Wonderful, Bob!
The newest applet is working very well.
Something funny but very sound:
go to
http://biomodel/Jmol/minimize/minimize.htm
Load the 2D caffeine, then click minimize several times until it stabilizes;
note the sp3 nitrogens
Now click on "recalculate aromaticity" and repeat several minimizations;
the N come now sp2. Great! Jmol really knows how!
For thyroxine it works pretty well on the first go, better after more
minimization cycles.
Tripalmitine takes time, but is working much better too (some of the
hydrogen pairs in each methylene group tend to stay together for a while).
A message in the console when minimization has ended would be useful.
And how about a clock cursor while it is running (as happens for isosurface
calculation) - I can see it running in the CPU monitor, as with isosurfaces.
This is very exciting!
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