Bob,
I like the no jitter approach, and I also enabled it on the model
editor. I had tried to do this on an earlier version on Jmol, and I
could not get it to work. The docs for 12.0 made it clear how to do this.
Sorry about that. The 3D to 2D thing was an attempt at humor. For our
model kit goals, user to user transmission of structures is important.
That's why I really liked your query string approach. To do that,
however, JME files are best. For "models" created in JME - no problem
with emailing with retention of stereochemistry. For a model engineered
by a student in the model editor, sending the model by email involved
first sending it from Jmol to JME - 3D to 2D. That's not the best, but
it makes for fast/easy transfer of Jmol models.
The best would be Jmol reading and writing JME files. That way
communication would be 3D to 3D both ways. Tom and I go way back with
the use of JME, and I just have a suspicion that Novartis is a factor in
JME going open source. I hope your suggestion toward this end meets with
success.
Yeah, I have to clean up documentation, including link help. Actually,
those little question marks on the editor screens are hover help links.
As you probably noticed, I tend to be verbose, and the biggest problem
may be that the hovers are too verbose. Maybe I should make the actual
link act as the hover trigger. I just don't like having a hover come up
in an application when all I want to do is click a link for action.
One more point: I ran across a note that you wrote about global Jmol
variables. This was very valuable in formation for me. Part of the
reason that I have so much written in a combination of JavaScript and
Jmol script is that I did not realize that a Jmol variable could have
global extent. This made binding conformation rotation to mouse actions
a breeze.
Otis
On 4/15/2010 6:56 PM, Robert Hanson wrote:
Otis -- by the way, I made the minimization "silent" automatically, so
you won't see the jittering in the latest version of Jmol. Are you
able to go 3D to 2D? I'm not finding that....
I suggest a title="..." attribute in those MM Load and MO Load
options. I have no idea what MM and MO refer to, but I'm guessing that
a quick tip would explain it. That goes for most of the other links.
People like to hover over a link and get a clue as to what it means.
Best way to learn -- better than "just click it" in my opinion.
Bob
On Wed, Apr 14, 2010 at 11:20 AM, Otis Rothenberger
<osrot...@chemagic.com <mailto:osrot...@chemagic.com>> wrote:
Ok, with a little help from Peter Ertl, I think I understand the
JME's 4
stereo bond rotation. Maybe this was all resolved on the group
exchange
previously, but I missed it if it was published.
The four stereo bond rotation will only work if it is relevant to two
attached chiral carbon atoms. For example, it works for:
http://chemagic.com/web_molecules/script_page_large.aspx?jme=7%206%20C%208.88%20-5.32%20C%204.03%20-5.32%20C%206.46%20-6.72%20Br%205.24%20-3.22%20C%207.67%20-4.62%20C%205.24%20-4.62%20C%206.46%20-5.32%201%205%201%202%206%201%203%207%201%204%206%201%205%207%201%206%207%201
The above uses Bob's newly invented email transfer of models via query
string. I just love it! On our site, the model loads into Jmol. On the
JME Draw screen, you can Depict it and play with it in JME. Sorry
about
not removing the hydrogens in the Depict. That's doable, but it's
a bit
buggy yet, so I'm still working on it. I should note, that the above
structure was created flat, so the sterechemistry represents what
Jmol's
jmeFile load decided to do with this flat structure.
If you cannot load the above structure it is 2-bromo-3-methylpentane,
which Jmol renders as (2S,3S)-2-bromo-3-methylpentane, at least on my
system.
Otis
--
Otis Rothenberger
chemagic.com <http://chemagic.com>
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Robert M. Hanson
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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
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Otis Rothenberger
chemagic.com
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proactively, and fine-tune applications for parallel performance.
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