Has something changed recently with defaults related to "autobond." Ball
and stick structures that were fine in the past seem to end up with nearly
every adjacent atom being bonded to each other (i.e. hydrogens bond to their
carbon as well as to each other) .
Questions:
1. What are the default values and typical values for:
bondTolerance
minBondDistance
and most importantly, what are the units for these (I was surprised the docs
described these as "decimal" as opposed to decimal in angstroms or something
else)?
2. Have later versions of Java possibly caused a change in how these
parameters are initially set? We've been running with a frozen version of
Jmol on our website and just noticed problems with methyl groups. Since our
code and data have not changed, Java update seem like the only source of
changes.
--Andrew
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