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

[Robert H. <ha...@st...>]

sorry -- got buried during BCCE

On Mon, Aug 2, 2010 at 10:51 AM, Otis Rothenberger <osr...@ch...>wrote:

> 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?
>
>
Shouldn't be a problem.... done.


> 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/
>
>
Great. Why don't you see if you can contact them and suggest they give us a
direct link to the 3D mol file.
Also check that stereochemistry for bonds and atoms is working there.


> 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
>
>
>
>
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900