Re: [Jmol-users] final testing appreciated

2008-10-04 Thread Robert Hanson
I still think it's a Java caching problem on your machine.

Try downloading RC17. That runs fine for me.

On Mon, Sep 29, 2008 at 12:17 PM, Rolf Huehne <[EMAIL PROTECTED]>wrote:

> Robert Hanson wrote:
> > Hmm. This could be a mix of signed applet versions. Try using
> >
> > jmolInitialize(".","JmolAppletSigned.jar")
> >
> > so that it is definitely picking up just the one JAR file.
> >
> > I'll try
> >
> > jmolInitialize(".","JmolAppletSigned0.jar")
> >
> > and see if I forgot to include something in one of the Jar files. Could
> be
> > -- those were reorganized recently.
> >
>
> I tried this already. All 4 possible applet names show the same error:
>
>  JmolApplet.jar
>  JmolApplet0.jar
>  JmolAppletSigned.jar
>  JmolAppletSigned0.jar
>
> You can try it yourself with the unsigned applet at this URL:
>
>
> http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=2arc&JMOLVERSION=11.6.RC16
>
> When I try this URL on WinXP (Java 1.6.0_07, Firefox 2.0.0.14, IE
> 7.0.5730.11) I get a "java.security.AccessControlException" instead of
> the error reported for Java 1.4 on Linux.
>
>
> Regards,
> Rolf
>
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phone: 507-786-3107


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Re: [Jmol-users] final testing appreciated

2008-10-04 Thread Thomas Stout
Great!  Thanks very much -- that's very useful.
-Tom

(google is amazing!)

On Thu, Sep 25, 2008 at 8:15 AM, Angel Herraez <[EMAIL PROTECTED]> wrote:

> Just found this (well, not me, Google of course):
>
> Clearing Java cache on Linux, Mac, Windows:
> http://www.uwplatt.edu/oit/howto/java-cache.html
>
>
>
>
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Re: [Jmol-users] final testing appreciated

2008-10-01 Thread Robert Hanson
same problem

On Wed, Oct 1, 2008 at 8:47 AM, Rolf Huehne <[EMAIL PROTECTED]> wrote:

> Robert Hanson wrote:
> > Final testing appreciated for Jmol 11.6. Anything you can do to try to
> break
> > it would be great.
> >
>
> The following commands that used to work at least until 11.5.35 give an
> error message in 11.6.RC17:
>
>  bound_box = getProperty("boundboxInfo", "vector");
>  vector_x  = bound_box.x;
>
> script ERROR: unexpected end of script command
> line 1 command 1 of  file null:
>  vector_x = bound_box . >> x <<
>
> Regards,
> Rolf
>
> -
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phone: 507-786-3107


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Re: [Jmol-users] final testing appreciated

2008-10-01 Thread Robert Hanson
yeah, I know what that is thanks.

On Wed, Oct 1, 2008 at 8:47 AM, Rolf Huehne <[EMAIL PROTECTED]> wrote:

> Robert Hanson wrote:
> > Final testing appreciated for Jmol 11.6. Anything you can do to try to
> break
> > it would be great.
> >
>
> The following commands that used to work at least until 11.5.35 give an
> error message in 11.6.RC17:
>
>  bound_box = getProperty("boundboxInfo", "vector");
>  vector_x  = bound_box.x;
>
> script ERROR: unexpected end of script command
> line 1 command 1 of  file null:
>  vector_x = bound_box . >> x <<
>
> Regards,
> Rolf
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
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> prizes
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> ___
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> 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
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Re: [Jmol-users] final testing appreciated

2008-10-01 Thread Angel Herraez
Using 11.6.RC17 I get this error:

eval ERROR: el argumento no es válido
line 1 command 64 of  file null:
  { selected } . >> y << = 0

The offending script is 
select 2.0; spacefill off; wireframe 0.04;  color [xFF00FF]; 
{selected}.y = 0; 

It worked in 11.5.41 at least

(I seem to recall having problems with this before)


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Re: [Jmol-users] final testing appreciated

2008-10-01 Thread Rolf Huehne
Rolf Huehne wrote:
> Robert Hanson wrote:
>> Hmm. This could be a mix of signed applet versions. Try using
>>
>> jmolInitialize(".","JmolAppletSigned.jar")
>>
>> so that it is definitely picking up just the one JAR file.
>>
>> I'll try
>>
>> jmolInitialize(".","JmolAppletSigned0.jar")
>>
>> and see if I forgot to include something in one of the Jar files. Could be
>> -- those were reorganized recently.
>>
> 
> I tried this already. All 4 possible applet names show the same error:
> 
>   JmolApplet.jar
>   JmolApplet0.jar
>   JmolAppletSigned.jar
>   JmolAppletSigned0.jar
> 
> You can try it yourself with the unsigned applet at this URL:
> 
> http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=2arc&JMOLVERSION=11.6.RC16
> 
> When I try this URL on WinXP (Java 1.6.0_07, Firefox 2.0.0.14, IE
> 7.0.5730.11) I get a "java.security.AccessControlException" instead of
> the error reported for Java 1.4 on Linux.
> 

With Jmol 11.6.RC17 the reported specific error on Linux vanished but
now I get the "java.security.AccessControlException" on all systems.

