I've found this weird problem with jmolLink when using FFox 3+ (3.6.15)
on Macintosh Snow Leopard (10.6.6). The same problem has been around
for a while and the recent Java security update has no effect on it.
If the .spt file has underscore on it, the loading with jmolLink
fails with the
Please make a demo page and send us the link as well as submitting a bug
report to both Bugzilla and Java.
Q: If you rename your script file some_script.txt, does it work?
Q: Does the console history indicate the proper name of the file?
Q: Can you see the file using (from the Jmol console)
Speaking of public databases, this might be a time to test the facility that
has been in Jmol for quite some time -- the ability of the UNSIGNED applet
to access remote files via a JavaScript interface. I don't think anyone has
capitalized on this, but there is a St. Olaf server that is built into
Dear All:
I think the vibration animation state is being left out of the Jmol generated
state script for versions of Jmol 12.0.26 and above (may have started earlier).
Can others please verify that when they save a state script for a molecule
that is showing an animation of the vibration and
Two items concerning communication with Jmol caught my attention.
this one (Continuing Saga of Jmol Talking to Public Databases)
and Command line communication with the Jmolapplication?
I'm not sure if it is really relevant to the method that I'm using.
I'm using visual basic (VB) as a front
Jonathan,
I'm using 12.1.35. With the cyclohexane chair flip, running the captured
state seems to be starting the animation at the frame captured.
I don't think the state script will pass list size limits. I'll send it to
you as an attachment for comparison to your state script. I tried to
Michael,
OK, you definitely have my attention. Communication between Jmol and local
applications is a great idea. I have a few questions:
1) Are you doing this with the applet or the application?
2) It sounds like you are currently talking to Jmol with your VB code
independent of traditional
Oops, Jonathan is talking about vibration on not animation on. I
misunderstood the request. He definitely needs more checkers on this. I'm
may have an appropriate SPARTAN file. If so, I'll check it.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL
I assume the applet. Bob Hanson can explain the details. I've not yet
written any scripts - I treat them as a black box, and make the minimum
changes to make it work.
My SeqViewprogram is meant to be a help to protein engineers. The
demo for globins is at:
On Tue, Mar 15, 2011 at 11:56 AM, Otis Rothenberger
osrot...@chemagic.comwrote:
Bob,
I think we still run into the cross domain security violation with the St
Olaf server.
Nope - no cross-domain server issues with JavaScript servers. Just HTML
servers. Could be odd browser issues -- that's
Hi, Michael. It's been to long for me to remember what the problems were in
direct communication with the browser window from VB.
--
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
So, Otis, what I am wondering about is whether you would allow us to add
jmolLoadAjax_STOLAF_NIH
to Jmol.js. It would allow any applet (or knowledgeable user on any applet's
page) to load any of the NIH models into Jmol directly, without need for the
signed applet. You can try this yourself for
Fixed for Jmol 12.1.40 and 12.0.37
On Tue, Mar 15, 2011 at 8:23 AM, Jonathan Gutow gu...@uwosh.edu wrote:
Dear All:
I think the vibration animation state is being left out of the Jmol
generated state script for versions of Jmol 12.0.26 and above (may have
started earlier). Can others
(it got broken in 12.0.RC6)
On Tue, Mar 15, 2011 at 8:23 AM, Jonathan Gutow gu...@uwosh.edu wrote:
Dear All:
I think the vibration animation state is being left out of the Jmol
generated state script for versions of Jmol 12.0.26 and above (may have
started earlier). Can others please
Bob,
Sure, add it. It's a powerful resource.
I looked at Jmol.js jmolLoadAjax_STOLAF_RCSB(). I get it now. I didn't know
you could do that.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
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