Bob:
I think this may be a stupid question, but...... I understand your nomenclature
diagram. Are you saying that the pages directory must be inside the jmol
directory which itself must be at the root (top level) of the site. That is,
that you must past through the jmol directory to get to the pages and
associated files.
This could explain some of my issues. I previously had various program index
files (i.e. Stereochemistry .html) in the same directory as as all of the jar
files. But I wanted to clean things up a bit. So I put all of the jmol files
in a directory of its own at the top level, beside the Stereochemistry.html
file. The actual program files are 2 levels below that in a directory called
Programs within which there is a Stereochemistry directory.
so /contains Jmol directory +Stereochemistry.HTML/Programs/Stereochemistry + 3
other program directories/the various stereochemistry HTML files which draw
upon directories for various image and pdb files.
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)
>
>
>
>
> ------------------------------------------------------------------------------
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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]
------------------------------------------------------------------------------
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