It occurs when using the 'script' or 'load' command if a server absolute
path is provided, e.g.:

  load /ImgLibPDB/tmp/pdb2arc.ent.gz

It doesn't occur if a complete URL is provided instead in the 'load'
command (which apparantly isn't possible with 'script'):

  load http://www.imb-jena.de/ImgLibPDB/tmp/pdb2arc.ent.gz

With Jmol 11.6.RC13 and earlier the problem doesn't exist.

Regards,
Rolf

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Re: [Jmol-users] final testing appreciated

2008-10-01 Thread Rolf Huehne
Robert Hanson wrote:
> Final testing appreciated for Jmol 11.6. Anything you can do to try to break
> it would be great.
> 

The following commands that used to work at least until 11.5.35 give an
error message in 11.6.RC17:

  bound_box = getProperty("boundboxInfo", "vector");
  vector_x  = bound_box.x;

script ERROR: unexpected end of script command
line 1 command 1 of  file null:
  vector_x = bound_box . >> x <<

Regards,
Rolf

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Re: [Jmol-users] final testing appreciated

2008-09-29 Thread Rolf Huehne
Robert Hanson wrote:
> Hmm. This could be a mix of signed applet versions. Try using
> 
> jmolInitialize(".","JmolAppletSigned.jar")
> 
> so that it is definitely picking up just the one JAR file.
> 
> I'll try
> 
> jmolInitialize(".","JmolAppletSigned0.jar")
> 
> and see if I forgot to include something in one of the Jar files. Could be
> -- those were reorganized recently.
> 

I tried this already. All 4 possible applet names show the same error:

  JmolApplet.jar
  JmolApplet0.jar
  JmolAppletSigned.jar
  JmolAppletSigned0.jar

You can try it yourself with the unsigned applet at this URL:

http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=2arc&JMOLVERSION=11.6.RC16

When I try this URL on WinXP (Java 1.6.0_07, Firefox 2.0.0.14, IE
7.0.5730.11) I get a "java.security.AccessControlException" instead of
the error reported for Java 1.4 on Linux.


Regards,
Rolf

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Re: [Jmol-users] final testing appreciated

2008-09-29 Thread Robert Hanson
Hmm. This could be a mix of signed applet versions. Try using

jmolInitialize(".","JmolAppletSigned.jar")

so that it is definitely picking up just the one JAR file.

I'll try

jmolInitialize(".","JmolAppletSigned0.jar")

and see if I forgot to include something in one of the Jar files. Could be
-- those were reorganized recently.

Bob


On Mon, Sep 29, 2008 at 11:03 AM, Rolf Huehne <[EMAIL PROTECTED]>wrote:

> Robert Hanson wrote:
> > Final testing appreciated for Jmol 11.6. Anything you can do to try to
> break
> > it would be great.
> >
> > One bug I know about seems to be that the applet stalls if a file load
> error
> > occurs. I'm onto that one.
> >
>
> I tried to use the signed applet but when I try to load a file I get the
> following Java error message:
>
> java.lang.NoSuchMethodError: java.lang.Thread.getId()J
>at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
>at
> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown
> Source)
>at
> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown
> Source)
>at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown
> Source)
>at java.lang.Thread.run(Thread.java:534)
>
> The same error also occurs if I use any of the "Load/Save" options in
> the popup menu and in the unsigned applet.
>
> Interestingly, the popup menu problem with 2 monitors (Jmol on the right
> monitor, popup menu on the left monitor) vanishes with the signed applet
> (Jmol + popup menu on the right monitor).
>
>  Test System 
>  Jmol   : 11.6.RC16
>  Java   : 1.4.2_18
>  OS : Linux, OpenSuSE 10.2
>  Browser: Firefox 2.0.0.16
> 
>
> Regards,
> Rolf
>
> -
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Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
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Re: [Jmol-users] final testing appreciated

2008-09-29 Thread Rolf Huehne
Robert Hanson wrote:
> Final testing appreciated for Jmol 11.6. Anything you can do to try to break
> it would be great.
> 
> One bug I know about seems to be that the applet stalls if a file load error
> occurs. I'm onto that one.
> 

I tried to use the signed applet but when I try to load a file I get the
following Java error message:

java.lang.NoSuchMethodError: java.lang.Thread.getId()J
at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown
Source)
at
org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown
Source)
at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source)
at java.lang.Thread.run(Thread.java:534)

The same error also occurs if I use any of the "Load/Save" options in
the popup menu and in the unsigned applet.

