Re: [Jmol-users] Java Update 65 Causing Issues?

[DCU]

Agreed - the last part is probably not essential, though a useful check if 
things don't work. My guess is that the problem lies with the 1st part, i.e. 
ensuring that Java on the visitor's computer is configured to permit it to use 
the visited Jmol website.


> On 30 Jul 2014, at 06:34, Robert Hanson  wrote:
> 
> 
> 
> 
>> On Tue, Jul 29, 2014 at 3:14 PM, Albert Pratt  wrote:
>>  
>> When version 65 was downloaded and installed it didn't work with Jmol.  
>> However, following advice, I configured Java (Start>Java>Configure 
>> Java>Security>Edit Site List) by including the URLs of relevant Jmol sites 
>> (the http:// prefix appears to be essential). I also checked that Java was 
>> enabled in Chrome36, Firefox31 and IE11.  
>> 
>> All three browsers now operate with test page 2 using Java 7, version 65.
> 
> This last part DEFINITELY should not be necessary. Java should be doing that 
> automatically when you first start up an applet. Maybe this is the issue with 
> 65.
> 
> 
>  
>> 
>> 
>> 
>>  
>> 
>> 
>> 
>>> On 29 July 2014 10:45, Robert Hanson  wrote:
>>> I've done that now -- it is on the "Installing Jmol" template.
>>> 
>>> 
 On Mon, Jul 28, 2014 at 10:52 AM, Robert Hanson  wrote:
 It would be good if someone would  get this into the Jmol wiki.
 
 
> On Sat, Jul 26, 2014 at 6:55 PM, Eric Martz  
> wrote:
> Dear Pshemak,
> 
> Thanks so much -- your suggestion enabled Java 7 update 65 to work
> with Jmol on my Windows 7 system.
> 
> 1. I used Control Panel, Programs, Uninstall to uninstall the
> non-working Java 7 update 65.
> 
> 2. Using the free Windows search program Agent Ransack (truly
> excellent, blows away Windows Explorer for finding system files), I
> located these:
> 
> C:\Users\Eric Martz\AppData\Roaming\Oracle
> C:\ProgramData\Oracle
> C:\Users\Eric Martz\AppData\LocalLow\Sun
> C:\ProgramData\Sun
> 
> I deleted all 4 of those directories and all their contents.
> 
> 3. I went to java.com and downloaded the installer for Java 7 update
> 65, and installed it. Now Jmol_S works again.
> 
> OTHER OBSERVATIONS
> 
> After uninstalling Java 7 update 65, and installing Java 7, update
> 60, Jmol_S worked. I wondered if then upgrading to 65 would run
> Jmol_S. It did NOT.
> 
> I have explained two ways to get Jmol to work again here:
> 
> http://proteopedia.org/wiki/index.php/Installing_and_enabling_Java#Windows
> 
> -Eric
> 
> At 7/25/14, you wrote:
> >I had similar problems (I reported them some time ago).  They were
> >limited to one Windows machine (Win 7, Firefox, Chrome, IE) of 3 tried
> >(Win 7 and Win 8).
> >
> >My problem was with the update procedure.  It was insufficient to
> >uninstall the old version, I had to delete (after uninstalling) all Java
> >directories (hiding under Oracle and even Sun Systems names in Users
> >directories).
> >
> >After clean up, it works fine.
> >
> >One curiosity: I have tested multiple Java applets (not just Jmol) and
> >only Jmol did not work for me (it never fully loaded to get to the
> >permission window, no error messages).
> >
> >Please report back if it work for you too.
> >
> >PM
> >
> >
> >
> >
> >On 7/25/2014 7:26 PM, Eric Martz wrote:
> > > In Windows 7, my tests indicate that Java 7 update 65 does not work
> > > with the current Jmol_S, or recent 14.0.17 Jmol_S. However, update 60
> > > does work.
> > >
> > > Do others confirm this?
> > >
> > > Previous emails indicate that Java 7 update 65 runs Jmol applet in
> > > Windows 8 (Angel H), and that Java 8 runs Jmol applet (Henry R, OS
> > > not specified?).
> > >
> > > However, on Windows 7, when I upgraded Java 7 from 60 to 65 today, I
> > > could not get the current Jmol_S applet to work in IE 11, Firefox 31,
> > > or Chrome (current).
> > >
> > > I tested Jmol 14.2.3
> > > http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
> > > and Jmol_S 14.0.17
> > > http://bioinformatics.org/firstglance/fgij/fg.htm?mol=1d66&JAVA
> > >
> > > Curiously, a very old old unsigned applet (11.4.RC3) worked in
> > > Firefox and Chrome (but not in IE).
> > > http://www.umass.edu/molvis/tutorials/dna/dnapairs.htm
> > >
> > > All the above test sites work fine with Java 7 update 65 on OS X
> > > (Mavericks) with Safari or Firefox.
> > >
> > > All the above test sites work fine with Java 7 update 65 on Windows
> > > XP in Firefox 31 or Internet Explorer 8.
> > >
> > > I then uninstalled Java from my Windows 7, downloaded and installed
> > > Java 7 update 60
> > > (x86 version).
> > >
> > http://www.oracle.com/technetwork/java/javase/downloads/java-archive-downloads-javase7-521261.html
> > > Everything worked again.
>

Re: [Jmol-users] Java Update 65 Causing Issues?

[Robert Hanson]

On Tue, Jul 29, 2014 at 3:14 PM, Albert Pratt  wrote:


> When version 65 was downloaded and installed it didn't work with Jmol.
>  However, following advice, I configured Java (Start>Java>Configure
> Java>Security>Edit Site List) by including the URLs of relevant Jmol sites
> (the http:// prefix appears to be essential). I also checked
>  that Java was
> enabled in Chrome36, Firefox31 and IE11.
>
> All three browsers now operate with test page 2 using Java 7, version 65.
>
>
>
This last part DEFINITELY should not be necessary. Java should be doing
that automatically when you first start up an applet. Maybe this is the
issue with 65.




>
>
>
>
>
>
>
> On 29 July 2014 10:45, Robert Hanson  wrote:
>
>> I've done that now -- it is on the "Installing Jmol" template.
>>
>>
>> On Mon, Jul 28, 2014 at 10:52 AM, Robert Hanson 
>> wrote:
>>
>>> It would be good if someone would  get this into the Jmol wiki.
>>>
>>>
>>> On Sat, Jul 26, 2014 at 6:55 PM, Eric Martz 
>>> wrote:
>>>
 Dear Pshemak,

 Thanks so much -- your suggestion enabled Java 7 update 65 to work
 with Jmol on my Windows 7 system.

