On Jul 21, 2010, at 5:38 PM, Angel Herráez wrote:
> Now that's really tough to diagnose...
>
> 1. I'm not sure what yourhttp:// 192... means. Are you running a local
> webserver? Do you
> see exactly the same problem when you run from a real server?
Yes. The 192 address is the apache
Now that's really tough to diagnose...
1. I'm not sure what yourhttp:// 192... means. Are you running a local
webserver? Do you
see exactly the same problem when you run from a real server?
2. Please try this
http://wiki.jmol.org/index.php/Jmol_Applet_Deployment_Local#Activating_UseComman
OK. I tried the following script after killing Firefox, clearing all caches,
restarting Firefox. This is on my local machine using the http:// 192.
approach to launching.
jmolInitialize("../jmol","JmolApplet.jar");
var script = 'load "Structures/molecul
Ah but that is what I am trying to avoid at the moment. However, that
always works for me. And the signed applet always works. I don't think it is
a path issue based on the fact that including the load script in the jmolApplet
function works fine and the path is the same.
About "smashin
Hi Boris
Two suggestions:
http://chemapps.stolaf.edu/jmol/docs/#jmolmathjmolvariables
see "Read-Only Variables" like _currentModelNumberInFile, _modelNumber
http://jmol.sourceforge.net/jslibrary/#jmolSetCallback
see "animFrameCallback"
http://chemapps.stolaf.edu/jmol/docs/#setcallback
"set Ani
To whom it may concern:
I want to use jmol for visualization of molecular structures
and trajectories of molecular dynamics runs.
For this I convert the trajectories into a single file with
consecutive snapshots. This part is running just fine. However,
it would be great if it would be possible t
Phil, your test page in my Firefox WinXP:
first time: empty applet, no errors
reload: model displays OK
I read this as timing problem: the page tries to load the model before the
applet has finished
downloading. Second time it is cached, so it works. And no Java errors anytime.
Your problem: y
Phil,
On Windows 7:
FF = loads applet and model
Chrome = Loads blank applet only
MSIE = nada - blank page.
All latest browser versions.
Otis
Otis Rothenberger
chemagic.com
On 7/21/2010 2:53 PM, Philip Bays wrote:
I have been clearing the cache regularly -- before each try -- and
restarting
Interesting. For me, your version of my page loads in Firefox, but the model
does not load in Safari.I will try Otis's timing suggestion -- and change
the - to = :-(
Phil
On Jul 21, 2010, at 2:45 PM, Angel Herráez wrote:
>>
I have been clearing the cache regularly -- before each try -- and restarting
the browser. I am on a mac and use a utility (Cocktail -- though it might be
better in a glass) to clear all browser caches, including java.
Try this URL: http://www.saintmarys.edu/~pbays/JStest/HTMLFiles/ST1.html
I
Phil,
Another thought re Angel's suggestion that it is a file access problem:
Use absolute (from Web root) rather than relative paths:
jmolApplet([450, 460], 'load /models/2-chlorobutane_(R).mol; javascript
"jmolInit()";')
Otis
Otis Rothenberger
chemagic.com
On 7/21/2010 2:32 PM, Angel H
>
Phil,
Although the error message is confusing, you may be correct about
timing. The following approach might work:
jmolApplet([450, 460], 'javascript "jmolInit()";')
A while back I raised the issue of the javascript command not working in
MSIE, but I was flat out wrong on that point. If your
Hi Phil
Don't despair.
> But I also read that using the server and accessing by
> http://192.blah.blah.blah will behave like the
> eventual campus web site site will -- and that the above arrangement of files
> is not necessary.
1.
If you read the pages from a server, yes, any folder arrangem
I've just encountered a bug with a script that selects or deselects previously
selected residue.
Example : on http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm load a
multiple chain pdb file (as 1d66)
- set selectionhalos on (to make things clearer)
- select selected and not 56:B
chains
On 7/20/2010 7:27 PM, Robert Hanson wrote:
to draw the isosurface you need to use the isosurface command, not the
load command. I think that's the only problem. Note that older
isosurfaces had some of the atoms present -- this was removed in the
latest version of JVXL, but could be reinserted i
Hi again,
I managed to fix this. It was a problem with my browser, not jmol, but I'm
writing the solution here in case it helps someone else.
Thanks for your help,
Matthew
Firefox 3.5.9 on Fedora 11
Firefox was using the OpenJDK runtime environment and the associated IcedTea
plugin. I installe
MiKTeX rendering an empty pdf doc has already been mentioned, and was
in the instructions in the wiki. I've now added more clarification
regarding the need for the several IDTFConverter files.
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