Interestingly, the popup menu problem with 2 monitors (Jmol on the right
monitor, popup menu on the left monitor) vanishes with the signed applet
(Jmol + popup menu on the right monitor).

 Test System 
 Jmol   : 11.6.RC16
 Java   : 1.4.2_18
 OS : Linux, OpenSuSE 10.2
 Browser: Firefox 2.0.0.16


Regards,
Rolf

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Re: [Jmol-users] final testing appreciated

2008-09-29 Thread Angel Herraez
I've added some information about clearing Java cache and other Java-
related stuff into the Wiki: main page > Running Jmol > Solving Java 
Problems
Also linked from Running Jmol Application and Running Jmol Applet

Any confirmation or correction of that info from the Mac or Linux 
users will be welcome --I cannot test those systems.


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Re: [Jmol-users] final testing appreciated

2008-09-25 Thread Angel Herraez
Just found this (well, not me, Google of course):

Clearing Java cache on Linux, Mac, Windows:
http://www.uwplatt.edu/oit/howto/java-cache.html




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Re: [Jmol-users] final testing appreciated

2008-09-25 Thread Robert Hanson
It's the Java cache.

On Thu, Sep 25, 2008 at 9:55 AM, Thomas Stout <[EMAIL PROTECTED]>wrote:

>
> That sounds like a good explanation, but unfortunately I had the same
> problem on both WinXP and linux & I also cleared the FF cache on both
> platforms (in addition to re-starting FF and also re-starting the computer
> (WinXP).  I may go back and try it again, but like I said, I'm happily
> using the signed Applet now
>
> -Tom
>
> PS - No, I did NOT clear the java cache -- I have no idea how to do that
> under linux!!
>
>
>
> On Thu, Sep 25, 2008 at 1:35 AM, Angel Herraez <[EMAIL PROTECTED]>wrote:
>
>> El 24 Sep 2008 a las 17:35, Thomas Stout escribió:
>> > Oh, I restarted everything - including the computer and re-downloaded
>>
>>
>> My experience with Firefox (Win) is that on some occasions it caches
>> the applet and insists on using the cached copy even after restart
>> and even if a new applet version is being tried. Apart from trying
>> hard reload of page, closing and reopening Firefox, you may need to
>> clear Firefox and/or Java caches.
>> That would explain Tom's problem, since only the unsigned RC14 applet
>> would have been cached and the signed one would eb recognized as a
>> different one.
>>
>>
>> -
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>> challenge
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>> world
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>
>
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>


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Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] final testing appreciated

2008-09-25 Thread Thomas Stout
That sounds like a good explanation, but unfortunately I had the same
problem on both WinXP and linux & I also cleared the FF cache on both
platforms (in addition to re-starting FF and also re-starting the computer
(WinXP).  I may go back and try it again, but like I said, I'm happily
using the signed Applet now

-Tom

PS - No, I did NOT clear the java cache -- I have no idea how to do that
under linux!!



On Thu, Sep 25, 2008 at 1:35 AM, Angel Herraez <[EMAIL PROTECTED]> wrote:

> El 24 Sep 2008 a las 17:35, Thomas Stout escribió:
> > Oh, I restarted everything - including the computer and re-downloaded
>
>
> My experience with Firefox (Win) is that on some occasions it caches
> the applet and insists on using the cached copy even after restart
> and even if a new applet version is being tried. Apart from trying
> hard reload of page, closing and reopening Firefox, you may need to
> clear Firefox and/or Java caches.
> That would explain Tom's problem, since only the unsigned RC14 applet
> would have been cached and the signed one would eb recognized as a
> different one.
>
>
> -
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Re: [Jmol-users] final testing appreciated

2008-09-25 Thread Robert Hanson
also, you can add parameters like that as though they were callbacks:

jmolInitialize("./", "JmolApplet.jar")
jmolSetCallback("draggable", true)
jmolApplet(400)

On Thu, Sep 25, 2008 at 3:31 AM, Angel Herraez <[EMAIL PROTECTED]> wrote:

> Re: draggable applet
>
> Here is a partial copy of my previous post (4 Sep.)
>
> --- Forwarded message follows ---
> [...]
> I've tested it and it works. The applet detaches (Firefox 3 and
> Chrome) and stays as a borderless window with a tiny close button
> (that returns it to the browser), no way to resize. Maybe useless,
> but cool!
>
> This is the code I've used:
>
> jmolInitialize("./", "JmolApplet.jar")
>  jmolSetDocument(0)
>  var s= jmolApplet(400)
>  s = jmolAppletAddParam(s,"draggable", "true")
>  document.write(s)
>  jmolSetDocument(document)
>
> --- End of forwarded message ---
>
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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
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Re: [Jmol-users] final testing appreciated

2008-09-25 Thread Angel Herraez
Re: draggable applet

Here is a partial copy of my previous post (4 Sep.)