 1. I used Control Panel, Programs, Uninstall to uninstall the
 non-working Java 7 update 65.

 2. Using the free Windows search program Agent Ransack (truly
 excellent, blows away Windows Explorer for finding system files), I
 located these:

 C:\Users\Eric Martz\AppData\Roaming\Oracle
 C:\ProgramData\Oracle
 C:\Users\Eric Martz\AppData\LocalLow\Sun
 C:\ProgramData\Sun

 I deleted all 4 of those directories and all their contents.

 3. I went to java.com and downloaded the installer for Java 7 update
 65, and installed it. Now Jmol_S works again.

 OTHER OBSERVATIONS

 After uninstalling Java 7 update 65, and installing Java 7, update
 60, Jmol_S worked. I wondered if then upgrading to 65 would run
 Jmol_S. It did NOT.

 I have explained two ways to get Jmol to work again here:


 http://proteopedia.org/wiki/index.php/Installing_and_enabling_Java#Windows

 -Eric

 At 7/25/14, you wrote:
 >I had similar problems (I reported them some time ago).  They were
 >limited to one Windows machine (Win 7, Firefox, Chrome, IE) of 3 tried
 >(Win 7 and Win 8).
 >
 >My problem was with the update procedure.  It was insufficient to
 >uninstall the old version, I had to delete (after uninstalling) all
 Java
 >directories (hiding under Oracle and even Sun Systems names in Users
 >directories).
 >
 >After clean up, it works fine.
 >
 >One curiosity: I have tested multiple Java applets (not just Jmol) and
 >only Jmol did not work for me (it never fully loaded to get to the
 >permission window, no error messages).
 >
 >Please report back if it work for you too.
 >
 >PM
 >
 >
 >
 >
 >On 7/25/2014 7:26 PM, Eric Martz wrote:
 > > In Windows 7, my tests indicate that Java 7 update 65 does not work
 > > with the current Jmol_S, or recent 14.0.17 Jmol_S. However, update
 60
 > > does work.
 > >
 > > Do others confirm this?
 > >
 > > Previous emails indicate that Java 7 update 65 runs Jmol applet in
 > > Windows 8 (Angel H), and that Java 8 runs Jmol applet (Henry R, OS
 > > not specified?).
 > >
 > > However, on Windows 7, when I upgraded Java 7 from 60 to 65 today, I
 > > could not get the current Jmol_S applet to work in IE 11, Firefox
 31,
 > > or Chrome (current).
 > >
 > > I tested Jmol 14.2.3
 > > http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
 > > and Jmol_S 14.0.17
 > > http://bioinformatics.org/firstglance/fgij/fg.htm?mol=1d66&JAVA
 > >
 > > Curiously, a very old old unsigned applet (11.4.RC3) worked in
 > > Firefox and Chrome (but not in IE).
 > > http://www.umass.edu/molvis/tutorials/dna/dnapairs.htm
 > >
 > > All the above test sites work fine with Java 7 update 65 on OS X
 > > (Mavericks) with Safari or Firefox.
 > >
 > > All the above test sites work fine with Java 7 update 65 on Windows
 > > XP in Firefox 31 or Internet Explorer 8.
 > >
 > > I then uninstalled Java from my Windows 7, downloaded and installed
 > > Java 7 update 60
 > > (x86 version).
 > >
 >
 http://www.oracle.com/technetwork/java/javase/downloads/java-archive-downloads-javase7-521261.html
 > > Everything worked again.
 > >
 > > Eric
 > >
 > >
 > >



 --
 Want fast and easy access to all the code in your enterprise? Index and
 search up to 200,000 lines of code with a free copy of Black Duck
 Code Sight - the same software that powers the world's largest code
 search on Ohloh, the Black Duc

Re: [Jmol-users] Java Update 65 Causing Issues?

[Albert Pratt]

Eric, Robert,

The procedure I used worked for both the "unsigned Jmol applet" and "signed
Jmol applet" options on the test page.

Albert




On 30 July 2014 00:22, Eric Martz  wrote:

>  Angel: you could simply put a link in the Jmol wiki to
> http://proteopedia.org/w/Installing_and_enabling_Java#Windows
> where solutions to the Java update 65 problem are given. Once the bug in
> the Java installer is fixed in a new update, I will remove that yellow
> block.
>
> Reminder to everyone: the procedure successfully used by Albert Pratt
> (presumably for unsigned Jmol applets) is documented here:
> http://proteopedia.org/w/Installing_and_enabling_Java
>
> Eric
>
> On 7/29/14 4:14 PM, Albert Pratt wrote:
>
> Recently I needed to install Java 7, version 65 (with Windows 7, Home
> Premium) and took the opportunity to do a complete uninstall of  earlier
> Java versions (e-mails below) using Fix 1
> in
> Protopedia
> ,
> deleting *all* Oracle and Sun sub-directories in:
> C:\Users\*your-name*\AppData\Roaming\
> C:\Users\*your-name*\AppData\LocalLow\
> C:\ProgramData\ .
>
>  Java 7, version 60, had previously worked with the caffeine Jmol model
> in test page 2 , among
> others sites.
>
> When version 65 was downloaded and installed it didn't work with Jmol.
>  However, following advice, I configured Java (Start>Java>Configure
> Java>Security>Edit Site List) by including the URLs of relevant Jmol sites
> (the http:// prefix appears to be essential). I also checked
>  that Java was
> enabled in Chrome36, Firefox31 and IE11.
>
> All three browsers now operate with test page 2 using Java 7, version 65.
>
>
>
>
>
>
>
>
>
> On 29 July 2014 10:45, Robert Hanson  wrote:
>
>> I've done that now -- it is on the "Installing Jmol" template.
>>
>>
>> On Mon, Jul 28, 2014 at 10:52 AM, Robert Hanson 
>> wrote:
>>
>>> It would be good if someone would  get this into the Jmol wiki.
>>>
>>>
>>> On Sat, Jul 26, 2014 at 6:55 PM, Eric Martz 
>>> wrote:
>>>
 Dear Pshemak,

 Thanks so much -- your suggestion enabled Java 7 update 65 to work
 with Jmol on my Windows 7 system.

 1. I used Control Panel, Programs, Uninstall to uninstall the
 non-working Java 7 update 65.

 2. Using the free Windows search program Agent Ransack (truly
 excellent, blows away Windows Explorer for finding system files), I
 located these:

 C:\Users\Eric Martz\AppData\Roaming\Oracle
 C:\ProgramData\Oracle
 C:\Users\Eric Martz\AppData\LocalLow\Sun
 C:\ProgramData\Sun

 I deleted all 4 of those directories and all their contents.

