Menu
▾
▴
Re: [Jmol-users] Solving Jmol loading problems
|
From: Jochen J. <joc...@fi...> - 2025-06-03 10:44:35
|
Hi Mark!
JSmol always took percentages, this allows for resizing. It follows the outer box, as long as at some point there is an outbox that has a defined size.
Jochen
On 2 Jun 2025, at 20:31, Mark Perri <pe...@so...> wrote:
Hi Jochen,
I forgot to say, I set height and width as pixel values instead of percentages before I initialized it. I didn't know JSmol accepted percentages.
Thanks,
Mark
On Mon, Jun 2, 2025 at 3:52 AM Jochen Junker <joc...@fi...<mailto:joc...@fi...>> wrote:
Hi Mark!
It is about jmolc, yes.
It is initialized at line 1722 in function InitAfter():
Jmol.setDocument(0);
Jmol.getApplet("jmolc", InfoC);
t = Jmol.getAppletHtml(jmolc);
d = document.getElementById("jsmol_container");
setInnerHTML(d,t);
The block is initially set to display none, it is set to display as block later. This 3D viewer will not always be shown.
This is exactly the same code as for v14, where it works.
Jochen
On 2 Jun 2025, at 00:02, Mark Perri <pe...@so...<mailto:pe...@so...>> wrote:
Hi Jochen,
Are you talking about jmolc? I can't find where it's created in your source. But it's not getting loaded correctly: jmolc._applet is null.
If you do:
document.getElementById("jsmol_container").innerHTML="";
document.getElementById("jsmol_container").innerHTML=Jmol.getAppletHtml("jmolc",Info);
It will load.
The css is also display:none, but I'm not sure if that's because it's not loaded correctly.
Thanks,
Mark
On Sun, Jun 1, 2025 at 11:58 AM Jochen Junker <joc...@fi...<mailto:joc...@fi...>> wrote:
Hi Bob!
Thank you and Angel for your input. I have had my share of cache related issues, so I can rule that out.
0. Try a different browser. Sometimes one is ahead of another in JavaScript, and there is some change there.
I normally do my development on Firefox because of the Debugger. The same error happens on Safari and Chrome. On Chrome I got the most meaningful error message: “IndexSizeError: Failed to execute 'getImageData' on 'CanvasRenderingContext2D': The source width is 0."
But, I do not get any errors on the console. On the console I see the normal messages that the applet was started.
1. Use URL option ?j2sdebugcode
? can be & or # as needed if you already have query fields in the URL.
Unfortunately this does not work in this case.
2. Open the browser developer console debugger or source tab and click stop on errors, including caught errors
The page always throws and catches a few errors as it loads in order to check the browser for comparability issues. So push through those until the error you are seeing is thrown.
There is also at least one error that does not generally affect loading that should not be there but I have not worried about it. Maybe you can tell me how to get around that.
In V14 I get the CORS error, but that is it.
In V16 I get no significant errors from Jmol.
IndexSizeError: Index or size is negative or greater than the allowed amount
This error is interesting because I think it is new. I have not seen it before, at least stated as such. Traditionally JavaScript does not throw array out of bounds exceptions except for negative numbers. Probably a counter went negative.
This error seems to be related to using clipping in canvas’ drawImage function:
https://stackoverflow.com/questions/19338032/canvas-indexsizeerror-index-or-size-is-negative-or-greater-than-the-allowed-a
3. Another option is to use the _J2S option. The value of that should be the full path to a j2s directory on another path or domain. This allows direct comparison between two versions on the same or different machines.
4. At this point if I am still not seeing the exact problem I start setting debugging break points, reloading the page to see what is going on at some particular point. This invariably at least identifies the problem.
5. Worst case process is to run two versions side by side with break points in the same place looking for differences. This ultimately discovers the issue. It's a huge help to have one working version. This is a famous truck and one that I use regularly on the Java side. I always start with the SwingJS code and then power that to the legacy only when it is working in SwingJS.
6. Be patient and confident that whatever the problem is, it is most likely something very simple.
7. Send us a link to the failing page. Several people reading this can give it a try. Only do the above if you are interested in the challenge.
As suggested, I have set up 2 pages just differing in the Jmol version.
Version 14 here: https://toratheu.de/compare14?cocon1720457998896<https://ddec1-0-en-ctp.trendmicro.com/wis/clicktime/v1/query?url=https%3a%2f%2ftoratheu.de%2fcompare14%3fcocon1720457998896&umid=e537e692-ac4a-4dd0-bf50-88055a9654fd&rct=1748833820&auth=1bcda6227c1853a98db9a85322c3ec3db27ad845-d5e736e3d28bd18eeddde7ca638bc20c5a453f8c>
Version 16 here: https://toratheu.de/compare16?cocon1720457998896<https://ddec1-0-en-ctp.trendmicro.com/wis/clicktime/v1/query?url=https%3a%2f%2ftoratheu.de%2fcompare16%3fcocon1720457998896&umid=e537e692-ac4a-4dd0-bf50-88055a9654fd&rct=1748833820&auth=1bcda6227c1853a98db9a85322c3ec3db27ad845-3b80a51ffb6967446e8ad29ff7eb355ba2c951f9>
This pages are on a development server. Opening the pages will give 2 XHR 404 errors, which are handled gracefully and do not relate to Jmol. Besides that the Debugger in Firefox does not give out any errors. To see the other instances of Jmol working on the Version 16 page you have to click the 3D/2D toggle in the results window (Title: Total of 28 Constitutions found). I have embedded the Jmol loading messages in an other window, makes it easier to follow.
I have also managed to identify where the error happens, a screenshot of the location follows. Maybe that helps.
Best Regards,
Jochen
<Screenshot 2025-06-01 at 15.54.10.png>
_______________________________________________
Jmol-users mailing list
Jmo...@li...<mailto:Jmo...@li...>
https://lists.sourceforge.net/lists/listinfo/jmol-users
_______________________________________________
Jmol-users mailing list
Jmo...@li...<mailto:Jmo...@li...>
https://lists.sourceforge.net/lists/listinfo/jmol-users
_______________________________________________
Jmol-users mailing list
Jmo...@li...<mailto:Jmo...@li...>
https://lists.sourceforge.net/lists/listinfo/jmol-users
_______________________________________________
Jmol-users mailing list
Jmo...@li...
https://lists.sourceforge.net/lists/listinfo/jmol-users
|