--- Forwarded message follows ---
[...]
I've tested it and it works. The applet detaches (Firefox 3 and 
Chrome) and stays as a borderless window with a tiny close button 
(that returns it to the browser), no way to resize. Maybe useless, 
but cool! 

This is the code I've used: 

jmolInitialize("./", "JmolApplet.jar") 
  jmolSetDocument(0) 
  var s= jmolApplet(400) 
  s = jmolAppletAddParam(s,"draggable", "true") 
  document.write(s) 
  jmolSetDocument(document) 

--- End of forwarded message ---

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Re: [Jmol-users] final testing appreciated

2008-09-25 Thread Angel Herraez
El 24 Sep 2008 a las 17:35, Thomas Stout escribió:
> Oh, I restarted everything - including the computer and re-downloaded 


My experience with Firefox (Win) is that on some occasions it caches 
the applet and insists on using the cached copy even after restart 
and even if a new applet version is being tried. Apart from trying 
hard reload of page, closing and reopening Firefox, you may need to 
clear Firefox and/or Java caches.
That would explain Tom's problem, since only the unsigned RC14 applet 
would have been cached and the signed one would eb recognized as a 
different one.


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Re: [Jmol-users] final testing appreciated

2008-09-25 Thread Angel Herraez
El 24 Sep 2008 a las 16:06, Robert Hanson escribió:

> OH, OK, I'm glad that worked. I had heard about that and was 
> wondering about it. Is that what then allows one to drag the applet 
> out of the window and onto the desktop?

As I understand, the "draggable" is a feature of applets in the new 
Java 6u10 (still in RC, or beta). I've tried it and it works with 
Jmol and JChemPaint (if seems to be a general feature) but I think it 
has to be activated when inserting the applet; I'll chase my test 
code and post it here if anyone is interested --frankly I don't see 
the utility.

As for the Firefox/Mac Java fix, it was an old issue with Apple Java 
versions and Firefox, but In had understood that is was soulve din 
recent versions of Java and/or Firefox. It seems not the case.
This is documented at
http://wiki.jmol.org:81/index.php/Support/Osx



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Re: [Jmol-users] final testing appreciated

2008-09-24 Thread rob yang

Not sure about the dragging to desktop part. I tried out of curiosity without 
success. But the java plugin made the applet working again in ff3, so yeah!

-Rob

Date: Wed, 24 Sep 2008 16:06:54 -0500
From: [EMAIL PROTECTED]
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] final testing appreciated

OH, OK, I'm glad that worked. I had heard about that and was wondering about 
it. Is that what then allows one to drag the applet out of the window and onto 
the desktop?

Bob



On Wed, Sep 24, 2008 at 3:45 PM, rob yang <[EMAIL PROTECTED]> wrote:






I installed this: 
http://sourceforge.net/project/showfiles.php?group_id=107955&package_id=116499&release_id=591572


Date: Wed, 24 Sep 2008 15:40:50 -0500
From: [EMAIL PROTECTED]
To: jmol-users@lists.sourceforge.net

Subject: Re: [Jmol-users] final testing appreciated

so do we conclude that the firefox3/Mac issue is resolved? What was the 
download you had to do to get that working?


Bob


On Wed, Sep 24, 2008 at 3:38 PM, rob yang <[EMAIL PROTECTED]> wrote:






Angel,
The same html was working in firefox2 indeed. Firefox3 was giving me errors 
roughly 80% of time (works occasionally without any intentional tweaking to the 
browser). I just installed the java plugins as recommended by browsercheck, and 
now I am indeed admiring my jmol webpage in firefox3 without any problem.



