The reason the crosslinks command acts on pseudobonds is because it was for chemical cross-links between molecular structures where the crosslinks are pseudobonds and you of course want to distinguish the pseudobonds from the bonds in that case. So the crosslinks command works on pseudobonds because that is best for what it was intended for. While a command option could be added to allow it to work on bonds, it is messy because ChimeraX implements Bonds and Pseudobonds as different classes and the crosslinks code has places where it explicitly makes collections of Pseudobonds. Handling a mix of Bonds and Pseudobonds would be especially troublesome. Converting bonds to pseudobonds could be done with a Python script but the marker set code would not recognize the pseudobonds since it always links markers with bonds. So it is not a great solution to convert bonds to pseudobonds as then you would lose the capabilities that act on bonds. So I don’t have a great suggestion for you. This does seem like a poor design in ChimeraX.

On Mar 2, 2019, at 7:20 AM, Jun Ha Song <junhasong@berkeley.edu> wrote:

Dear RBVI,

I want to use few command lines that are exclusively available for pseudobonds. The problem is that my model is consisted of markers and links, and there seems like no possible way for me to simply transfer bonds into pseudobonds.

What commands like crosslinks histogram provide seems way to good for it to be limited for pseudobonds only. Is there a technical reason why such command is only applicable with pseudobonds? Can commands in Chimera/ChimeraX that work with pseudobonds easily be adapted to work with bonds, or is that too much of technical difficulty?

If it is not feasible, is there a way to turn bonds into pseudobonds?

Best,
Junha Song.
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