Phil-
The Jmol related problem changes work for me on XP with Firefox, Chrome,
and MSIE.
Java 1.6.0_19
Firefox 3.6.3
Is it possible that your use of innerHTML to load a the original applet
is causing issues on some browsers/platforms when you use the newer Jmol
applet?
Another thought: Would jmol.js make the problem go away? I went kicking
and screaming into the use of jmol.js. I mean kicking and screaming! But
the switch solved a lot of problems for me.
Otis
On 6/8/2010 9:00 AM, Philip Bays wrote:
But here are the issues:
1. The programs have worked in the past, and were even working last
week, I think. They were written about 5 years ago and have been in
use since then with classes. (This was pre-Hanson time).
2. I have reorganized the site with appropriate (I think) adjustments
in paths, so the issue of location would be a possibility, but I would
think that non-Mozilla browsers would also not work if that was the case.
3. I observe the issue both locally and on my web site.
4. The first file is loaded fine. It is subsequent reloads of
molecules into the applet that fail. They are loaded from the same place.
5. I have a colleague who has tried the site from a windows machine.
IE works, Firefox does not load the applet at all. She is running
Java 1.5x.
6. I have upgraded to the latest version of Jmol in the process.
7. I am running Java 1.6
Here is a URL to observe:
www.saintmarys.edu/~pbays/Stereochemistry.html
<http://www.saintmarys.edu/%7Epbays/Stereochemistry.html>
Phil
On Jun 8, 2010, at 8:44 AM, Jonathan Gutow wrote:
Phil,
This is a problem specifically with how Mozilla browsers on the Mac
pass local paths. This has been a problem for years. For local
running of pages on a Mac you need to use a different browser. The
issue is that the Mozilla browsers insist on passing absolute paths
through the javascript. This causes a security exception when
running locally. Mozilla browsers work fine from the web. I don't
think we've ever tried to report this as it isn't an issue for pages
from servers.
Maybe we need to add something to the Wiki. The information is
included in my WebExport tutorial in the section on testing locally.
Jonathan
On Jun 8, 2010, at 12:03 AM, [email protected]
<mailto:[email protected]> wrote:
Message: 5
Date: Mon, 7 Jun 2010 18:16:44 -0400
From: Philip Bays <[email protected] <mailto:[email protected]>>
Subject: [Jmol-users] Java exception
To: Jmol Jmol <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected]
<mailto:[email protected]>>
Content-Type: text/plain; charset=us-ascii
For a number of years I have had a series of tutorials that students
have successfully used. I was using a pretty old version of Jmol
and recently updated the website, incorporating a newer version
(11.8.24). The tutorials using Jmol work fine on the Mac for all
browsers except Mozilla (Firefox, Camino, Seamonkey). On these
browsers the applet loads and the first structure is shown.
However, subsequent reloads of the applet fail. They fail
completely on windows machines with Firefox but run with IE. In the
Firefox applet window on the mac I get the statement:
java.security.AccessControlException: access denied
The Java console gives a permissions error as shown below.
FileManager.getAtomSetCollectionFromFile(Acyclic/M4/S.pdb)
//Acyclic/M4/S.pdb
FileManager opening
file:/Users/pbays/Sites/Programs/Stereochemistry/Acyclic/M4/S.pdb
file ERROR:
file:/Users/pbays/Sites/Programs/Stereochemistry/Acyclic/M4/S.pdb
java.security.AccessControlException: access denied
(java.io.FilePermission
/Users/pbays/Sites/Programs/Stereochemistry/Acyclic/M4/S.pdb read)
openFile(Acyclic/M4/S.pdb): 275 ms
eval ERROR: java.security.AccessControlException: access denied
(java.io.FilePermission
/Users/pbays/Sites/Programs/Stereochemistry/Acyclic/M4/S.pdb read)
----
load >> "Acyclic/M4/S.pdb" <<
Any quick clue as to what is happening and what changed? FYI: I did
try 12.0RC12 and it behaved the same way.
Phil
J. Philip Bays
Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
(574) 284-4663
[email protected] <mailto:[email protected]>
Dr. Jonathan H. Gutow
Chemistry Department [email protected] <mailto:[email protected]>
UW-Oshkosh Office: 920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow
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J. Philip Bays
Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
(574) 284-4663
[email protected] <mailto:[email protected]>
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Otis Rothenberger
chemagic.com
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