Hi Andrew
> 1. What are the default values and typical values for:
>
> bondTolerance
> minBondDistance
Type "show state". There you will find the current settings.
I am seeing as default:
set autoBond true;
set bondTolerance 0.45;
set minBondDistance 0.4;
> 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)?
In general terms (if there's an exception it should be clearly indicated),
"decimal" values in
Jmol are always angstroms. "Integer" are pixels or some other unit relevant to
the specific
command.
> 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.
I see this unlikely, but I'm no expert in Java. And if that's the only thing
you changed...
You might post an example of molecule file so we can check.
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