[chimerax-users] Selecting atoms outside (or inside) a density map's contour

[Mateusz Dobrychłop]

Dear ChimeraX Team,

I'm a structural bioinformatician working on my PhD thesis. I've been a long time user of Chimera, and I'm now using ChimeraX to create figures for my dissertation. I genuinely love both programs. Thank you for creating them.

I found myself stuck trying to perform one operation in ChimeraX that is very easy to perform in Chimera.

What I'm trying to do is select (and color) all atoms of an atomic model, that are located outside of a density map's contour.

In Chimera, I was able to just select the model and use the shortcut "ac oa" and that was it. Unfortunately I am not able to find a way to do that in ChimeraX.

I even tried to select the atoms in Chimera, then save the selected atoms as a PDB file, and then the inverted selection as a separate PDB file, and then open the two files in ChimeraX and color them separately. This could even work for a full atom representation, but does not work well for ribbon representation. That said, if the solution to my problem could be to somehow transfer the list of atoms that are outside the map from Chimera to ChimeraX, that would work for me as well.

I will appreciate any tips and suggestions!

Kind regards,
Mateusz
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