-Rob

> From: [EMAIL PROTECTED]
> To: jmol-users@lists.sourceforge.net


> Date: Wed, 24 Sep 2008 22:21:06 +0200
> Subject: Re: [Jmol-users] final testing appreciated
> 
> Rob, you must take with caution that diagnostics. Browsercheck is rather old* 
> and its report 


> is based on the browser identity (userAgent), not by testing the features.
> Do you mean that Firefox 2 was working correctly and Firefox 3 fails, on the 
> same MacOS? 
> If so, it's probably not that reason then, since both versions should pass 
> (or fail) the test in 


> the  same way.
> 
> 
> (* I just found that when the browser is compatible, it doesn't report any 
> messages, but only 
> the green box. This is due to a bad code, using  ==  instead of = for an 
> assignment. I'm after 


> the fix)
> 
> 
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes


> Grand prize is a trip for two to an Open Source event anywhere in the world
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> https://lists.sourceforge.net/lists/listinfo/jmol-users



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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



 

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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



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Re: [Jmol-users] final testing appreciated

2008-09-24 Thread Thomas Stout
Oh, I restarted everything - including the computer and re-downloaded all of
the gzipped, the zip-ped and the full-source included versions!  Not a big
deal to me since I've switched over to the signed applet in order to provide
local file loading and image saving...

-Tom


On Wed, Sep 24, 2008 at 11:58 AM, Robert Hanson <[EMAIL PROTECTED]> wrote:

> Tom, could be your browser didn't get fully closed. You have to make sure
> all browser windows are closed and then restart the browser to use a newer
> version of the applet. Just putting it in a directory and navigating to a
> page won't do it. The release files are fine.
>
> Bob
>
>
> On Wed, Sep 24, 2008 at 12:16 PM, Thomas Stout <[EMAIL PROTECTED]>wrote:
>
>>
>> One oddity that I've just noticed: I downloaded 11.6.RC16 (several times
>> in the last 24 hours) and find that if I run the stand alone or load the
>> signed applet, they report version 11.6.RC16.  However, if I run the
>> un-signed Applet, it is still reporting version 11.6.RC14 -- is this known
>> and/or intentional?
>>
>> Cheers,
>> Tom
>>
>>
>> On Mon, Sep 22, 2008 at 4:14 PM, Robert Hanson <[EMAIL PROTECTED]>wrote:
>>
>>> Final testing appreciated for Jmol 11.6. Anything you can do to try to
>>> break it would be great.
>>>
>>> One bug I know about seems to be that the applet stalls if a file load
>>> error occurs. I'm onto that one.
>>>
>>> Bob
>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Professor of Chemistry
>>> 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
>>>
>>> -
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>> challenge
>>> Build the coolest Linux based applications with Moblin SDK & win great
>>> prizes
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>>> world
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>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>> -
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win great
>> prizes
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>> world
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>> ___
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>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> 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
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
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Re: [Jmol-users] final testing appreciated

2008-09-24 Thread Robert Hanson
OH, OK, I'm glad that worked. I had heard about that and was wondering about
it. Is that what then allows one to drag the applet out of the window and
onto the desktop?

Bob


On Wed, Sep 24, 2008 at 3:45 PM, rob yang <[EMAIL PROTECTED]> wrote:

>  I installed this:
> http://sourceforge.net/project/showfiles.php?group_id=107955&package_id=116499&release_id=591572
>
> --
> Date: Wed, 24 Sep 2008 15:40:50 -0500
> From: [EMAIL PROTECTED]
> To: jmol-users@lists.sourceforge.net
> Subject: Re: [Jmol-users] final testing appreciated
>
> so do we conclude that the firefox3/Mac issue is resolved? What was the
> download you had to do to get that working?
>
> Bob
>
>
> On Wed, Sep 24, 2008 at 3:38 PM, rob yang <[EMAIL PROTECTED]> wrote:
>
>  Angel,
> The same html was working in firefox2 indeed. Firefox3 was giving me errors
> roughly 80% of time (works occasionally without any intentional tweaking to
> the browser). I just installed the java plugins as recommended by
> browsercheck, and now I am indeed admiring my jmol webpage in firefox3
> without any problem.
>
> -Rob
>
> > From: [EMAIL PROTECTED]
> > To: jmol-users@lists.sourceforge.net
> > Date: Wed, 24 Sep 2008 22:21:06 +0200
> > Subject: Re: [Jmol-users] final testing appreciated
> >
> > Rob, you must take with caution that diagnostics. Browsercheck is rather
> old* and its report
> > is based on the browser identity (userAgent), not by testing the
> features.
> > Do you mean that Firefox 2 was working correctly and Firefox 3 fails, on
> the same MacOS?
> > If so, it's probably not that reason then, since both versions should
> pass (or fail) the test in
> > the same way.
> >
> >
> > (* I just found that when the browser is compatible, it doesn't report
> any messages, but only
> > the green box. This is due to a bad code, using == instead of = for an
> assignment. I'm after
> > the fix)
> >
> >
> > -
> > This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> > Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> > Grand prize is a trip for two to an Open Source event anywhere in the
> world
> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > ___
> > Jmol-users mailing list
> > Jmol-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> --
> Use Windows Live Messenger to send messages to your buddies on their mobile
> phones Find out more on our PC to Mobile website <http://www.pc2mobile.ca>
>
> -
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> challenge
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> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> 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
>
> --
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
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> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Professor of Chemistry
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
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Re: [Jmol-users] final testing appreciated

2008-09-24 Thread rob yang

I installed this: 
http://sourceforge.net/project/showfiles.php?group_id=107955&package_id=116499&release_id=591572

Date: Wed, 24 Sep 2008 15:40:50 -0500
From: [EMAIL PROTECTED]
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] final testing appreciated

so do we conclude that the firefox3/Mac issue is resolved? What was the 
download you had to do to get that working?