 3. I went to java.com and downloaded the installer for Java 7 update
 65, and installed it. Now Jmol_S works again.

 OTHER OBSERVATIONS

 After uninstalling Java 7 update 65, and installing Java 7, update
 60, Jmol_S worked. I wondered if then upgrading to 65 would run
 Jmol_S. It did NOT.

 I have explained two ways to get Jmol to work again here:


 http://proteopedia.org/wiki/index.php/Installing_and_enabling_Java#Windows

 -Eric

 At 7/25/14, you wrote:
 >I had similar problems (I reported them some time ago).  They were
 >limited to one Windows machine (Win 7, Firefox, Chrome, IE) of 3 tried
 >(Win 7 and Win 8).
 >
 >My problem was with the update procedure.  It was insufficient to
 >uninstall the old version, I had to delete (after uninstalling) all
 Java
 >directories (hiding under Oracle and even Sun Systems names in Users
 >directories).
 >
 >After clean up, it works fine.
 >
 >One curiosity: I have tested multiple Java applets (not just Jmol) and
 >only Jmol did not work for me (it never fully loaded to get to the
 >permission window, no error messages).
 >
 >Please report back if it work for you too.
 >
 >PM
 >
 >
 >
 >
 >On 7/25/2014 7:26 PM, Eric Martz wrote:
 > > In Windows 7, my tests indicate that Java 7 update 65 does not work
 > > with the current Jmol_S, or recent 14.0.17 Jmol_S. However, update
 60
 > > does work.
 > >
 > > Do others confirm this?
 > >
 > > Previous emails indicate that Java 7 update 65 runs Jmol applet in
 > > Windows 8 (Angel H), and that Java 8 runs Jmol applet (Henry R, OS
 > > not specified?).
 > >
 > > However, on Windows 7, when I upgraded Java 7 from 60 to 65 today, I
 > > could not get the current Jmol_S applet to work in IE 11, Firefox
 31,
 > > or Chrome (current).
 > >
 > > I tested Jmol 14.2.3
 > > http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
 > > and Jmol_S 14.0.17
 > > http://bioinformatics.org/firstglance/

Re: [Jmol-users] Java Update 65 Causing Issues?

[Eric Martz]

Angel: you could simply put a link in the Jmol wiki to
http://proteopedia.org/w/Installing_and_enabling_Java#Windows
where solutions to the Java update 65 problem are given. Once the bug in 
the Java installer is fixed in a new update, I will remove that yellow 
block.


Reminder to everyone: the procedure successfully used by Albert Pratt 
(presumably for unsigned Jmol applets) is documented here:

http://proteopedia.org/w/Installing_and_enabling_Java

Eric

On 7/29/14 4:14 PM, Albert Pratt wrote:
Recently I needed to install Java 7, version 65 (with Windows 7, Home 
Premium) and took the opportunity to do a complete uninstall of  
earlier Java versions (e-mails below) using Fix 1 
in 
Protopedia 
, 
deleting /all/ Oracle and Sun sub-directories in:

C:\Users\/your-name/\AppData\Roaming\
C:\Users\/your-name/\AppData\LocalLow\
C:\ProgramData\ .

Java 7, version 60, had previously worked with the caffeine Jmol model 
in test page 2 , 
among others sites.


When version 65 was downloaded and installed it didn't work with Jmol. 
 However, following advice, I configured Java (Start>Java>Configure 
Java>Security>Edit Site List) by including the URLs of relevant Jmol 
sites (the http:// prefix appears to be essential). I also checked 
 that Java was 
enabled in Chrome36, Firefox31 and IE11.


All three browsers now operate with test page 2 using Java 7, version 65.








On 29 July 2014 10:45, Robert Hanson > wrote:


I've done that now -- it is on the "Installing Jmol" template.


On Mon, Jul 28, 2014 at 10:52 AM, Robert Hanson
mailto:hans...@stolaf.edu>> wrote:

It would be good if someone would  get this into the Jmol wiki.


On Sat, Jul 26, 2014 at 6:55 PM, Eric Martz
mailto:ema...@microbio.umass.edu>>
wrote:

Dear Pshemak,

Thanks so much -- your suggestion enabled Java 7 update 65
to work
with Jmol on my Windows 7 system.

1. I used Control Panel, Programs, Uninstall to uninstall the
non-working Java 7 update 65.

2. Using the free Windows search program Agent Ransack (truly
excellent, blows away Windows Explorer for finding system
files), I
located these:

C:\Users\Eric Martz\AppData\Roaming\Oracle
C:\ProgramData\Oracle
C:\Users\Eric Martz\AppData\LocalLow\Sun
C:\ProgramData\Sun

I deleted all 4 of those directories and all their contents.

3. I went to java.com  and downloaded the
installer for Java 7 update
65, and installed it. Now Jmol_S works again.

OTHER OBSERVATIONS

After uninstalling Java 7 update 65, and installing Java
7, update
60, Jmol_S worked. I wondered if then upgrading to 65
would run
Jmol_S. It did NOT.

I have explained two ways to get Jmol to work again here:


http://proteopedia.org/wiki/index.php/Installing_and_enabling_Java#Windows

-Eric

At 7/25/14, you wrote:
>I had similar problems (I reported them some time ago).
 They were
>limited to one Windows machine (Win 7, Firefox, Chrome,
IE) of 3 tried
>(Win 7 and Win 8).
>
>My problem was with the update procedure.  It was
insufficient to
>uninstall the old version, I had to delete (after
uninstalling) all Java
>directories (hiding under Oracle and even Sun Systems
names in Users
>directories).
>
>After clean up, it works fine.
>
>One curiosity: I have tested multiple Java applets (not
just Jmol) and
>only Jmol did not work for me (it never fully loaded to
get to the
>permission window, no error messages).
>
>Please report back if it work for you too.
>
>PM
>
>
>
>
>On 7/25/2014 7:26 PM, Eric Martz wrote:
> > In Windows 7, my tests indicate that Java 7 update 65
does not work
> > with the current Jmol_S, or recent 14.0.17 Jmol_S.
However, update 60
> > does work.
> >
> > Do others confirm this?
> >
> > Previous emails indicate that Java 7 update 65 runs
Jmol applet in
> > Windows 8 (Angel H), and that Java 8 runs Jmol applet
(Henry R, OS
> > not specified?).

Re: [Jmol-users] Java Update 65 Causing Issues?

