Hi Chase, It’s principally because ChimeraX has to work with structures lacking explicit hydrogens, and so while it knows the valence of each atom. it doesn’t necessarily know the order of a particular bond due to tautomerism. Also, some bonds may have a non-integral order, e.g. aromatic ring bonds or carboxylates. It can also be tricky to orient the multiple lines, e.g. you may want to orient the double/triple bonds orthogonal to the view direction whereas you would want non-integral bonds to lie in the relevant plane, unless there isn’t one (e.g. phosphates)!
Anyway, it’s kind of a headache, which is why we haven’t done anything about it so far. Certainly something could be done, at least for fully protonated structures, but ChimeraX lacks so many features that we do know how to implement and implement well that we haven’t been motivated to add ones where we’re not even sure what we would do…
—Eric
Eric Pettersen
UCSF Computer Graphics Lab
Dear ChimeraX,
I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms.
Thank you, Chase Smith
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| | Chair, Department of Pharmaceutical Sciences & Associate Professor of Medicinal Chemistry | | School of Pharmacy | | MCPHS University |
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