[Jmol-users] Three related points: JME Question, IU SMILES note, NIH SMILES note

[Otis R. <osr...@ch...>]

Bob,

JME automatically creates a bromonium ion (and other onium ions) when it 
is chemically logical. When this ion is transferred to Jmol, it is 
rendered as the Unknown atom, Xx. The problem is really any three 
character string ion created by Jmol (e.g. Cl+). I can script around 
this, but script around is another term for work around, and I know 
that's a term you do not like. Is this problem addressable inside Jmol?

By the way, I notice that the IU 2D to 3D SMILES site is up again. It 
has been down for a while. There has been one significant change. An 
unreadable SMILES returns and empty molfile. This allows graceful error 
message scripting.

The NIH SMILES translator, a new discovery for me, is incredible:

http://cactus.nci.nih.gov/translate/

I can pass a Jmol SMILES to it directly and get the 3d molfile return, 
but an intervening NIH page prevents direct loading into Jmol. Still the 
site produces a quality 2D to 3D translation with lightning speed.

The ability to keep track of a stereo SMILES in an evolving Jmol model 
kit model was a wonderful addition to Jmol.

Otis

-- 
Otis Rothenberger
chemagic.com