Hi Joe, it looks like you did everything just right.. So I'm not sure what you mean by "It gives the CCP4 map but it is not a real space model-map as expected.". What makes you think this is not a real-space model-calculated map? It should be, it is expected to be.. Pavel On 1/22/24 01:53, joe.wilson2023 wrote:

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 wrote:

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