@Brenton,
> user guide and I don't know how [atom-expression] and [bond-type] is
> meant to look like for my example. My current example is metamizole and
> I'd like a double bond to go between C17 and C18, any idea what code I'd
> have to use?
That would be like
connect (C17) (C18) double
or maybe
connect (atomno=17) (atomno=18) double
@Pierluigi,
Aomatic is tricky to deine properly. Jmol has "calculate aromatic", but you
need to experiment; I don't think it can be used automatically for any
molecule with success.
Another isuue is the location of the dotted bond: it does not always come in
the inner side of the ring. You can change whatever default arrangement you
get, but it has to be done per case.
> In effect, it would be interesting to set up JMol to use aromatic
> character as a default when it has to work with organic structures.
How would you define that you have an organic structure?
> When I use it in the classical way, receving the molecule from JSME
> through a call to an external server (NIH server), the 3D model shows
> the double ond sof benzene as common double bonds. Is there a way to
> set up by which the aromatic rings can be displayed in a way that can
> show immediately that the are aromatic (i.e. with an "internal" double
> bond with respect to the ring)?
Try the above "calculate aromatic" and/or "connect .... aromatic"
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