Hi everybody,
Inversely to what Pavel wrote, just if you want to get a limited-resolution map of the Coulomb potential (and not anything else), eventually with a resolution that varies over the map
regions, Section 5.2 of the manuscript
https://arxiv.org/abs/2412.14350
exactly explains how to do this. I guess, if this critical, Phenix teams can routinely add such an option.
With best wishes,
Sacha Urzhumtsev
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
On 4/2/25 10:52, James Holton wrote:
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:
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?
--
Ricardo Diogo Righetto
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