Hi Max

Have you explored the "connect" command?

>From your last description, I think that might do what you want.
It's easy to select atom pairs by distance, and then you could "reconnect" 
them and apply color and thickness of bond

https://chemapps.stolaf.edu/jmol/docs/#connect

·
 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28871 Alcalá de Henares  (Madrid), Spain


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