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.
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)?
Just to see:
http://37.59.114.153/STdM/index.php/it/esercizi/disegnare-molecole-in-2d-e-3d
to draw some aromatic molecule and see how the 3D molecule is
displayed in JSMol.
If you have some further suggestion to improve how the molecule is
displayed, it would be nice for me to chenge my code to show to the
users better images.
Note that the site is still in final developing and the english part
should be totally revised ( it comes from automatic translation by
Google directly driven by Joomla) and some modification should be made
to introduce in the head the required javascript declarations, so the
english pages do not work properly at this moment.....
Many thanks to all for you help and advices,
Bye,
Pierluigi
Il sabato 27 settembre 2014, Brenton Horne <[email protected]> ha
scritto:
> Hi Angel
>
> Thanks for the tip; but I have looked up the connect function in the
> 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?
>
> Thanks for your time,
> Brenton
>
> On 27/09/2014 6:26 PM, Angel Herráez wrote:
> > Hi Brenton
> >
> > 1. If you edit manually the pdb file, you can add CONECT records for the
> > double bonds. But it is better -and more flexible- to use Jmol scripts
> (which
> > may be embedded in the pdb file or applied from within the page) with the
> > "connect" command. This allows to set partial and aromatic bonds.
> >
> > 2. Jmol has "calculate aromatic" and "connect aromatic". You may or not
> like
> > how they look, but it is the same idea as in your example.
> > You could also draw a ring inside the atom ring (cycle) to depict
> aromaticity;
> > that is not automatic, but a decoration you might build using the "draw"
> > command.
> >
> >
> >
> >
> >
> >
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