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
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] wrote:
>
>> Message: 5
>> Date: Mon, 7 Jun 2010 18:16:44 -0400
>> From: Philip Bays <[email protected]>
>> Subject: [Jmol-users] Java exception
>> To: Jmol Jmol <[email protected]>
>> Message-ID: <[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]
>>
>
>
>
> Dr. Jonathan H. Gutow
> Chemistry Department [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]
------------------------------------------------------------------------------
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