Angel is correct. So that we are not comparing apples and oranges here,
my Jmol load from JME is loading the JME file. This is important to note
because way back when this 2D ---> 3d transition started, JME was the
only player. In helping me with this, Bob optimized the transition for
JME files directly. SMILES ---> 3D in Jmol came later.
The reason that the initial focus was on the JME files is that they
contained the stereo information that Bob needed to do some initial z
axis shifting prior to UFF. As things developed, I simply stayed with
the JME file load, and there is a direct pathway for these to load built
into Jmol by Bob.
I do some tweaking on my end after load. If you want to see an
un-tweaked (pure Jmol) load of a JME file, draw a structure using our
model kit, go to the Edit screen, and run the following JavaScript:
~jmolScript('var mod="' + '' + document.getElementById(jme1).jmeFile() +
'";load "@mod"')
http://chemagic.com/web_molecules/script_page_large.aspx
Tilde is required! What you see is pure Jmol loading a JME file from the
JME editor. It's probably not relevant in this discussion, but don't
forget that Resolver will do a SMILES ---> to JME file translation.
Otis
Otis Rothenberger
chemagic.com
On 7/26/2011 2:23 PM, Angel Herráez wrote:
> (Sorry, I'm away on holidsya and can't follow this as closely as I would like)
>
> Paul, I think that all my sketcher pages use MOL format for transfer to Jmol,
> while Otis' JME
> is probably using either SMILES or JME strings. That's likely the cause of
> the diiferent
> behaviour with planar 3-substituted carbons (which I have observed regularly
> too; happy to
> see there are better ways to convince Jmol now to add that H)
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Magic Quadrant for Content-Aware Data Loss Prevention
> Research study explores the data loss prevention market. Includes in-depth
> analysis on the changes within the DLP market, and the criteria used to
> evaluate the strengths and weaknesses of these DLP solutions.
> http://www.accelacomm.com/jaw/sfnl/114/51385063/
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------------------------------------------------------------------------------
Magic Quadrant for Content-Aware Data Loss Prevention
Research study explores the data loss prevention market. Includes in-depth
analysis on the changes within the DLP market, and the criteria used to
evaluate the strengths and weaknesses of these DLP solutions.
http://www.accelacomm.com/jaw/sfnl/114/51385063/
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