Bob


On Wed, Sep 24, 2008 at 3:38 PM, rob yang <[EMAIL PROTECTED]> wrote:






Angel,
The same html was working in firefox2 indeed. Firefox3 was giving me errors 
roughly 80% of time (works occasionally without any intentional tweaking to the 
browser). I just installed the java plugins as recommended by browsercheck, and 
now I am indeed admiring my jmol webpage in firefox3 without any problem.


-Rob

> From: [EMAIL PROTECTED]
> To: jmol-users@lists.sourceforge.net

> Date: Wed, 24 Sep 2008 22:21:06 +0200
> Subject: Re: [Jmol-users] final testing appreciated
> 
> Rob, you must take with caution that diagnostics. Browsercheck is rather old* 
> and its report 

> is based on the browser identity (userAgent), not by testing the features.
> Do you mean that Firefox 2 was working correctly and Firefox 3 fails, on the 
> same MacOS? 
> If so, it's probably not that reason then, since both versions should pass 
> (or fail) the test in 

> the  same way.
> 
> 
> (* I just found that when the browser is compatible, it doesn't report any 
> messages, but only 
> the green box. This is due to a bad code, using  ==  instead of = for an 
> assignment. I'm after 

> the fix)
> 
> 
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes

> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/

> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users


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-- 
Robert M. Hanson
Professor of Chemistry
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



_

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Re: [Jmol-users] final testing appreciated

2008-09-24 Thread Robert Hanson
so do we conclude that the firefox3/Mac issue is resolved? What was the
download you had to do to get that working?

Bob


On Wed, Sep 24, 2008 at 3:38 PM, rob yang <[EMAIL PROTECTED]> wrote:

>  Angel,
> The same html was working in firefox2 indeed. Firefox3 was giving me errors
> roughly 80% of time (works occasionally without any intentional tweaking to
> the browser). I just installed the java plugins as recommended by
> browsercheck, and now I am indeed admiring my jmol webpage in firefox3
> without any problem.
>
> -Rob
>
> > From: [EMAIL PROTECTED]
> > To: jmol-users@lists.sourceforge.net
> > Date: Wed, 24 Sep 2008 22:21:06 +0200
> > Subject: Re: [Jmol-users] final testing appreciated
> >
> > Rob, you must take with caution that diagnostics. Browsercheck is rather
> old* and its report
> > is based on the browser identity (userAgent), not by testing the
> features.
> > Do you mean that Firefox 2 was working correctly and Firefox 3 fails, on
> the same MacOS?
> > If so, it's probably not that reason then, since both versions should
> pass (or fail) the test in
> > the same way.
> >
> >
> > (* I just found that when the browser is compatible, it doesn't report
> any messages, but only
> > the green box. This is due to a bad code, using == instead of = for an
> assignment. I'm after
> > the fix)
> >
> >
> > -
> > This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> > Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> > Grand prize is a trip for two to an Open Source event anywhere in the
> world
> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > ___
> > Jmol-users mailing list
> > Jmol-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> --
> Use Windows Live Messenger to send messages to your buddies on their mobile
> phones Find out more on our PC to Mobile website <http://www.pc2mobile.ca>
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
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> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Professor of Chemistry
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
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
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Re: [Jmol-users] final testing appreciated

2008-09-24 Thread rob yang

Angel,
The same html was working in firefox2 indeed. Firefox3 was giving me errors 
roughly 80% of time (works occasionally without any intentional tweaking to the 
browser). I just installed the java plugins as recommended by browsercheck, and 
now I am indeed admiring my jmol webpage in firefox3 without any problem.

