ChemTube3D http://www.chemtube3d.com was ready for the day of reckoning and has
migrated to JSmol.
I would like to thank Bob Hanson and the rest of the community for their
outstanding efforts to allow us to replicate the superb experience that was
Jmol, but now miraculously without Java.
I
I've been trying my page today with both Java and JS versions of Jmol.
While JS of course works fine, I get a weird problem with the Java version
- the applet loads fine, but I can't seem to load files into it. Anyone has
experience with this, or knows if it could be related with the changes in
On 16 Jan 2014, at 09:43, Greeves, Nick ngree...@liverpool.ac.uk wrote:
ChemTube3D http://www.chemtube3d.com was ready for the day of reckoning and
has migrated to JSmol.
I would like to thank Bob Hanson and the rest of the community for their
outstanding efforts to allow us to replicate
Bob,
The previous problem persists. When I request the page to show a drop-down
menu of frames/frame names, Chrome's javascript console still offers:
Uncaught ReferenceError: JmolApplet0 is not defined.
Initializing jsmol is new to me. Maybe I'm doing it wrong. I have var Info
defined
I am having trouble getting Jsmol to load gzipped files as well. Can someone
point me to the exact place to enter my server address in Jmol2.js? I’ve done
this for the two places where a search for “php” turned up.
Unzipped files are loading fine.
Thanks,
David
~~~
Hi David
Jmol2.js has this:
Jmol.Info = { // overrides jmolInitialize()
//jarPath: java,
//jarFile: JmolAppletSigned0.jar,
//j2sPath: j2s,
use: HTML5, // could be JAVA or HTML5
disableJ2SLoadMonitor: false,
disableInitialConsole: true
}
You need this:
[...]
use: HTML5,
serverURL:
Matt,
There was some list discussion of this a while back, and I'm still not sure
what was recommended at the time. The discussion related to the use of the
following in the head JavaScript prior to the body declaration:
var jmolApplet0;
I think the statement was made that this was no longer
Robert Lancashire brought this to my attention:
https://blogs.oracle.com/java-platform-group/entry/upcoming_exception_site_list_in?msgid=3-9509477622
The basic idea is that if you have unsigned applets -- older applets or
ones that you are self-signing -- then you can test them on your own local
Thanks, Otis.
Yes, the page has the var declaration in head.
It seems the applet loads and all the other aspects of the page work
properly. The error occurs when trying script containing
jmol.getpropertyasarray. I tried w/ and w/o declaration in head, but it
did not make a difference.
Matt
Simone, could you try Jmol 14.1.6_dev, please? See
http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.15.zip
That's the version with the fix for the [object Array] problem.
On Thu, Jan 16, 2014 at 4:50 AM, Simone Sturniolo simonesturni...@gmail.com
wrote:
I've been trying my page today
Capital J?
Uncaught ReferenceError: JmolApplet0 is not defined.
On Thu, Jan 16, 2014 at 9:00 AM, Kubasik, Matt mkuba...@fairfield.eduwrote:
Bob,
The previous problem persists. When I request the page to show a
drop-down menu of frames/frame names, Chrome's javascript console still
Wow! Good catch, Bob!
But correcting to lowercase j in
var InfoM = Jmol.GetPropertyAsArray(jmolApplet0,modelinfo.models.name)
Now offers in Chrome's javasccript console:
Uncaught TypeError: Object #Object has no method 'GetPropertyAsArray'
Matt
On 1/16/14 10:04 AM, Robert Hanson
Nah, now JSmol enters into some infinite or very long loop when loading the
file and Firefox crashes (it happens on the line Script:
file:///home/wml08325/Desktop/MagresViewHg/MagresView_1_2bis/jsmol/JSmol.min.js:331).
Simone
2014/1/16 Robert Hanson hans...@stolaf.edu
Right, the weak link now
Jiayi,
Yes, I fully appreciate the difficulty.
Be sure to use Eclipse or, if you must, some other programming environment.
Then you can follow function call links forwards and backwards, and walk
through the code using breakpoints. If you don't have this capability, you
will go crazy.
The
lower case g. :)
On Thu, Jan 16, 2014 at 10:16 AM, Kubasik, Matt mkuba...@fairfield.eduwrote:
Wow! Good catch, Bob!
But correcting to lowercase j in
var InfoM = Jmol.GetPropertyAsArray(jmolApplet0,modelinfo.models.name)
Now offers in Chrome's javasccript console:
Uncaught TypeError:
Unbelievable. Thanks!
I'm sure I'll be back...
On 1/16/14 10:28 AM, Robert Hanson hans...@stolaf.edu wrote:
lower case g. :)
On Thu, Jan 16, 2014 at 10:16 AM, Kubasik, Matt
mkuba...@fairfield.edu wrote:
Wow! Good catch, Bob!
But correcting to lowercase j in
var InfoM =
Thanks, Bob, Otis, and the list for your help.
Still needing some cleaning up (especially wrt echoing frame names), the
page is here:
http://www.neon22.com/jsmol/jsmol/jsmolvib.htm
Matt
On 1/16/14 10:41 AM, Kubasik, Matt mkuba...@fairfield.edu wrote:
Unbelievable. Thanks!
