Dear Jmol users,
I can display the following applet: http://jmol.sourceforge.net/demo/atoms/
under windows xp(firefox) linux(fedora 12, 64 bits; firefox 3.5.10)
without any problem.
Now when create my applet (very basic) using caffeine.xyz @
Hi,
This sounds like the same error that I had recently on Fedora 11. It
comes with OpenJDK by default but you need to uninstall that and
install the one from Sun, along with the associated plug in for
firefox. Please see my most recent post, and/or you might have to ask
your IT Support for help
Matthew Betts wrote:
Please see my most recent post, and/or you might have to ask
your IT Support for help (I found it a bit tricky anyway).
That's now also at
http://wiki.jmol.org/index.php/Troubleshooting/Applet#The_applet_is_di
splayed.2C_other_problems
I gave something along the following a try using 12.0.RC27_dev (signed applet)
isosurface laplacian cutoff 0.2 sign C5_lap.cube;color isosurface
translucent;write C5.idtf;
and it produced a .idtf and a .idtf.tex file of non zero length. But they were
very small (4k/8K) and looked empty to
Henry, it's a long time since I did my small contribution to
exporters and so don't remember well the support (well, in fact I did
not work on idtf export, only vrml and x3d), but I did one molecular
isosurface the other day, so they must be supported. Maybe it's
related to size.
Rzepa, Henry h.rz...@imperial.ac.uk a écrit :
I think that conversion to eg .idtf only works on certain models,
and perchance not on surfaces?
oh no; in slide no 8 of http://vdlee.free.fr/cyclo_jmol.pdf you will
find two iso-surfaces created by an export to a .idtf file
For what its
Please send all trouble cases to me if you can. Some sort of bug -- unless
it's really just a memory issue. Still...
Bob
On Fri, Jul 23, 2010 at 8:43 AM, avder...@univ-montp2.fr wrote:
Rzepa, Henry h.rz...@imperial.ac.uk a écrit :
I think that conversion to eg .idtf only works on
try
jmolInitialize(../jmol, JmolApplet.jar);
just to see if the implementation of Java is having problems with
progressive class loading.
On Fri, Jul 23, 2010 at 7:15 AM, FyD f...@q4md-forcefieldtools.org wrote:
Dear Jmol users,
I can display the following applet:
Dear Matthew Jmol users,
This sounds like the same error that I had recently on Fedora 11. It
comes with OpenJDK by default but you need to uninstall that and
install the one from Sun, along with the associated plug in for
firefox. Please see my most recent post, and/or you might have to ask
I have now loaded three files onto my campus server: ST1.html, ST2.html, and
ST3.html. The files are identical except that I have commented out, or in,
various script lines.
ST1: A simple load of a molecule into a jmol applet followed by an alert,
dismissal of which allows another molecule
Hi,
Did you enable the plugin with the final step mentioned on the jmol wiki?:
open Firefox, select Tools Addons, and enable the Java plug-in
You may also need to disable the IcedTea plugin (which uses openjdk)
from the same menu.
- should I install jre 1.6.x or 1.5.x from sun ?
I
ST1.html:
You should NEVER do this:
script
var script = 'load Structures/molecule4.pdb';
jmolApplet([500,500],script);
/script
script
alert(Load another structure);
var script2 = 'load Structures/chlorophyll.pdb';
jmolScript(script2);
Ever ever ever! That is just asking for trouble. No one
Again, never do this! (same reason, and in MSIE the applet will not
ever be loaded before the prompt returns)
UseCommandThread probably shouldn't be played with, either.
script type = text/javascript
jmolInitialize(../jmol,JmolApplet.jar);
//jmolInitialize(../jmol,JmolApplet.jar);
Phil, instead of an alert, use an anchor tag that we can click on after the
applet loads. That's the only valid test here. What again were you trying to
test?
Bob
On Fri, Jul 23, 2010 at 10:52 AM, Robert Hanson hans...@stolaf.edu wrote:
Again, never do this! (same reason, and in MSIE the
Quoting Matthew Betts matthew.be...@bioquant.uni-heidelberg.de:
Did you enable the plugin with the final step mentioned on the jmol wiki?:
open Firefox, select Tools Addons, and enable the Java plug-in
I cannot because it is not found.
