On 10-9-2006 11:50, Bob Hanson wrote: > I think this is out of my league. > > I don't think it is the job of display programs, such as Jmol, to try and calculate things as complicated as H-bonding. This "bonding" should be calculated externally and then encoded into the input file explicitly so the display program just needs to turn it on or off. If Jmol wants to become a full-fledged structure-editing program then that is a whole different story. But, deciding what is and isn't a "bond" is quite non-trivial and when you are dealing with things, such as protons, you can't even "see" (crystallographically) it gets even trickier.
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