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 https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html 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
Hi Ricardo, Maybe have a look at this example here: https://cci.lbl.gov/docs/cctbx/script_1/ Someone else could possible tell you how to tinker with the CCTBX scattering registry to achieve coulomb potential map rather than an electron density map. Rob
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 https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html 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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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:
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 https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html 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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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
De : Pavel Afonine
participants (5)
-
Alexandre OURJOUMTSEV -
James Holton -
Pavel Afonine -
Ricardo Righetto -
robert＠oeffner.net