You may also need to disable the IcedTea plugin
I have the following error in Eclipse
DescriptionResourcePathLocationType
The method getAtomSetCollectionFromReader(String, null, BufferedReader,
null) is undefined for the type SmarterJmolAdapter
TestSmarterJmolAdapter.javaJmol/test/org/jmol/adapter/smarterline
223Java
(2nd version of this message, the previous one did not make its way to the list
yet)
I am currently working on a viewer that embeds a sequence display with
mouseover capability : when the user hovers a residue in the sequence, a
command is sent to Jmol so that the corresponding residue is
How are you launching the browser? Are you typing firefox on a command
line or clicking on a toolbar icon?
I have run into situations where there is more than one version of the
browser installed on my CentOS machine (aka, RHEL) and the two methods point
to different installations. Firefox
I am trying to test whether I understand jmol.js. Obviously I do not:-( But
I understand what you are saying. I will be along presently. Actually, we
are probably leaving town the first of the week and you will not here from me
for a while, for which everyone is probably happy:-)
Phil
On Fri, Jul 23, 2010 at 9:18 AM, Paul Pillot
paul.pil...@ac-orleans-tours.fr wrote:
I wrote a small test to see if the setcallback was in cause in the drop of
performance :
a javascript for loop calls 20 times in a row the jmolscript method. The
time for the end of each script is reported
FYI, I run into the same problem in the Firefox version of our Jmol
Interface, except using a JmolScript call in a pickCallback method.
On Fri, Jul 23, 2010 at 12:52 PM, Robert Hanson hans...@stolaf.edu wrote:
On Fri, Jul 23, 2010 at 9:18 AM, Paul Pillot
paul.pil...@ac-orleans-tours.fr
Here's what I know:
With the signed applet, the default is to have useCommandThread=TRUE, and
with the unsigned applet, it is FALSE.
With the signed applet, you can have a problem opening some files if you do
not useCommandThread. If you have problems with the signed applet opening
files, let me
If you write your callback in Jmol script and call it directly from the
hover using a Jmol function. Perhaps?
n Fri, Jul 23, 2010 at 9:18 AM, Paul Pillot paul.pil...@ac-orleans-tours.fr
wrote:
(2nd version of this message, the previous one did not make its way to the
list yet)
I am currently
OH, THAT test. I'm going to remove _dev now for RC27.
On Fri, Jul 23, 2010 at 11:17 AM, Nicolas Vervelle nverve...@gmail.comwrote:
I have the following error in Eclipse
DescriptionResourcePathLocationType
The method getAtomSetCollectionFromReader(String, null, BufferedReader,
OK Bob, et. al.:
I have tried to mimic a piece of one of your pages, namely:
http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm
I also tried to view this page in Firefox, but you are using the signed applet.
Everything I have tried, even the stuff I should never, ever, ever
--
*We're sorry...*
The page you are looking for:
*/~pbays/JSTest/HTMLFiles/NT1.html*
On Fri, Jul 23, 2010 at 2:44 PM, Philip Bays pb...@saintmarys.edu wrote:
OK Bob, et. al.:
I have tried to mimic a piece of one of your pages, namely:
Thanks Michael, Wayne and Bob for that,
- the negative numbers noticed by Wayne, were just a design issue, nothing to
worry about.
- regarding the useCommandThread directive, I used it for my project when I
discovered that firefox refused to load subsequent files in the applet. My
development
Phil and Bob,
I'm confused about Bob's last note, but the following point may be relevant:
I get the same message as below, but it looks like Phil is on a Unix
system - case sensitive.
http://www.saintmarys.edu/~pbays/JSTest/HTMLFiles/NT1.html does not
exist, buts
http://www.saintmarys.edu/~pbays/JStest/HTMLFiles/NT1.html
On Jul 23, 2010, at 3:44 PM, Philip Bays wrote:
OK Bob, et. al.:
I have tried to mimic a piece of one of your pages, namely:
http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm
I also tried to view this page in
Yes, I suspect they do have a different security for localHost. No doubt
people have tried to weasel in on that port to extract information that is
really local, not remote.
I do think that the signed applet is the way to go with any local
application. It's not just file location. It's all the
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