[Albert Pratt]

Recently I needed to install Java 7, version 65 (with Windows 7, Home
Premium) and took the opportunity to do a complete uninstall of  earlier
Java versions (e-mails below) using Fix 1
in
Protopedia
,
deleting *all* Oracle and Sun sub-directories in:
C:\Users\*your-name*\AppData\Roaming\
C:\Users\*your-name*\AppData\LocalLow\
C:\ProgramData\ .

Java 7, version 60, had previously worked with the caffeine Jmol model in test
page 2 , among others
sites.

When version 65 was downloaded and installed it didn't work with Jmol.
 However, following advice, I configured Java (Start>Java>Configure
Java>Security>Edit Site List) by including the URLs of relevant Jmol sites
(the http:// prefix appears to be essential). I also checked
 that Java was
enabled in Chrome36, Firefox31 and IE11.

All three browsers now operate with test page 2 using Java 7, version 65.









On 29 July 2014 10:45, Robert Hanson  wrote:

> I've done that now -- it is on the "Installing Jmol" template.
>
>
> On Mon, Jul 28, 2014 at 10:52 AM, Robert Hanson 
> wrote:
>
>> It would be good if someone would  get this into the Jmol wiki.
>>
>>
>> On Sat, Jul 26, 2014 at 6:55 PM, Eric Martz 
>> wrote:
>>
>>> Dear Pshemak,
>>>
>>> Thanks so much -- your suggestion enabled Java 7 update 65 to work
>>> with Jmol on my Windows 7 system.
>>>
>>> 1. I used Control Panel, Programs, Uninstall to uninstall the
>>> non-working Java 7 update 65.
>>>
>>> 2. Using the free Windows search program Agent Ransack (truly
>>> excellent, blows away Windows Explorer for finding system files), I
>>> located these:
>>>
>>> C:\Users\Eric Martz\AppData\Roaming\Oracle
>>> C:\ProgramData\Oracle
>>> C:\Users\Eric Martz\AppData\LocalLow\Sun
>>> C:\ProgramData\Sun
>>>
>>> I deleted all 4 of those directories and all their contents.
>>>
>>> 3. I went to java.com and downloaded the installer for Java 7 update
>>> 65, and installed it. Now Jmol_S works again.
>>>
>>> OTHER OBSERVATIONS
>>>
>>> After uninstalling Java 7 update 65, and installing Java 7, update
>>> 60, Jmol_S worked. I wondered if then upgrading to 65 would run
>>> Jmol_S. It did NOT.
>>>
>>> I have explained two ways to get Jmol to work again here:
>>>
>>>
>>> http://proteopedia.org/wiki/index.php/Installing_and_enabling_Java#Windows
>>>
>>> -Eric
>>>
>>> At 7/25/14, you wrote:
>>> >I had similar problems (I reported them some time ago).  They were
>>> >limited to one Windows machine (Win 7, Firefox, Chrome, IE) of 3 tried
>>> >(Win 7 and Win 8).
>>> >
>>> >My problem was with the update procedure.  It was insufficient to
>>> >uninstall the old version, I had to delete (after uninstalling) all Java
>>> >directories (hiding under Oracle and even Sun Systems names in Users
>>> >directories).
>>> >
>>> >After clean up, it works fine.
>>> >
>>> >One curiosity: I have tested multiple Java applets (not just Jmol) and
>>> >only Jmol did not work for me (it never fully loaded to get to the
>>> >permission window, no error messages).
>>> >
>>> >Please report back if it work for you too.
>>> >
>>> >PM
>>> >
>>> >
>>> >
>>> >
>>> >On 7/25/2014 7:26 PM, Eric Martz wrote:
>>> > > In Windows 7, my tests indicate that Java 7 update 65 does not work
>>> > > with the current Jmol_S, or recent 14.0.17 Jmol_S. However, update 60
>>> > > does work.
>>> > >
>>> > > Do others confirm this?
>>> > >
>>> > > Previous emails indicate that Java 7 update 65 runs Jmol applet in
>>> > > Windows 8 (Angel H), and that Java 8 runs Jmol applet (Henry R, OS
>>> > > not specified?).
>>> > >
>>> > > However, on Windows 7, when I upgraded Java 7 from 60 to 65 today, I
>>> > > could not get the current Jmol_S applet to work in IE 11, Firefox 31,
>>> > > or Chrome (current).
>>> > >
>>> > > I tested Jmol 14.2.3
>>> > > http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
>>> > > and Jmol_S 14.0.17
>>> > > http://bioinformatics.org/firstglance/fgij/fg.htm?mol=1d66&JAVA
>>> > >
>>> > > Curiously, a very old old unsigned applet (11.4.RC3) worked in
>>> > > Firefox and Chrome (but not in IE).
>>> > > http://www.umass.edu/molvis/tutorials/dna/dnapairs.htm
>>> > >
>>> > > All the above test sites work fine with Java 7 update 65 on OS X
>>> > > (Mavericks) with Safari or Firefox.
>>> > >
>>> > > All the above test sites work fine with Java 7 update 65 on Windows
>>> > > XP in Firefox 31 or Internet Explorer 8.
>>> > >
>>> > > I then uninstalled Java from my Windows 7, downloaded and installed
>>> > > Java 7 update 60
>>> > > (x86 version).
>>> > >
>>> >
>>> http://www.oracle.com/technetwork/java/javase/downloads/java-archive-downloads-javase7-521261.html
>>> > > Everything worked again.
>>> > >
>>> > > Eric
>>> > >
>>> > >
>>> > >
>>>
>>>
>>>
>>> -

Re: [Jmol-users] Java Update 65 Causing Issues?

[Angel Herráez]

I can put those descriptions  in the wiki, but I am not sure the situation is 
clear.

On 28 Jul 2014 at 10:52, Robert Hanson wrote:
> It would be good if someone would get this into the Jmol wiki.


--
Infragistics Professional
Build stunning WinForms apps today!
Reboot your WinForms applications with our WinForms controls. 
Build a bridge from your legacy apps to the future.
http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java Update 65 Causing Issues?

[Robert Hanson]

I've done that now -- it is on the "Installing Jmol" template.


