ChimeraX can now find hydrogens bonds. The “hbonds” command is very similar to the same command in Chimera 1. The principal difference is that since ChimeraX uses cylinders instead of lines to depict the hydrogen bonds, the “lineType” and “lineWidth” keywords have been replaced with “dashes” and “radius” (and the hydrogen bonds are now dashed by default). Full details are available with “help hbonds” or at this link:
Unfortunately, the hydrogen bond computation is also slower than in Chimera 1. We are working on that.
—Eric
Eric Pettersen
UCSF Computer Graphics Lab