Hi,
The Jmol extension now has simple tags for loading molecules directly with a
SMILES string or a PDB code.
Examples are available at
http://wiki.jmol.org/index.php/MediaWiki/Basic_Example
Nico
2010/11/23 Angel Herráez <angel.herr...@uah.es>
> Nico,
>
> > Can Jmol show a molecule having just a SMILES string ?
>
> Yes, Jmol can do it, but
> 1. it relies on an external server being available (it does the calculation
> from smiles to 3D)
> 2. we need the signed applet for that (which is a concern for WP, since the
> Java security
> warning to load the signed applet may deter users)
>
> > If so, what are the commands that need to be executed ?
>
> load "$CCCNC"
> /the quotes may be omiited is the string is not conflictive)
>
>
> > I think we could add a syntax for Wikipedia where a user would simply
> have to add something like
> > <smiles>XXXX</smiles> todisplay the molecule in Jmol.
>
> Maybe, to display a link that will open a popup or insert a DIV with Jmol
>
>
> > Also, can Jmol retrieve a molecular file using only an identifier (like
> getting the molecule on the
> > pdbdatabase) ?
>
> Again, yes. From the PDB server using the PDB 4-character ID.
> Same concerns: signed applet, external server.
> Syntax is
>
> load "=1CRN"
>
>
>
>
>
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