On Mon, Jul 28, 2014 at 10:52 AM, Robert Hanson  wrote:

> It would be good if someone would  get this into the Jmol wiki.
>
>
> On Sat, Jul 26, 2014 at 6:55 PM, Eric Martz 
> wrote:
>
>> Dear Pshemak,
>>
>> Thanks so much -- your suggestion enabled Java 7 update 65 to work
>> with Jmol on my Windows 7 system.
>>
>> 1. I used Control Panel, Programs, Uninstall to uninstall the
>> non-working Java 7 update 65.
>>
>> 2. Using the free Windows search program Agent Ransack (truly
>> excellent, blows away Windows Explorer for finding system files), I
>> located these:
>>
>> C:\Users\Eric Martz\AppData\Roaming\Oracle
>> C:\ProgramData\Oracle
>> C:\Users\Eric Martz\AppData\LocalLow\Sun
>> C:\ProgramData\Sun
>>
>> I deleted all 4 of those directories and all their contents.
>>
>> 3. I went to java.com and downloaded the installer for Java 7 update
>> 65, and installed it. Now Jmol_S works again.
>>
>> OTHER OBSERVATIONS
>>
>> After uninstalling Java 7 update 65, and installing Java 7, update
>> 60, Jmol_S worked. I wondered if then upgrading to 65 would run
>> Jmol_S. It did NOT.
>>
>> I have explained two ways to get Jmol to work again here:
>>
>> http://proteopedia.org/wiki/index.php/Installing_and_enabling_Java#Windows
>>
>> -Eric
>>
>> At 7/25/14, you wrote:
>> >I had similar problems (I reported them some time ago).  They were
>> >limited to one Windows machine (Win 7, Firefox, Chrome, IE) of 3 tried
>> >(Win 7 and Win 8).
>> >
>> >My problem was with the update procedure.  It was insufficient to
>> >uninstall the old version, I had to delete (after uninstalling) all Java
>> >directories (hiding under Oracle and even Sun Systems names in Users
>> >directories).
>> >
>> >After clean up, it works fine.
>> >
>> >One curiosity: I have tested multiple Java applets (not just Jmol) and
>> >only Jmol did not work for me (it never fully loaded to get to the
>> >permission window, no error messages).
>> >
>> >Please report back if it work for you too.
>> >
>> >PM
>> >
>> >
>> >
>> >
>> >On 7/25/2014 7:26 PM, Eric Martz wrote:
>> > > In Windows 7, my tests indicate that Java 7 update 65 does not work
>> > > with the current Jmol_S, or recent 14.0.17 Jmol_S. However, update 60
>> > > does work.
>> > >
>> > > Do others confirm this?
>> > >
>> > > Previous emails indicate that Java 7 update 65 runs Jmol applet in
>> > > Windows 8 (Angel H), and that Java 8 runs Jmol applet (Henry R, OS
>> > > not specified?).
>> > >
>> > > However, on Windows 7, when I upgraded Java 7 from 60 to 65 today, I
>> > > could not get the current Jmol_S applet to work in IE 11, Firefox 31,
>> > > or Chrome (current).
>> > >
>> > > I tested Jmol 14.2.3
>> > > http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
>> > > and Jmol_S 14.0.17
>> > > http://bioinformatics.org/firstglance/fgij/fg.htm?mol=1d66&JAVA
>> > >
>> > > Curiously, a very old old unsigned applet (11.4.RC3) worked in
>> > > Firefox and Chrome (but not in IE).
>> > > http://www.umass.edu/molvis/tutorials/dna/dnapairs.htm
>> > >
>> > > All the above test sites work fine with Java 7 update 65 on OS X
>> > > (Mavericks) with Safari or Firefox.
>> > >
>> > > All the above test sites work fine with Java 7 update 65 on Windows
>> > > XP in Firefox 31 or Internet Explorer 8.
>> > >
>> > > I then uninstalled Java from my Windows 7, downloaded and installed
>> > > Java 7 update 60
>> > > (x86 version).
>> > >
>> >
>> http://www.oracle.com/technetwork/java/javase/downloads/java-archive-downloads-javase7-521261.html
>> > > Everything worked again.
>> > >
>> > > Eric
>> > >
>> > >
>> > >
>>
>>
>>
>> --
>> Want fast and easy access to all the code in your enterprise? Index and
>> search up to 200,000 lines of code with a free copy of Black Duck
>> Code Sight - the same software that powers the world's largest code
>> search on Ohloh, the Black Duck Open Hub! Try it now.
>> http://p.sf.net/sfu/bds
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department 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
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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
--
Infragistics Professional
Build stunning WinForms apps tod

Re: [Jmol-users] Java Update 65 Causing Issues?

[Robert Hanson]

Has this been reported to Oracle? That's critical.


On Tue, Jul 15, 2014 at 10:45 PM, Pshemak Maslak  wrote:

>  I can confirm that observations. All my (remaining) Jmol (Java)
> instances show as "gray" squares. There are no error messages in the Java
> console (in fact, loading of the page with the app does not trigger opening
> of the console even if it is set up to open).
>
> Other java applets on the same site work fine (and the Java console opens
> when they load).
>
> PM
>
>
>
>
> On 7/15/2014 8:03 PM, David Hibbitts wrote:
>
>  After updating Java today, I've been unable to run jmol on my webpage:
>
>
> http://atlas.che.virginia.edu/mm/dim.php?user=ddh9r&jobid=82043&struct=Dimer_Mode.res
>
>  or any others that i've tried, including:
>
>  http://jmol.sourceforge.net/demo/atoms/
>
>  Java itself, however, seems to work as expected on
>
>  http://java.com/en/download/installed.jsp
>
>  and
>
>  http://javatester.org/version.html
>
>  Turning on the console in the Java control panel shows that the console
> doesn't run at all when on jmol pages, but does run on the testing pages.
> Is anyone else noticing this issue?
>
>  (Testing a different pc with an older version of Java (Update 55)
> confirms that all pages above work as expected).
>
>  Thanks,
>
>  David Hibbitts
>
>
> --
> Want fast and easy access to all the code in your enterprise? Index and
> search up to 200,000 lines of code with a free copy of Black Duck
> Code Sight - the same software that powers the world's largest code
> search on Ohloh, the Black Duck Open Hub! Try it now.http://p.sf.net/sfu/bds
>
>
>
> ___
> Jmol-users mailing 
> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> Want fast and easy access to all the code in your enterprise? Index and
> search up to 200,000 lines of code with a free copy of Black Duck
> Code Sight - the same software that powers the world's largest code
> search on Ohloh, the Black Duck Open Hub! Try it now.
> http://p.sf.net/sfu/bds
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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
--
Infragistics Professional
Build stunning WinForms apps today!
Reboot your WinForms applications with our WinForms controls. 
Build a bridge from your legacy apps to the future.
http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java Update 65 Causing Issues?

[Robert Hanson]

It would be good if someone would  get this into the Jmol wiki.


