Dear Bob,
To sum up,
I tried different webBrowsers and OS :
Finally:
a) Using Safari / Mac os Snow Leopard is ok, signed and non signed applet
b) Using Safari / Mac os Lion doesn't work ("You do not have java Applets
enabled ...", while
I have allowed "applications downloaded from anywhere" in the security
configuration,
while the java applet module is activated in "Java preferences" ...)
c) Using Mozilla / Mac os Snow Leopard doesn't work : the Mozilla application
is freezing after
the PDB file name is required to the user...
d) Using Mozilla / Mac os Lion works fine with the non-signed jMol applet,
but fails with the signed applet
Thanks again for your help!
Have a nice week-end.
Eric
Le 8 oct. 2012 à 20:57, Robert Hanson a écrit :
> Oh, right. Maybe not. But that's not the problem. No changes have been made
> in Jmol.js recently. You agree it's all working at my site, right? Then you
> just have not got the right files yet. Really all you need are the three
> files in
>
> http://chemapps.stolaf.edu/jmol/docs/examples-12/test/
>
> and then also
>
> http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol.js
> http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned.jar
>
> Right? That's all that page is using. I have no idea what's going on if that
> doesn't work for you. Nothing special about our server here....
>
>
>
> Bob
>
>
>
> On Mon, Oct 8, 2012 at 1:40 PM, eric henon <eric.he...@univ-reims.fr> wrote:
> Hi Bob,
>
> Thanks for the archive. Unfortunately, there is no Jmol.js file in this
> archive. I downloaded the last
> version (13.0.6), and Jmol.js is there ( but some others .js files are
> lacking compared to the
> archive you sent to me (JmolCore-auto.js, JmolCoreTest.js, JmolJSmol.js) ).
>
> However, my jBox application does not run properly on 13.0.6 version: the pdb
> is not loaded.
> It is not a problem of java (I employed FireFox); all the jMol buttons,
> CheckBox, ... appear,
> the jmol applet is sized to 800, but remains empty. The jMolScript("load
> 2PO6.pdb")
> command seems to be the problem, or maybe also the jMolSetCallback command
> (?).
>
> Also, the jMolScript("console") does not appear
> so that I cannot debug easily.
>
> I tried with the 13.0.4, ..., 12.2.34 versions: it does not work (same
> problem as above described).
> It only works with my old 12.2.21 jMol version.
> Have you carried out successfully my jMol application using a recent version
> of jMol ?
>
> Thanks in advance.
> Eric
>
>
>
>
>
> Le 8 oct. 2012 à 01:41, Robert Hanson a écrit :
>
>> Glad to hear that. I think it's a problem of not having the up-to-date
>> files. If it is working at my site it's because I have the latest fixes
>> there. So consider extracting the relevant .js files from
>> http://chemapps.stolaf.edu/jmol/Jmol-13.zip
>>
>> I just realized that I had not been updating some of the JmolJSO JavaScript
>> library files correctly there. So that might be part of it. But they are
>> there now.
>>
>> Bob
>>
>>
>>
>>
>> On Sun, Oct 7, 2012 at 3:29 PM, eric henon <eric.he...@univ-reims.fr> wrote:
>> Hi Bob,
>>
>> It's very strange because :
>>
>> 1) Actually, that works (no "lag" problem any more) using your link to the
>> modified jBox.html/Signed
>>
>> 2) One of the difference was that you use "JmolAppletSigned.jar in place of
>> "true" in jmolInitialize method.
>> But that is not the reason why it works now (I tested sucessfully your code
>> with either true or molAppletSigned.jar)
>>
>> The other difference was that I put the tweak (buffering the jMolScript
>> instructions)
>> in the first tag : <script src=./Jmol.js" type=...> rather than putting it
>> in another <script> tag.
>> But the jMolScript buffering was working nevertheless.
>>
>> 3) Moreover, curiously, using your link works now fine with my "Lion Safari
>> web Browser".
>>
>> Let me recall to you that I posted a mail some days ago about this problem,
>> i.e.
>> I got the following message "You do not have Java applets enabled in your
>> web Browser..."
>> when loading this jmol application within my Safari on my Lion i mac
>> (there is no problem using the Safari on a Snow Leopard Mac os system ...).
>>
>> Thus, at present time, using
>>
>> a) "FireFox/Lion Mac os" on my own (local) Jmol application/Signed works
>> fine (no lag, no problem of "enabling java")
>> b) "Safari /Lion Mac os" on my own (local) Jmol application/Signed does
>> not work : "You do not have Java applets enabled in your web Browser..."
>> c) "Safari /Lion Mac os" on your (http) Jmol application/Signed does work !
>> no problem of "You do not have Java applets enabled in your web Browser..."
>>
>> Thanks Bob, for your help on the "lag" problem.
>> If you have any idea concerning the other problem, thanks in advance.
