Hello Ian
I'm sorry to say that I have no experience with CIF files. That ? character is
quite a bad
choice.
I had a similar problem once with PDB files having * in their atom IDs, and
solved it using
? as the wildcard. Not usable for you ;.(
Regarding your javascript method, the problem of javascript running ahead of
Jmol
loading is frequent. In my experience, the only safe solution is to have Jmol
call the
javascript, and to include that call in the jmolApplet() call itself.
So, it could be something like
jmolApplet(300, 'load myFile.cif; javascript "parseAtoms()"; ')
and have this javascript:
function parseAtoms()
{
var atomList = jmolGetPropertyAsArray("atomInfo", "all");
(etc.)
return ...whatever Jmol script commands
}
The JS function should return a string with the Jmol script
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