[phenixbb] phenix.mtriage output model-map

[joe.wilson2023]

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 <pafonine at lbl.gov> 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
>
>
>
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