>>
>> Have a nice evening.
>> Eric
>>
>>
>>
>>
>>
>> Le 7 oct. 2012 à 19:38, Robert Hanson a écrit :
>>
>>> Are you seeing the same problem at
>>> http://chemapps.stolaf.edu/jmol/docs/examples-12/test/jBox.html ?
>>>
>>> (enter
>>>
>>> =1crn
>>>
>>> in the input box, for instance)
>>>
>>>
>>> That's working fine for me.
>>>
>>> Bob
>>>
>>>
>>> On Sun, Oct 7, 2012 at 6:56 AM, eric henon <eric.he...@univ-reims.fr> wrote:
>>> Robert,
>>>
>>> many thanks for your answer.
>>> It is a very nice "tweak" to buffer jMolScript instructions like that.
>>> I did it.
>>>
>>> Unfortunately, the "lag" problem remains when using jmolInitialize(".",
>>> true); (signed Applet mode)
>>> whatever using the Safari or FireFox web browser.
>>>
>>> Did you observe the same problem ?
>>>
>>> Thanks again.
>>> Eric
>>>
>>>
>>> Le 6 oct. 2012 à 22:12, Robert Hanson a écrit :
>>>
>>>> Eric, there are a number of problems with that page. I don't know about
>>>> the signed/unsigned business, but first let's get this part fixed:
>>>>
>>>> // calculate the three dimensions of the box
>>>> jmolScript("Vx = (V1.x - V5.x)");
>>>> jmolScript("Vy = (V1.y - V5.y)");
>>>> jmolScript("Vz = (V1.z - V5.z)");
>>>> jmolScript("a = sqrt(Vx*Vx + Vy*Vy + Vz*Vz)");
>>>>
>>>> jmolScript("Vx = (V1.x - V3.x)");
>>>> jmolScript("Vy = (V1.y - V3.y)");
>>>> jmolScript("Vz = (V1.z - V3.z)");
>>>> jmolScript("b = sqrt(Vx*Vx + Vy*Vy + Vz*Vz)");
>>>>
>>>> jmolScript("Vx = (V1.x - V2.x)");
>>>> jmolScript("Vy = (V1.y - V2.y)");
>>>> jmolScript("Vz = (V1.z - V2.z)");
>>>> jmolScript("c = sqrt(Vx*Vx + Vy*Vy + Vz*Vz)");
>>>>
>>>>
>>>> // calculate the box volume
>>>> jmolScript("volume = a * b * c ");
>>>> vol=jmolEvaluate("volume%1");
>>>> aa =jmolEvaluate("a%1");
>>>> bb =jmolEvaluate("b%1");
>>>> cc =jmolEvaluate("c%1");
>>>>
>>>>
>>>> This will not work properly and is very inefficient. First, get all those
>>>> script calls into one string:
>>>>
>>>> "Vx = (V1.x - V5.x);Vy = (V1.y - V5.y);Vz = (V1.z - V5.z);a = sqrt(Vx*Vx +
>>>> Vy*Vy + Vz*Vz);Vx = (V1.x - V3.x)..."
>>>>
>>>> With that in mind, you should probably just use:
>>>>
>>>> "V1.distance(V5)"
>>>>
>>>> But the more important thing is that jmolScript is asynchronous, and
>>>> jmolEvaluate is not. Really what you want is this:
>>>>
>>>> a = jmolEvaluate(V1.distance(V5))
>>>> b = jmolEvaluate(V1.distance(V3))
>>>> c = jmolEvaluate(V1.distance(V2))
>>>> vol = a * b * c
>>>>
>>>> you can do the rounding in JavaScript.
>>>>
>>>>
>>>> But.... on the other hand, it will work fine with just this little tweak:
>>>>
>>>> At the top of your script tag, add this to buffer the script into Jmol:
>>>>
>>>> jmolScript0 = jmolScript;
>>>>
>>>> script = ""
>>>> jmolScript = function(a) {
>>>> // buffer these into jmol -- jmolScript() by itself clears the buffer
>>>> if (a) {
>>>> script += ";" + a;
>>>> } else {
>>>> jmolScript0(script);
>>>> script = "";
>>>> }
>>>> }
>>>>
>>>> then add
>>>>
>>>> jmolScript()
>>>>
>>>> just before
>>>>
>>>> vol=jmolEvaluate("volume%1");
>>>>
>>>> and just at the end of the drawBox() function.
>>>>
>>>> You should be all set.
>>>>
>>>> Really a very cool page!
>>>>
>>>> Bob
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Fri, Oct 5, 2012 at 11:20 PM, eric henon <eric.he...@univ-reims.fr>
>>>> wrote:
>>>> Dear all,
>>>>
>>>> once more I meet one
>>>> problem using my jMol code (attached).
>>>>
>>>> When using the signed applet,
>>>> the applet becomes very very slow.