On Sat, Jul 26, 2014 at 6:55 PM, Eric Martz 
wrote:

> Dear Pshemak,
>
> Thanks so much -- your suggestion enabled Java 7 update 65 to work
> with Jmol on my Windows 7 system.
>
> 1. I used Control Panel, Programs, Uninstall to uninstall the
> non-working Java 7 update 65.
>
> 2. Using the free Windows search program Agent Ransack (truly
> excellent, blows away Windows Explorer for finding system files), I
> located these:
>
> C:\Users\Eric Martz\AppData\Roaming\Oracle
> C:\ProgramData\Oracle
> C:\Users\Eric Martz\AppData\LocalLow\Sun
> C:\ProgramData\Sun
>
> I deleted all 4 of those directories and all their contents.
>
> 3. I went to java.com and downloaded the installer for Java 7 update
> 65, and installed it. Now Jmol_S works again.
>
> OTHER OBSERVATIONS
>
> After uninstalling Java 7 update 65, and installing Java 7, update
> 60, Jmol_S worked. I wondered if then upgrading to 65 would run
> Jmol_S. It did NOT.
>
> I have explained two ways to get Jmol to work again here:
>
> http://proteopedia.org/wiki/index.php/Installing_and_enabling_Java#Windows
>
> -Eric
>
> At 7/25/14, you wrote:
> >I had similar problems (I reported them some time ago).  They were
> >limited to one Windows machine (Win 7, Firefox, Chrome, IE) of 3 tried
> >(Win 7 and Win 8).
> >
> >My problem was with the update procedure.  It was insufficient to
> >uninstall the old version, I had to delete (after uninstalling) all Java
> >directories (hiding under Oracle and even Sun Systems names in Users
> >directories).
> >
> >After clean up, it works fine.
> >
> >One curiosity: I have tested multiple Java applets (not just Jmol) and
> >only Jmol did not work for me (it never fully loaded to get to the
> >permission window, no error messages).
> >
> >Please report back if it work for you too.
> >
> >PM
> >
> >
> >
> >
> >On 7/25/2014 7:26 PM, Eric Martz wrote:
> > > In Windows 7, my tests indicate that Java 7 update 65 does not work
> > > with the current Jmol_S, or recent 14.0.17 Jmol_S. However, update 60
> > > does work.
> > >
> > > Do others confirm this?
> > >
> > > Previous emails indicate that Java 7 update 65 runs Jmol applet in
> > > Windows 8 (Angel H), and that Java 8 runs Jmol applet (Henry R, OS
> > > not specified?).
> > >
> > > However, on Windows 7, when I upgraded Java 7 from 60 to 65 today, I
> > > could not get the current Jmol_S applet to work in IE 11, Firefox 31,
> > > or Chrome (current).
> > >
> > > I tested Jmol 14.2.3
> > > http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
> > > and Jmol_S 14.0.17
> > > http://bioinformatics.org/firstglance/fgij/fg.htm?mol=1d66&JAVA
> > >
> > > Curiously, a very old old unsigned applet (11.4.RC3) worked in
> > > Firefox and Chrome (but not in IE).
> > > http://www.umass.edu/molvis/tutorials/dna/dnapairs.htm
> > >
> > > All the above test sites work fine with Java 7 update 65 on OS X
> > > (Mavericks) with Safari or Firefox.
> > >
> > > All the above test sites work fine with Java 7 update 65 on Windows
> > > XP in Firefox 31 or Internet Explorer 8.
> > >
> > > I then uninstalled Java from my Windows 7, downloaded and installed
> > > Java 7 update 60
> > > (x86 version).
> > >
> >
> http://www.oracle.com/technetwork/java/javase/downloads/java-archive-downloads-javase7-521261.html
> > > Everything worked again.
> > >
> > > Eric
> > >
> > >
> > >
>
>
>
> --
> Want fast and easy access to all the code in your enterprise? Index and
> search up to 200,000 lines of code with a free copy of Black Duck
> Code Sight - the same software that powers the world's largest code
> search on Ohloh, the Black Duck Open Hub! Try it now.
> http://p.sf.net/sfu/bds
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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
--
Infragistics Professional
Build stunning WinForms apps today!
Reboot your WinForms applications with our WinForms controls. 
Build a bridge from your legacy apps to the future.
http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java Update 65 Causing Issues?

[Eric Martz]

Dear Pshemak,

Thanks so much -- your suggestion enabled Java 7 update 65 to work 
with Jmol on my Windows 7 system.

1. I used Control Panel, Programs, Uninstall to uninstall the 
non-working Java 7 update 65.

2. Using the free Windows search program Agent Ransack (truly 
excellent, blows away Windows Explorer for finding system files), I 
located these:

C:\Users\Eric Martz\AppData\Roaming\Oracle
C:\ProgramData\Oracle
C:\Users\Eric Martz\AppData\LocalLow\Sun
C:\ProgramData\Sun

I deleted all 4 of those directories and all their contents.

3. I went to java.com and downloaded the installer for Java 7 update 
65, and installed it. Now Jmol_S works again.

OTHER OBSERVATIONS

After uninstalling Java 7 update 65, and installing Java 7, update 
60, Jmol_S worked. I wondered if then upgrading to 65 would run 
Jmol_S. It did NOT.

I have explained two ways to get Jmol to work again here:

http://proteopedia.org/wiki/index.php/Installing_and_enabling_Java#Windows

-Eric

At 7/25/14, you wrote:
>I had similar problems (I reported them some time ago).  They were
>limited to one Windows machine (Win 7, Firefox, Chrome, IE) of 3 tried
>(Win 7 and Win 8).
>
>My problem was with the update procedure.  It was insufficient to
>uninstall the old version, I had to delete (after uninstalling) all Java
>directories (hiding under Oracle and even Sun Systems names in Users
>directories).
>
>After clean up, it works fine.
>
>One curiosity: I have tested multiple Java applets (not just Jmol) and
>only Jmol did not work for me (it never fully loaded to get to the
>permission window, no error messages).
>
>Please report back if it work for you too.
>
>PM
>
>
>
>
>On 7/25/2014 7:26 PM, Eric Martz wrote:
> > In Windows 7, my tests indicate that Java 7 update 65 does not work
> > with the current Jmol_S, or recent 14.0.17 Jmol_S. However, update 60
> > does work.
> >
> > Do others confirm this?
> >
> > Previous emails indicate that Java 7 update 65 runs Jmol applet in
> > Windows 8 (Angel H), and that Java 8 runs Jmol applet (Henry R, OS
> > not specified?).
> >
> > However, on Windows 7, when I upgraded Java 7 from 60 to 65 today, I
> > could not get the current Jmol_S applet to work in IE 11, Firefox 31,
> > or Chrome (current).
> >
> > I tested Jmol 14.2.3
> > http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
> > and Jmol_S 14.0.17
> > http://bioinformatics.org/firstglance/fgij/fg.htm?mol=1d66&JAVA
> >
> > Curiously, a very old old unsigned applet (11.4.RC3) worked in
> > Firefox and Chrome (but not in IE).
> > http://www.umass.edu/molvis/tutorials/dna/dnapairs.htm
> >
> > All the above test sites work fine with Java 7 update 65 on OS X
> > (Mavericks) with Safari or Firefox.
> >
> > All the above test sites work fine with Java 7 update 65 on Windows
> > XP in Firefox 31 or Internet Explorer 8.
> >
> > I then uninstalled Java from my Windows 7, downloaded and installed
> > Java 7 update 60
> > (x86 version).
> > 
> http://www.oracle.com/technetwork/java/javase/downloads/java-archive-downloads-javase7-521261.html
> > Everything worked again.
> >
> > Eric
> >
> >
> >


