun 2024 at 13:53, Jon Cooper < 0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > Comparing maps sounds justi. A like the sort of thing the Uppsala suite > did. Maybe you can find an old binary for mapman or mapman2(?) or compile > it from Martin Winn's github page. The closest I can find is EDSTATS which > I think is in the old ccp4 gui. > > Best wishes, Jon Cooper. > jon.b.coo...@protonmail.com > > Sent from Proton Mail Android > > > -------- Original Message -------- > > On 14/06/2024 20:58, Matt Mcleod 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 > > > ------------------------------ > > 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/
