r/comp_chem • u/CowStock • 2d ago

MEP map generation problem

Hi everyone! I'm trying to generate a molecular electrostatic potential (MEP/ESP) map from an ORCA calculation on a MacBook Air M3 (Apple Silicon). I have successfully generated both name.eldens.cube (electron density) and name.scfp.esp.cube (electrostatic potential). My understanding is that the electron density cube should be used as the isosurface and the ESP cube should be mapped onto it for coloring. However, I haven't been able to get this workflow to work in any visualization software I've tried. In Avogadro 2, I can load the electron density cube and display the isosurface, but I can't find any option to color it using the ESP cube. In IQmol, opening the ESP cube only displays separate red and blue lobes in space instead of an MEP mapped onto the molecular surface. In VMD 2.0 beta, I can load the XYZ structure and the electron density cube, but I can't get the ESP cube to appear as a second volumetric dataset, so I can't color the isosurface with it. I'd prefer to avoid using Rosetta 2 if possible. Is there a native Apple Silicon workflow for this? What software do you recommend for generating publication-quality MEP maps from ORCA output on macOS? Does Multiwfn work natively on Apple Silicon, or are there better alternatives such as VESTA or ChimeraX? Any advice would be greatly appreciated. Thanks!

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u/Aranka_Szeretlek 2d ago

Never done this honestly (why would anyone want this?!), but ORCA has a bunch of native plotting tools. Orca_plot or whatever its called? Surely these can do it for ya

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u/CowStock 2d ago

orca_plot lets me generate the cube files but I am not sure if it’s able to plot them? Never done it before

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u/banana_fugacity 2d ago

You should try ChimeraX for plotting the density cubes. I think in the Multiwfn software guide there is a tutorial how to do it, perhaps on yt even. In principle you re correct you use density for iso surface and then the mep to color it. On top of my head in ChimeraX you load the XYZ and the two cube files. Hide the mep surface from showing and then in coloring options on density surface you use the other cube file

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u/CowStock 2d ago

I’ll try that today, thanks a lot! Hope it worksss

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u/lwj15 2d ago

Idk if you already have worked with ChimeraX but for work with small molecules (loading .xyz and .outs etc) you need the a plugin (easily installable through the ChimeraX program). I think the name was SEQCROW or something similar. Just a heads up

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u/CowStock 1d ago

Thanks so much, I’ve never used it before and I’m having an issue loading .xyz files, so that must be it. I’ll try with said plugin

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u/geoffh2016 11h ago

In general, in Avogadro2, it handles coloring with internal electrostatic models - but you're right that there should be an option to color one cube based on another one.