I'm sure I'll be
David,
Found it…
Warning: I have no idea what I’m doing, and I could be breaking everything. By
trial and error I discovered the following:
I couldn’t get gz file download to work by putting anything in the jmol2.js
file. I thought the “serverURL belonged between lines 38 and 37, but that
This might explain the erratic behaviour. It seems to work now and then, with
not clear pattern.
Eve the simple example by Angel at
http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not
working. It will freeze while calculating, render the surface, and maybe draw
and
Chris, are you calling Jmol2.js before or after JSmol.min.js?
That could be a reason for parameters not being applied.
JSmol.min.js includes some defaults.
I think you need Jmol2.js after it.
--
CenturyLink Cloud:
Good sleuthing. I have added serverURL to the default Info block in
Jmol2.js and added a comment about it there.
If you can avoid making any changes to JSmol.min.js, that's wise. A real
headache to maintain if you do.
I don't recommend making this entry relative unless you are absolutely
certain
On 01/16/2014 06:14 PM, Jaime Prilusky wrote:
This might explain the erratic behaviour. It seems to work now and then, with
not clear pattern.
Eve the simple example by Angel at
http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is
not working. It will freeze while
On 01/16/2014 06:14 PM, Jaime Prilusky wrote:
This might explain the erratic behaviour. It seems to work now and then, with
not clear pattern.
Eve the simple example by Angel at
http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is
not working. It will freeze while
then that's a bug. That should work perfectly.
Bob
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs,
Rolf: Thank you for testing on other browsers and platforms. While developing I
stay on Mac.
Bob: I hope that this detailed report might help you find a solution for the
problem.
Jaim
On Jan 16, 2014, at 8:14 PM, Rolf Huehne rhue...@fli-leibniz.de wrote:
On 01/16/2014 06:14 PM, Jaime
Yes, I think I found it. *delay 0.01 *should work even though *refresh *does
not:
*set echo top leftecho working...*
*delay 0.01*
*echo*
Please try that; I'll also get *refresh *working. Testing now.
On Thu, Jan 16, 2014 at 1:27 PM, Jaime Prilusky
jaime.prilu...@weizmann.ac.il wrote:
http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.16b.zip
--- should fix this refeshing problem.
On Thu, Jan 16, 2014 at 2:01 PM, Robert Hanson hans...@stolaf.edu wrote:
Yes, I think I found it. *delay 0.01 *should work even though *refresh *does
not:
*set echo top leftecho
Angel,
Yes, I think I’m calling the JSmol.min.js file first.
In the header of the html page, I’ve got this
script type=text/javascript src=../../reuse/JSmol.min.js/script
script type=text/javascript src=../../reuse/Jmol.js/script
!--location of renamed Jmol2.js library--
Hi Chris
Uff that's complex to diagnose.
I'm not sure what is going wrong; it does sound reasonable.
I wold try to pool data and avoid defining Info values in two places. I.e.,
move
all declarattion into Jmol2.js or (less likely) into the page
Or, at least if unavoidable, don't declare
Thank you for the new version.
I would say that now the sequence is as follows:
it starts calculating the surface, freezing the browser
then appears the message, draws, disappears the message.
The message should appear before starting the long calculation time.
Again, this is on Mac. Maybe
Dear Bob,
On Safari Mac, with jsmol 14.1.6_dev_2014.01.16 , the notice while working
performs great with delay 0.1 instead of refresh
Thank you for the suggestion.
Jaim
On Jan 16, 2014, at 10:10 PM, Jaime Prilusky
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Thank
Hi,
If you have a central database of models located on a remote server (like
the PDB), and you are using JSmol as a local viewer and editor, how would
you save to the central server, rather than the local machine?
I know Jmol 13+ could do this by sending the output of write to a URL,
but I
Bob, Angel, Christopher,
Thanks for all your help so far with the gzipped files.
Still not working.
Any advice would be GREATLY appreciated.
Thanks in advance,
David
Here is what I’ve done (thanks Bob, for these instructions):
1. Opened JSmol.min.js and added js/Jmol2.js to it.
2. Saved
nah. impossible. I wonder if what you are seeing is the time it takes to
load the modular components. If you have turned off the loading monitor,
you may think nothing is happening -- or the calculation has started. I
have a quite variable connection here in Jamaica (especially working
through my
You can only load binary files from your local machine if you are using
FireFox, I believe. And maybe just on a PC. I can't remember. Any chance
that is your problem?
What is happening is that your machine does not support asynchronous binary
file transfer using AJAX, so it has to go to a server
Data is sent to a server via a simple http call, which can be a POST or
not. This can be done with a WRITE command, but you can also just use the
load() function. The key is to have ?POST? in the URL being loaded and
then if you want specifically the PNGJ binary data sent, you add _PNGJBIN_
to
I would say that this is not a delay caused by loading, unless modules or model
get unloaded in the middle.
The Scene Authoring Tool in Proteopedia allows me to render and remove
isosurface over and over again on the same loaded model with the click of a
button. All components should be
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