There must be some place in the code to change it to always dashed, but somebody else would have to advise on that…
To have all hydrogen bonds start out dashed, after line 991 of <your Chimera>/share/FindHBond/base.py (which should be “pbg.lineWidth = lineWidth”) add:
pbg.lineType = chimera.Dash
with the same indentation as the preceding line. On a Mac, “<your Chimera>” will be Chimera.app/Contents/Resources.
—Eric
Eric Pettersen
UCSF Computer Graphics Lab