--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java Update 65 Causing Issues?

[Pshemak Maslak]

I had similar problems (I reported them some time ago).  They were 
limited to one Windows machine (Win 7, Firefox, Chrome, IE) of 3 tried 
(Win 7 and Win 8).

My problem was with the update procedure.  It was insufficient to 
uninstall the old version, I had to delete (after uninstalling) all Java 
directories (hiding under Oracle and even Sun Systems names in Users 
directories).

After clean up, it works fine.

One curiosity: I have tested multiple Java applets (not just Jmol) and 
only Jmol did not work for me (it never fully loaded to get to the 
permission window, no error messages).

Please report back if it work for you too.

PM




On 7/25/2014 7:26 PM, Eric Martz wrote:
> In Windows 7, my tests indicate that Java 7 update 65 does not work
> with the current Jmol_S, or recent 14.0.17 Jmol_S. However, update 60
> does work.
>
> Do others confirm this?
>
> Previous emails indicate that Java 7 update 65 runs Jmol applet in
> Windows 8 (Angel H), and that Java 8 runs Jmol applet (Henry R, OS
> not specified?).
>
> However, on Windows 7, when I upgraded Java 7 from 60 to 65 today, I
> could not get the current Jmol_S applet to work in IE 11, Firefox 31,
> or Chrome (current).
>
> I tested Jmol 14.2.3
> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
> and Jmol_S 14.0.17
> http://bioinformatics.org/firstglance/fgij/fg.htm?mol=1d66&JAVA
>
> Curiously, a very old old unsigned applet (11.4.RC3) worked in
> Firefox and Chrome (but not in IE).
> http://www.umass.edu/molvis/tutorials/dna/dnapairs.htm
>
> All the above test sites work fine with Java 7 update 65 on OS X
> (Mavericks) with Safari or Firefox.
>
> All the above test sites work fine with Java 7 update 65 on Windows
> XP in Firefox 31 or Internet Explorer 8.
>
> I then uninstalled Java from my Windows 7, downloaded and installed
> Java 7 update 60
> (x86 version).
> http://www.oracle.com/technetwork/java/javase/downloads/java-archive-downloads-javase7-521261.html
> Everything worked again.
>
> Eric
>
>
> --
> Want fast and easy access to all the code in your enterprise? Index and
> search up to 200,000 lines of code with a free copy of Black Duck
> Code Sight - the same software that powers the world's largest code
> search on Ohloh, the Black Duck Open Hub! Try it now.
> http://p.sf.net/sfu/bds
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users


--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java Update 65 Causing Issues?

[Eric Martz]

In Windows 7, my tests indicate that Java 7 update 65 does not work 
with the current Jmol_S, or recent 14.0.17 Jmol_S. However, update 60 
does work.

Do others confirm this?

Previous emails indicate that Java 7 update 65 runs Jmol applet in 
Windows 8 (Angel H), and that Java 8 runs Jmol applet (Henry R, OS 
not specified?).

However, on Windows 7, when I upgraded Java 7 from 60 to 65 today, I 
could not get the current Jmol_S applet to work in IE 11, Firefox 31, 
or Chrome (current).

I tested Jmol 14.2.3
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
and Jmol_S 14.0.17
http://bioinformatics.org/firstglance/fgij/fg.htm?mol=1d66&JAVA

Curiously, a very old old unsigned applet (11.4.RC3) worked in 
Firefox and Chrome (but not in IE).
http://www.umass.edu/molvis/tutorials/dna/dnapairs.htm

All the above test sites work fine with Java 7 update 65 on OS X 
(Mavericks) with Safari or Firefox.

All the above test sites work fine with Java 7 update 65 on Windows 
XP in Firefox 31 or Internet Explorer 8.

I then uninstalled Java from my Windows 7, downloaded and installed 
Java 7 update 60
(x86 version).
http://www.oracle.com/technetwork/java/javase/downloads/java-archive-downloads-javase7-521261.html
Everything worked again.

Eric


--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java Update 65 Causing Issues

[Robert Hanson]

On Thu, Jul 17, 2014 at 10:54 AM, Pshemak Maslak  wrote:


> Does  ___JmolVersion="14.2.3_2014.07.12"  works with Java 7.65? Where
> can this version be downloaded?
>

The latest is currently at SourceForge. See
https://sourceforge.net/projects/jmol/files/

Hoping to get a bug-fix update in this weekend. Just didn't  get to it this
week.

Bob

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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
--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java Update 65 Causing Issues

[Angel Herráez]

I have just updated from Java 7.0_60 to 7.0_65 and the page
> > The test page: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm 

loads the Jmol_S applet just fine in Firefox 30, Win8.1
--after accepting the "signed applet by Integrated Graphics" dialog

I suggest that you thoroughly clean your java cache, Pshemak, just in 
case



--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java Update 65 Causing Issues

[Rzepa, Henry S]

On 17 Jul 2014, at 16:54, Pshemak Maslak  wrote:

> Jmol (v14.1.16) is not agreeing with Java 7.65 update (both Windows and 
> OS X, several browsers).
> 
> The test page: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm 
> "JSmol/Java" link works with Java 7.51, it does not load with Java 7.65 
> (no error messages, see below).
> 
I am running Java 8.11  and 
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED  works fine.



signature.asc
Description: Message signed with OpenPGP using GPGMail
--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Java Update 65 Causing Issues

[Pshemak Maslak]

Jmol (v14.1.16) is not agreeing with Java 7.65 update (both Windows and 
OS X, several browsers).