-Rob

> From: [EMAIL PROTECTED]
> To: jmol-users@lists.sourceforge.net
> Date: Wed, 24 Sep 2008 22:21:06 +0200
> Subject: Re: [Jmol-users] final testing appreciated
> 
> Rob, you must take with caution that diagnostics. Browsercheck is rather old* 
> and its report 
> is based on the browser identity (userAgent), not by testing the features.
> Do you mean that Firefox 2 was working correctly and Firefox 3 fails, on the 
> same MacOS? 
> If so, it's probably not that reason then, since both versions should pass 
> (or fail) the test in 
> the  same way.
> 
> 
> (* I just found that when the browser is compatible, it doesn't report any 
> messages, but only 
> the green box. This is due to a bad code, using  ==  instead of = for an 
> assignment. I'm after 
> the fix)
> 
> 
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

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Re: [Jmol-users] final testing appreciated

2008-09-24 Thread Angel Herráez
Rob, you must take with caution that diagnostics. Browsercheck is rather old* 
and its report 
is based on the browser identity (userAgent), not by testing the features.
Do you mean that Firefox 2 was working correctly and Firefox 3 fails, on the 
same MacOS? 
If so, it's probably not that reason then, since both versions should pass (or 
fail) the test in 
the  same way.


(* I just found that when the browser is compatible, it doesn't report any 
messages, but only 
the green box. This is due to a bad code, using  ==  instead of = for an 
assignment. I'm after 
the fix)


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Re: [Jmol-users] final testing appreciated

2008-09-24 Thread rob yang

Bob,
Yes, Jmol has been working great for me before I upgraded to firefox3. I know 
it's a browser problem because it still works great on safari and IE7. After 
doing the browser check, I now know why and it has nothing to do with Jmol. It 
is because firefox3 on mac's don't "support LiveConnect communications between 
JavaScript and Java applets." This explains why jmol applet loads just fine on 
my webpage, but the error occurs whenever buttons are clicked. 
Thank you.

Here's the full explaination given by browsercheck for reference:
--
Netscape/Mozilla/FireFox on Macintosh do not have access to the
latest Java release and therefore do not support LiveConnect
communications between JavaScript and Java applets. The Jmol
applet itself will function properly. However, web pages constructed
with HTML controls such as buttons, checkboxes, and links will not
function properly because the controls cannot send the script commands
to the Jmol applet.We recommend that you consider using Safari
or another Macintosh browser that supports LiveConnect communications
between JavaScript and Java applets.Or, you can try installing and using the 
Macintosh OS X Java Plug-in fromjavaplugin.sourceforge.net



  
Operating System

  mac

  
  

  Web browser


  mozilla

  
  

  Browser version


  5

  
  

  navigator.userAgent


  Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.0.1) 
Gecko/2008070206 Firefox/3.0.1

  
  

  has getElementById()


  true

  
  

  navigator.javaEnabled()


  false
--


Date: Wed, 24 Sep 2008 13:44:51 -0500
From: [EMAIL PROTECTED]
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] final testing appreciated

Rob,

This message is from some version of browsercheck, I think. 

When you go here:

http://jmol.sourceforge.net/browsercheck/


do you get that same message?

I suspect the problem is that somebody's HTML needs updating. 

Does Jmol work fine for you in general, anyway?

Bob



On Wed, Sep 24, 2008 at 12:03 PM, rob yang <[EMAIL PROTECTED]> wrote:










Final testing appreciated for Jmol 11.6. Anything you can do to try to break it 
would be great. 

Has anyone had problems with Jmol applet when using firefox 3? I sometimes 
(strangely not always) get the following error:


Your web browser is not fully compatible with Jmol
browser: mozilla   version: 5   os: mac
mozilla/5.0 (macintosh; u; intel mac os x 10.5; en-us; rv:1.9.0.1) 
gecko/2008070206 firefox/3.0.1



-Rob



 

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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



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Re: [Jmol-users] final testing appreciated

2008-09-24 Thread Robert Hanson
Rob,

This message is from some version of browsercheck, I think.

When you go here:

http://jmol.sourceforge.net/browsercheck/

do you get that same message?

I suspect the problem is that somebody's HTML needs updating.

Does Jmol work fine for you in general, anyway?

Bob



On Wed, Sep 24, 2008 at 12:03 PM, rob yang <[EMAIL PROTECTED]> wrote:

>
>
> --
>
>
> Final testing appreciated for Jmol 11.6. Anything you can do to try to
> break it would be great.
>
> Has anyone had problems with Jmol applet when using firefox 3? I sometimes
> (strangely not always) get the following error:
>
> Your web browser is not fully compatible with Jmol
> browser: mozilla   version: 5   os: mac
> mozilla/5.0 (macintosh; u; intel mac os x 10.5; en-us; rv:1.9.0.1)
> gecko/2008070206 firefox/3.0.1
>
>
> -Rob
>
> --
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Professor of Chemistry
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
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Re: [Jmol-users] final testing appreciated

2008-09-24 Thread Robert Hanson
Tom, could be your browser didn't get fully closed. You have to make sure
all browser windows are closed and then restart the browser to use a newer
version of the applet. Just putting it in a directory and navigating to a
page won't do it. The release files are fine.

