Hello Johannes As you may know, H-bond calculation in Jmol is limited to certain situations (mostly proteins) and has evolved (expanded) during the last years.
I am not sure about your problem, first I thought it may be related to the file format not being pdb. But since you say that you can do it from the console, then it may be some kind of bug. Maybe there was a former limitation that has been removed in the script processor but not from the menu generator. Bob Hanson will be able to tell you. Anyway, have you tried with a pdb file, to see if there is a difference? I remember using the popup menu for calculate, so the ability is there.
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