Hi Ketul, CCmask evaluates the cross-correlation between your experimental map and the map that is calculated from the model. If you look at the formula, the map calculated from the model involves, among other things, atomic coordinates, B factors, and occupancies. This means that even if the model visually appears to fit the experimental density, but its occupancies or/and B factors are incorrect (e.g., not refined), then the CCmask can be very low.
I can try to help more if needed, but since this is going to be more Phenix specific (and this is the CCP4 mailing list!), I'd prefer to do it either off-list or on phenixbb. All the best, Pavel On Tue, Jan 9, 2024 at 9:57 PM Ketul Saharan <ktsaharan1...@gmail.com> wrote: > Dear CCP4 community, > > I am building a structure model from ~3.0 Å resolution cryo-EM map. The > structure consists of seven chains, with each chain containing an N-, > middle, and C-terminal domain. Although I attempted to directly fit the > Alfa-fold model, it became evident that the protein exhibited some > movement, leading to poor fitting of N-terminal. To improve the fitting, I > segmented the alfa-fold model into two parts: i) the N-terminal and ii) the > middle and C-terminal domain. These fragments were then fitted into the > map. After a few rounds of refinement using coot and phenix, the model > effectively fitted all seven chains. > > The refinement resulted in a model to map correlation (CC mask) of over > 60% for the N-terminus. *However, even though the model appeared to fit > well inside the map, particularly in the middle and C-terminus regions, the > refining consistently resulted in a map to model correlation of 0%.* > > For your perusal, I have included the snapshot of the phenix refinement > results, the correlation graph, and the fitted model within the map > (displaying one chain out of seven). > > I am not able to figure out why the correlation is so poor even after fine > fitting of model to map. > > Any support in resolving this issue would be much appreciated. > > > Thank, > > Ketul Saharan > > > > -- > > Ketul Saharan > > Senior Research Fellow (Ph.D. Scholar) > > Laboratory of Macromolecular Crystallography (Lab-8) > > Institute of Life Sciences > > Nalco Square, Chandrasekharpur > > Bhubaneswar – 751023 > > Odisha State, INDIA > > > > Phone: +91 8708290889 > 124.png > <https://drive.google.com/file/d/1qYE_ge1M99zbkUt_g4JF3bNfEyDUelkS/view?usp=drive_web> > correlation.tif > <https://drive.google.com/file/d/1bogOk15bImYXSLCPcnrUfC9gRH0cGame/view?usp=drive_web> > map to model.tif > <https://drive.google.com/file/d/1y-QXMOwWslOTg2PRjS91PFf-gh1obiEt/view?usp=drive_web> > > ------------------------------ > > 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/