Bob


On Wed, Sep 24, 2008 at 12:16 PM, Thomas Stout <[EMAIL PROTECTED]>wrote:

>
> One oddity that I've just noticed: I downloaded 11.6.RC16 (several times in
> the last 24 hours) and find that if I run the stand alone or load the signed
> applet, they report version 11.6.RC16.  However, if I run the un-signed
> Applet, it is still reporting version 11.6.RC14 -- is this known and/or
> intentional?
>
> Cheers,
> Tom
>
>
> On Mon, Sep 22, 2008 at 4:14 PM, Robert Hanson <[EMAIL PROTECTED]> wrote:
>
>> Final testing appreciated for Jmol 11.6. Anything you can do to try to
>> break it would be great.
>>
>> One bug I know about seems to be that the applet stalls if a file load
>> error occurs. I'm onto that one.
>>
>> Bob
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> 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
>>
>> -
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win great
>> prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the
>> world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
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> ___
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Professor of Chemistry
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
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Re: [Jmol-users] final testing appreciated

2008-09-24 Thread Robert Hanson
I'll check into that.

On Wed, Sep 24, 2008 at 12:16 PM, Thomas Stout <[EMAIL PROTECTED]>wrote:

>
> One oddity that I've just noticed: I downloaded 11.6.RC16 (several times in
> the last 24 hours) and find that if I run the stand alone or load the signed
> applet, they report version 11.6.RC16.  However, if I run the un-signed
> Applet, it is still reporting version 11.6.RC14 -- is this known and/or
> intentional?
>
> Cheers,
> Tom
>
>
> On Mon, Sep 22, 2008 at 4:14 PM, Robert Hanson <[EMAIL PROTECTED]> wrote:
>
>> Final testing appreciated for Jmol 11.6. Anything you can do to try to
>> break it would be great.
>>
>> One bug I know about seems to be that the applet stalls if a file load
>> error occurs. I'm onto that one.
>>
>> Bob
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> 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
>>
>> -
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win great
>> prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the
>> world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
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> ___
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
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>


-- 
Robert M. Hanson
Professor of Chemistry
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
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Re: [Jmol-users] final testing appreciated

2008-09-24 Thread Thomas Stout
One oddity that I've just noticed: I downloaded 11.6.RC16 (several times in
the last 24 hours) and find that if I run the stand alone or load the signed
applet, they report version 11.6.RC16.  However, if I run the un-signed
Applet, it is still reporting version 11.6.RC14 -- is this known and/or
intentional?

Cheers,
Tom


On Mon, Sep 22, 2008 at 4:14 PM, Robert Hanson <[EMAIL PROTECTED]> wrote:

> Final testing appreciated for Jmol 11.6. Anything you can do to try to
> break it would be great.
>
> One bug I know about seems to be that the applet stalls if a file load
> error occurs. I'm onto that one.
>
> Bob
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> 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
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
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Re: [Jmol-users] final testing appreciated

2008-09-24 Thread Thomas Stout
for what it's worth:  I have never seen that using FF 3 on WinXP or linux
...  I don't have a modern Mac, so have not been running Jmol there...

-Tom



On Wed, Sep 24, 2008 at 10:03 AM, rob yang <[EMAIL PROTECTED]> wrote:

>
>
> --
>
>
> Final testing appreciated for Jmol 11.6. Anything you can do to try to
> break it would be great.
>
> Has anyone had problems with Jmol applet when using firefox 3? I sometimes
> (strangely not always) get the following error:
>
> Your web browser is not fully compatible with Jmol
> browser: mozilla   version: 5   os: mac
> mozilla/5.0 (macintosh; u; intel mac os x 10.5; en-us; rv:1.9.0.1)
> gecko/2008070206 firefox/3.0.1
>
>
> -Rob
>
> --
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
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Re: [Jmol-users] final testing appreciated

2008-09-24 Thread rob yang





Final testing appreciated for Jmol 11.6. Anything you can do to try to break it 
would be great. 

Has anyone had problems with Jmol applet when using firefox 3? I sometimes 
(strangely not always) get the following error:

Your web browser is not fully compatible with Jmol
browser: mozilla   version: 5   os: mac
mozilla/5.0 (macintosh; u; intel mac os x 10.5; en-us; rv:1.9.0.1) 
gecko/2008070206 firefox/3.0.1


-Rob



_

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Re: [Jmol-users] final testing appreciated

2008-09-22 Thread Robert Hanson
(That's the SIGNED applet...)

On Mon, Sep 22, 2008 at 6:14 PM, Robert Hanson <[EMAIL PROTECTED]> wrote:

>
> One bug I know about seems to be that the applet stalls if a file load
> error occurs. I'm onto that one.
>
> Bob
>
>
>
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