Sounds like a Java bug.
On Tue, Jun 8, 2010 at 7:43 PM, Philip Bays <[email protected]> wrote:
> Bob: I think I do not understand signed applets, or at least not this one.
>
> I set one of my HTML files to call the signed applet. It calls it and
> gives me the signed applet dialog. As I look at it I have three
> choices -- run, cancel, or always trust. I understand Run and Always trust.
> But I assumed that Cancel meant "I'm getting out of here" and nothing
> would be loaded. However, the signed applet is loaded and everything is
> fine -- no java exceptions on all browsers.
>
> What is Cancel supposed to do?
>
>
> Phil
>
> On Jun 8, 2010, at 7:53 PM, Robert Hanson wrote:
>
> OK, THERE IS A WORK-AROUND:
>
> jmolInitialize....
> jmolSetCallback("UseCommandThread","true")
> jmolApplet....
>
> As far as I can tell, this brings you back to the old behavior. The JAR
> files can be anywhere, and the files Jmol reads can be anywhere in or
> beneath the JAR file directory. For example:
>
> jmolInitialize('../../test', 'JmolApplet.jar')
> jmolSetCallback("UseCommandThread","true")
> jmolApplet(400, 'load "../../test/proline_flat.sdf"')
> jmolButton('script "../../test/halos.spt"', 'test test2 script file: halos
> on Hs')
> jmolButton('minimize', 'minimize')
>
> No problem. Comment out that jmolSetCallback line, and we are back to the
> bad behavior.
>
>
> The notes I have on that read:
>
> * You can specify that the signed or unsigned applet or application should
> * use an independent command thread (EXCEPT for scripts containing the
> "javascript" command)
> *
> * [param name="useCommandThread" value="true"]
>
> I guess that's pretty important now. I'm pretty sure Jmol will detect the
> Jmol "javascript" command and not try to execute it using that command
> thread.
>
>
> The way it WAS (only affects the unsigned applet):
>
> On a web server, as long as the files are somewhere within the domain
> (usually something like www.stolaf.edu/), they could be anywhere.
>
> Locally, as long as all the files being read were in the directory
> containing the JAR files or in a subdirectory of that, that was fine. The
> HTML page could be anywhere.
>
> The way it IS NOW:
>
> No change for the web server.
>
> Locally, what used to apply only to the JAR files now applies also to the
> HTML page.
>
> The minimization /UFF business MUST be a Java bug. That's too weird. It
> appears that the Javascript thread can't open a resource that is in the Jar
> file but not within its directory. Huh? Must be a bug! But I will test a bit
> tonight.
>
>
>
>
>
> Bob
>
>
>
>
>
>
>
>
>> It appears to me that you are saying I need to move the
>> Stereochemistry.HTML (index file) into the Jmol directory.
>>
>> On another issue altogether. There is much emphasis on the Jmol page that
>> the program and applet are named Jmol, not jMol and not jmol. When I
>> download from the downloads page, I get a directory named jmol (all lower
>> case). That seems inconsistent with the specifications. when I first set
>> up the tutorials, I used Jmol and that was, I think what was downloaded. My
>> server is very particular about case and it has caused me headaches when I
>> have not remembered.
>>
>> Phil
>>
>> On Jun 8, 2010, at 12:57 PM, Robert Hanson wrote:
>>
>> OK, looks like there is a new Firefox security policy:
>>
>> For all local files accessed via JavaScript, both the JAR file AND the
>> HTML file must be on the path to that file.
>>
>> Pretty sure that's new.
>>
>> The fix for me was to move the Jmol-12.... directory into the pages
>> directory, modify the files, and it worked. Of course, this is an
>> EXCEPTIONAL drag!!! Kind of removes the possibility of using the local
>> applet within anything more than a single-directory context. Actually, the
>> solution looks like using this path set:
>>
>>
>> .... /jmol
>> .............[all jar files here]
>> ............./pages
>> .............[html here]
>>
>>
>> This basically makes impossible use of the unsigned applet on a local
>> machine.
>>
>>
>> On Tue, Jun 8, 2010 at 11:29 AM, Robert Hanson <[email protected]>wrote:
>>
>>> UFF.txt is a resource within the Jar file. Specifically it is in:
>>>
>>> JmolApplet0_Minimize.jar/org/jmol/minimize/forcefield
>>>
>>> JmolAppletSigned0_Minimize.jar/org/jmol/minimize/forcefield
>>>
>>>
>>> If you use
>>>
>>> set debug
>>>
>>>
>>> you should see its contents listed when the minimizer runs.