The test page: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm 
"JSmol/Java" link works with Java 7.51, it does not load with Java 7.65 
(no error messages, see below).

Does  ___JmolVersion="14.2.3_2014.07.12"  works with Java 7.65? Where 
can this version be downloaded?

Thanks,

PM







On 7/16/2014 2:19 AM, Rzepa, Henry S wrote:
> On 16 Jul 2014, at 04:45, Pshemak Maslak  wrote:
>
>> I can confirm that observations. All my (remaining) Jmol (Java) instances 
>> show as "gray" squares. There are no error messages in the Java console (in 
>> fact, loading of the page with the app does not trigger opening of the 
>> console even if it is set up to open).
>>
>> Other java applets on the same site work fine (and the Java console opens 
>> when they load).
>>
>> PM
>>
> I would also point out that there is Java 8 on the very near horizon,
>
> http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html
>
> I have been running  Java 8u5 for some months now (with no particular 
> problems on OS X, but 8u11 has just been released which  I have not tested), 
> but we should start testing both  7 AND 8 from now on.
>
> It is certainly true that as Oracle tightened the security sandbox for  Java, 
> we have had a period of significant instability (not least coping with all 
> those sites running  Java that have not replaced their unsigned  Jar’s with 
> signed ones).
>
> There are still a few functions of  Jmol that simply run too slowly in  JSmol 
> for  Java-Jmol to be phased out just yet (generating  .jvxl surfaces from 
> large cube files for example)  but  I suspect that day is going to have to 
> come. It might be useful to us all for a list of functions such as .jvxl 
> surface generation which simply cannot map to  JSmol to be created?
>
> Has anyone got any other suggestions for operations that really require  Jmol?


--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java Update 65 Causing Issues?

[Rolf Huehne]

On 07/16/2014 08:19 AM, Rzepa, Henry S wrote:
> There are still a few functions of  Jmol that simply run too slowly in  JSmol 
> for  Java-Jmol to be phased out just yet (generating  .jvxl surfaces from 
> large cube files for example)  but  I suspect that day is going to have to 
> come. It might be useful to us all for a list of functions such as .jvxl 
> surface generation which simply cannot map to  JSmol to be created?
>
> Has anyone got any other suggestions for operations that really require  Jmol?
>
I can't name specific operations but generally the number of atoms 
loaded is critical. But the range here is very wide, depending on 
hardware, operating system, browser and the current state of the running 
browser (e.g.: RAM available, other tasks, number of tabs).
On some systems it is fine until about 5000 atoms and then it is getting 
worse until you can't really work interactively with the mouse anymore. 
On other systems the limit is around 5 atoms (at least in a browser 
started freshly). And on my new MacBook Pro I can even work with about 
40 atoms in Safari, although rotation and zoom are already quite 
sluggish.

Regards,
Rolf

-- 

Rolf Huehne
Postdoc

Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@fli-leibniz.de
Website: http://www.fli-leibniz.de

   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Dennys Klein

VAT No: DE 153 925 464
Register of Associations: No. 230296, Amtsgericht Jena
Tax Number: 162/141/08228


--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java Update 65 Causing Issues?

[Angel Herráez]

David, your site runs well in my system (Firefox 29 Win, Java 
1.7.0_60)
after accepting a couple of warnings.
You must update the Jmol version you are using in the page. Jmol 14 
has properly signed applet that will give less warnings and blocking 
in new Javas.



--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java Update 65 Causing Issues?

[Rzepa, Henry S]

On 16 Jul 2014, at 04:45, Pshemak Maslak  wrote:

> I can confirm that observations. All my (remaining) Jmol (Java) instances 
> show as "gray" squares. There are no error messages in the Java console (in 
> fact, loading of the page with the app does not trigger opening of the 
> console even if it is set up to open).
> 
> Other java applets on the same site work fine (and the Java console opens 
> when they load).
> 
> PM
> 

I would also point out that there is Java 8 on the very near horizon,

http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html

I have been running  Java 8u5 for some months now (with no particular problems 
on OS X, but 8u11 has just been released which  I have not tested), but we 
should start testing both  7 AND 8 from now on.

It is certainly true that as Oracle tightened the security sandbox for  Java, 
we have had a period of significant instability (not least coping with all 
those sites running  Java that have not replaced their unsigned  Jar’s with 
signed ones). 

There are still a few functions of  Jmol that simply run too slowly in  JSmol 
for  Java-Jmol to be phased out just yet (generating  .jvxl surfaces from large 
cube files for example)  but  I suspect that day is going to have to come. It 
might be useful to us all for a list of functions such as .jvxl surface 
generation which simply cannot map to  JSmol to be created?  

Has anyone got any other suggestions for operations that really require  Jmol? 


signature.asc
Description: Message signed with OpenPGP using GPGMail
--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java Update 65 Causing Issues?

[Pshemak Maslak]

I can confirm that observations. All my (remaining) Jmol (Java) 
instances show as "gray" squares. There are no error messages in the 
Java console (in fact, loading of the page with the app does not trigger 
opening of the console even if it is set up to open).


Other java applets on the same site work fine (and the Java console 
opens when they load).


PM



On 7/15/2014 8:03 PM, David Hibbitts wrote:

After updating Java today, I've been unable to run jmol on my webpage:

http://atlas.che.virginia.edu/mm/dim.php?user=ddh9r&jobid=82043&struct=Dimer_Mode.res

or any others that i've tried, including:

http://jmol.sourceforge.net/demo/atoms/

Java itself, however, seems to work as expected on

http://java.com/en/download/installed.jsp

and

http://javatester.org/version.html

Turning on the console in the Java control panel shows that the 
console doesn't run at all when on jmol pages, but does run on the 
testing pages. Is anyone else noticing this issue?


(Testing a different pc with an older version of Java (Update 55) 
confirms that all pages above work as expected).


Thanks,

David Hibbitts


--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds


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


--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Java Update 65 Causing Issues?

[David Hibbitts]

After updating Java today, I've been unable to run jmol on my webpage:

http://atlas.che.virginia.edu/mm/dim.php?user=ddh9r&jobid=82043&struct=Dimer_Mode.res

or any others that i've tried, including:

http://jmol.sourceforge.net/demo/atoms/

Java itself, however, seems to work as expected on

http://java.com/en/download/installed.jsp

and

http://javatester.org/version.html

Turning on the console in the Java control panel shows that the console
doesn't run at all when on jmol pages, but does run on the testing pages.
Is anyone else noticing this issue?

(Testing a different pc with an older version of Java (Update 55) confirms
that all pages above work as expected).

Thanks,

David Hibbitts
--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users