>>>>
>>>> For example,
>>>> rotating my box into the jMol windows
>>>> (I built a box that I can translate, rotate, scale)
>>>> takes about 3-4s for each rotation, while
>>>> it is quasi-instantaneous using the unsigned applet.
>>>>
>>>> Thus, only adding the true parameter in the jmolInitialize
>>>> method substantially influences the performance
>>>> of the applet.
>>>>
>>>> Is it a "standard" behavior ?
>>>>
>>>> Thanks in advance.
>>>> Best regards.
>>>> Eric Henon
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Don't let slow site performance ruin your business. Deploy New Relic APM
>>>> Deploy New Relic app performance management and know exactly
>>>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>>>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>>>> http://p.sf.net/sfu/newrelic-dev2dev
>>>> _______________________________________________
>>>> Jmol-developers mailing list
>>>> Jmol-developers@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Robert M. Hanson
>>>> Larson-Anderson Professor of Chemistry
>>>> Chair, Chemistry Department
>>>> St. Olaf College
>>>> Northfield, MN
>>>> http://www.stolaf.edu/people/hansonr
>>>>
>>>>
>>>> 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
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Don't let slow site performance ruin your business. Deploy New Relic APM
>>>> Deploy New Relic app performance management and know exactly
>>>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>>>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>>>> http://p.sf.net/sfu/newrelic-dev2dev_______________________________________________
>>>> Jmol-developers mailing list
>>>> Jmol-developers@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>
>>> Eric Henon
>>> Professeur
>>> Universite de Reims Champagne-Ardenne
>>> Institut de Chimie Moleculaire de Reims
>>> http://www.univ-reims.fr/ICMR
>>> CNRS UMR 6229
>>> UFR des Sciences Exactes et Naturelles
>>> BP 1039
>>> 51687 Reims Cedex 2 (France)
>>> Tél./Fax : + 33 (0) 3 26 91 84 97
>>> eric.he...@univ-reims.fr
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Don't let slow site performance ruin your business. Deploy New Relic APM
>>> Deploy New Relic app performance management and know exactly
>>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>>> http://p.sf.net/sfu/newrelic-dev2dev
>>> _______________________________________________
>>> Jmol-developers mailing list
>>> Jmol-developers@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>
>>>
>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Larson-Anderson Professor of Chemistry
>>> Chair, Chemistry Department
>>> St. Olaf College
>>> Northfield, MN
>>> http://www.stolaf.edu/people/hansonr
>>>
>>>
>>> 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
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Don't let slow site performance ruin your business. Deploy New Relic APM
>>> Deploy New Relic app performance management and know exactly
>>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>>> http://p.sf.net/sfu/newrelic-dev2dev_______________________________________________
>>> Jmol-developers mailing list
>>> Jmol-developers@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>> Eric Henon
>> Professeur
>> Universite de Reims Champagne-Ardenne
>> Institut de Chimie Moleculaire de Reims
>> http://www.univ-reims.fr/ICMR
>> CNRS UMR 6229
>> UFR des Sciences Exactes et Naturelles
>> BP 1039
>> 51687 Reims Cedex 2 (France)
>> Tél./Fax : + 33 (0) 3 26 91 84 97
>> eric.he...@univ-reims.fr
>>
>>
>> ------------------------------------------------------------------------------
>> Don't let slow site performance ruin your business. Deploy New Relic APM
>> Deploy New Relic app performance management and know exactly
>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>> http://p.sf.net/sfu/newrelic-dev2dev
>> _______________________________________________
>> Jmol-developers mailing list
>> Jmol-developers@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> 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
>>
>>
>> ------------------------------------------------------------------------------
>> Don't let slow site performance ruin your business. Deploy New Relic APM
>> Deploy New Relic app performance management and know exactly
>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>> http://p.sf.net/sfu/newrelic-dev2dev_______________________________________________
>> Jmol-developers mailing list
>> Jmol-developers@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>
> Eric Henon
> Professeur
> Universite de Reims Champagne-Ardenne
> Institut de Chimie Moleculaire de Reims
> http://www.univ-reims.fr/ICMR
> CNRS UMR 6229
> UFR des Sciences Exactes et Naturelles
> BP 1039
> 51687 Reims Cedex 2 (France)
> Tél./Fax : + 33 (0) 3 26 91 84 97
> eric.he...@univ-reims.fr
>
>
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev
> _______________________________________________
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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
>
>
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev_______________________________________________
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
Eric Henon
Professeur
Universite de Reims Champagne-Ardenne
Institut de Chimie Moleculaire de Reims
http://www.univ-reims.fr/ICMR
CNRS UMR 6229
UFR des Sciences Exactes et Naturelles
BP 1039
51687 Reims Cedex 2 (France)
Tél./Fax : + 33 (0) 3 26 91 84 97
eric.he...@univ-reims.fr
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