Hi Pavel,
Thank you for your information.
I had a try with the cmd you suggested and I did get the mtz file.
While trying to use the mtz to get a real space map, I tried with
"phenxi.mtz2map model.cif.mtz"
Available map coefficients in this MTZ file:
['FMODEL,PHIFMODEL'] (skipping, add include_fmodel=True to include)
No model input - will output map(s) in unit cell.
After adding includ_fmodel=True. It gives the CCP4 map but it is not a real
space model-map as expected.
I may not get the right way to do this. Need further help.
Many thanks,
Joe
On Sat, Jan 20, 2024 at 5:07 AM Pavel Afonine
Hi Joe,
I am new to Phenix and using the phenix.mtriage to get the map-model FSC results. It gives the correct results at the same time I also want to produce the mode-map used for the FSC calculation. Is there an option for this? If not how can I reproduce the same model-map with another phenix command?
at the moment phenix.mtriage does not have an option to output the model-generated map. However, you can get such a map using a different Phenix tool (in the command line). Example:
phenix.fmodel model.pdb high_res=3.2 scattering_table=electron
where model.pdb is the file with your atomic model, high_res specifies resolution of the map, and scattering_table tells to use electron form factors.
This will produce an MTZ file with the Fourier map that is calculated as described in Section 2.1.1. here:
https://pubmed.ncbi.nlm.nih.gov/30198894/
Pavel