[phenixbb] phenix.mtriage output model-map

[Pavel Afonine]

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 <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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