Hi,

additionally:

- If you want an exact map (not a finite-resolution Fourier map), use:

phenix.model_map model.pdb scattering_table=electron

- We are close to making a multipolar model available for density calculations, which—if I understand correctly—is what you need to simulate Coulomb potential maps. This feature is not yet available to general Phenix users, but if you send me the model off-list, I can generate and send the map back to you.

Pavel

Ostensibly, all you need to do is run phenix.fmodel with scattering_table=electron .  And perhaps try to come up with what k_sol should be for the bulk solvent density.  There are caveats, of course, not the least of which is that, last I checked, the modified scattering from formal charges like ions vs neutral groups is not implemented.  I don't actually know of a program that handles things like charges. I've heard rumors that someone was working on full QM calculations of electrons moving through matter to try and get this "right", but I have not heard about any progress for some time.

Sorry can't be more helpful,

-James

On 4/2/2025 4:52 AM, Ricardo Righetto wrote:

Hi,

Apologies if I'm missing something obvious, but I was not able to find this in the documentation: is there a PHENIX tool for simulating Coulomb potential maps (aka "cryo-EM maps") from atomic models?

I'm looking for something like the molmap command in ChimeraX, but more accurate. One such alternative is the simulate program from cisTEM, but I figured PHENIX might also have something?

Thank you!

--
Ricardo Diogo Righetto

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