Bob,
With 12.1.4_dev the SMILES and compare issues have been pretty much
resolved:
1) A Jmol stereo SMILES submitted as input to the NIH translate site
now returns a molfile identical to the submitted model - i.e. no more
inversion.
2) smilesFromJmolMod1.find('SMILES',smilesFromJmolMod2) wo
Tom, the updated applet is now in
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
You can now indicate slab and polymer unit cell information on the LOAD
line, and you can also give unit cell vectors instead of a b c alpha beta
gamma information.
see http://chemapps.stolaf.edu/jmol/
Otis, the updated applet is now in
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
"compare" examples can be found at
http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm
On Mon, Aug 9, 2010 at 10:00 AM, Robert Hanson wrote:
> Otis, it will take some getting used to and some
Hi Wayne,
Can you explain a bit more how the conversion STATE->jmol script
conversion works? is this tool open source?
Andreas
On Sun, Aug 8, 2010 at 1:24 PM, Wayne Decatur wrote:
> Hi Andreas,
> I would posit that Proteopedia makes it possible to what you suggest
> presently. If you use the s
Geoff,
Terrific!
Be sure to add your site to the Jmol Wiki page
http://wiki.jmol.org/index.php/Websites_Using_Jmol
Bob Hanson
On Tue, Aug 3, 2010 at 2:38 PM, wrote:
> Dear Jmol users,
>
> In collaboration with Dr. Nicholas Provart at the University of
> Toronto, I have implemented the Jmol w
Perhaps. But really I suspect it's something different. The isosurfaces
should be completely different objects -- they are initiated independently
and then merged at parallel function exit.
I'm headed in to where my MacBook is now.
On Mon, Aug 9, 2010 at 6:00 AM, Charles Shubert wrote:
> Hi Bo
Otis, it will take some getting used to and some careful documentation, but
I think you will find this SMILES/SMARTS "find" business extraordinarily
useful. It is a bit tricky.
On Mon, Aug 9, 2010 at 9:35 AM, Otis Rothenberger wrote:
> Bob,
>
> I noticed that the return was either an array of a
Bob,
I noticed that the return was either an array of all of the atomIndexes
or null. The Boolean return for the statement was "on" or "off."
I picked up on the fact that the find was not associative from your
original discussion of the Jmol SMILES applet. I have to admit that I've
been appro
Hi Bob,
Sounds like the conference was a success.
As I noted in an earlier email, I'm generating the script and I don't exactly
know when a particular script will be generated, so I then to sprinkle extra
"subset"s and "select"s around to make sure that I know the selection state
when I send a
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