>>>
>>> Very odd that the system can't find it. This could be an odd threading
>>> issue -- the thread that runs from a click of a button is not the same
>>> thread that runs when you use the Jmol console or menu.
>>>
>>> Local files -- sounds like a Java bug. But I could be doing something
>>> slightly wrong there.
>>>
>>> Suggestions:
>>>
>>> compare application and applet.
>>>
>>>
>>>
>>> 2010/6/8 Angel Herráez <[email protected]>
>>>
>>> This is the summary and a test case:
>>>>
>>>> 1. Problem is there only for local files, not from server. Seems to
>>>> be related to Jmol reading text files (either scripts or the UFF.txt
>>>> file embedded somehow inside Jmol) from a folder where the applet
>>>> jars are but the webpage is not.
>>>>
>>>> Main_folder
>>>> |
>>>> -- Pages_folder
>>>> |
>>>> -- mypage.htm
>>>> |
>>>> -- Jmol_folder
>>>> |
>>>> -- *.jar files
>>>> -- Jmol.js
>>>> -- model.mol
>>>> -- test.spt
>>>>
>>>> 2. The problem shows for reading script files (that do no model
>>>> loading, just simple commands) and also for running "minimize"
>>>>
>>>> 3. The same script commands or the minimize command work fine when
>>>> issued from teh script console. It'sonly calling them from a
>>>> jmolButton or an <input type="button" onClick="jmolScript()"> that
>>>> causes the problem.
>>>>
>>>> 4. Same behaviour in 11.6, 11.8.24 and 12.0.RC17
>>>>
>>>> 5. Errors are like:
>>>>
>>>> For loading a script file:
>>>>
>>>> FileManager opening
>>>> file:/F:/webs/_Proyectos/_pruebas/Jmol_local_scripts/Jmol-
>>>> 12.0.RC17/halos.spt
>>>> script ERROR: script ERROR:
>>>> io error reading
>>>> file:/F:/webs/_Proyectos/_pruebas/Jmol_local_scripts/Jmol-
>>>> 12.0.RC17/halos.spt:
>>>> java.security.AccessControlException:
>>>> access denied (java.io.FilePermission
>>>> F:\webs\_Proyectos\_pruebas\Jmol_local_scripts\Jmol-
>>>> 12.0.RC17\halos.spt read)
>>>>
>>>>
>>>
>>>> For running minimize:
>>>>
>>>> Minimizing 17 atoms
>>>> minimize: initializing (steps = 100 criterion =
>>>> 0.0010000000474974513) ...
>>>> minimize: using org.jmol.minimize.forcefield.ForceFieldUFF
>>>> 17 atoms will be minimized.
>>>> minimize: creating bonds...
>>>> minimize: setting atom types...
>>>> Couldn't find file: UFF.txt
>>>> Exception null in getResource UFF.txt
>>>> 0 force field parameters read
>>>>
>>>>
>>>>
>>> I don't think these are related, but they might be both security settings
>>> issues. Pretty much that's what we are seeing changing in browser updates
>>> these days.
>>>
>>>
>>>
>>>
>>>> Test case is avalable at
>>>> http://biomodel.uah.es/angel/test/Jmol_local_scripts.zip
>>>> Unzip and run from disk, not from server.
>>>> (Uses monolithic applet for simplicity; I've tested with the split
>>>> applet too)
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
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>>>>
>>>
>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>>
>>>
>>> If nature does not answer first what we want,
>>> it is better to take what answer we get.
>>>
>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>
>>
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit. See the prize list and enter to win:
>>
>> http://p.sf.net/sfu/thinkgeek-promo_______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>> J. Philip Bays
>> Professor of Chemistry
>> Department of Chemistry and Physics
>> Saint Mary's College
>> Notre Dame, IN 46556
>> (574) 284-4663
>> [email protected]
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit. See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit. See the prize list and enter to win:
>
> http://p.sf.net/sfu/thinkgeek-promo_______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> J. Philip Bays
> Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> (574) 284-4663
> [email protected]
>
>
>
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit. See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit. See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
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