date:20151016

Re: [Jmol-users] Jmol 14.4.0_2015.10.14 - alert boxes - polyhedra

2015-10-16 Thread simon

I think I have found a possible bug in the polyhedra command.

By way of example, if I load this CIF at chemapps:

http://chemapps.stolaf.edu/jmol/jmol.php?source=http://scripts.iucr.org/cgi-bin/sendcif?hb0009

and try

polyhedra BONDS {aluminium}

I get

script ERROR: TypeError: a.equals is not a function  
J.shapespecial.Polyhedra set generate

Whereas doing the same with previous versions of Jmol worked.

Cheers

Simon

Quoting si...@publcif.co.uk:

> Otis:
>
> In my case its the "alert where Jmol formerly died without alert"
> problem you describe.
>
> I can live with alerts for failing scripts (i.e. they shouldn't fail
> in the first place if I do my job properly),
> but it is now clear that its not just one of my scripts that is
> failing with Jmol 14.4 (though they worked with previous versions).
>
> Looks like it may take some time to identify exactly where the  
> problems are...
>
> Thanks for the info anyway.
>
> Cheers
>
> Simon
>
>
> Quoting Otis Rothenberger :
>
>> Simon,
>>
>> I was seeing this where the script WAS completing after the alert
>> box was dismissed. Bob correctly pointed out that I was running some
>> Bootstrap related scripts that imposed JavaScript ?use strict.? When
>> I removed this from the Bootstrap related scripts, the problem
>> disappeared.
>>
>> However, like you, I continue to see these alert boxes where the
>> script has an error where previous versions of Jmol would have died
>> without the alert. One example of this is the following:
>>
>> Jmol.evaluateVar(jmolApplet0, "'hexane'.find('SMILES','CCC') > 0?)
>>
>> I know the script is ridiculous, but it happened because of an
>> answer key error. Earlier versions of Jmol did not throw an error
>> alert with this script.
>>
>> To summarize, I was seeing two problems - one seems to be corrected
>> by editing ?use strict? out of my Bootstrap .js files. The other
>> problem, alert where Jmol formerly died without alert, seems to
>> remain.
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>> On Oct 16, 2015, at 7:12 AM, si...@publcif.co.uk wrote:
>>>
>>> Just installed this.
>>>
>>> For some of my pages I now get alerts boxes popping up saying:
>>>
>>>  TypeError: a.equals is not a function try/catch path:
>>> 0 function (b,d)
>>>  args[0]=TypeError: a.equals is not a function
>>>  args[1]=function (){a.instantialize(this,arguments)}
>>> 1 JS.ScriptEval.executeCommands(a,b)
>>>  args[0]=false
>>>  args[1]=true
>>> 2 JS.ScriptEval.resumeEval(a)
>>>  args[0]=[JS.ScriptContext object]
>>> 3 function ()
>>>
>>> This occurs when running a script that renders polyhedra.
>>>
>>> Apart from the fact that a script that has worked for years now
>>> seems to fail,
>>> why does an alert box popup rather than just the messages being
>>> written to the console?
>>>
>>> Do I need to set something to turn off alerts in this version of Jmol?
>>>
>>> I'll try to figure out exactly what causes the script to fail, but in
>>> the meantime any help with preventing the alert boxes would be
>>> appreciated.
>>>
>>> Thanks
>>>
>>> Simon Westrip
>>>
>>>
>>>
>>>
>>>
>>> Quoting Robert Hanson :
>>>
 I have recompiled Jmol 14.4.0 with a newly signed certificate.

 This is important only if your site uses the Jmol Java applet.

 This applet will not work again until this update is installed. Your
 current applet will fail indicating that its certificate has been revoked.
 This fixes that issue. If you want, you may be able to just extract the
 jsmol/java directory from Jmol.zip and copy the JAR files to your site to
 the same directory. But I recommend you upload the entire package.

 You can see proper operation of the Java applet at

 http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED

 I am very sorry for this inconvenience.

 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

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

Re: [Jmol-users] Default rendering changeable?

2015-10-16 Thread Rolf Huehne

On 10/16/2015 07:56 PM, Angel Herráez wrote:
> Rolf, it probably does not affect your problem, but your script is not the 
> best
> example for this. Clearly, changing the vdw property does not take effect
> immediately, only when you issue a spacefill command, so that's not a good
> test
>
Angel, I disagree. What you describe is exactly why it is a good test. 
The default rendering includes invoking a 'spacefill' command.

And changing the van der Waals radii of atoms is one of the things I 
might want to do. So a solution where this doesn't work wouldn't really 
help me.

> Maybe this:
>
> set defaultLoadScript "set echo top left; echo finished loading; spacefill 
> 1.0 only;";
> load =1deh;
>
This wouldn't tell me anything about my question because the end result 
would be the same for both cases.

> For me, the model does load as 1 angstrom balls. Of course, it may be that it
> first loads with "default rendering" and is later restyled. I donot see any
> changes, the first display is 1A balls.
>
You usually will not see any difference because no refresh is done in 
between. But if I add a 'refresh' I can see the first rendering shortly 
before the final one:

set defaultLoadScript "set echo top left; echo finished loading; 
refresh; spacefill 1.0 only;"
load =1deh;

> I am not yet sure what you aim at by "nothing should be rendered"
> spacefill off, wireframe off, cartoons off; ?
> hide all ?
>
It is aimed at avoiding to waste time for any kind of unwanted rendering 
for any atom. I might need for example only 'spacefill' with customized 
radii.

I don't really know if 'Hide all' would help because I don't know what 
is still done for the hidden atoms.

Regards,
Rolf
-- 

Rolf Huehne
Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

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

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Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Burkhard Zinner

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


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Re: [Jmol-users] Default rendering changeable?

2015-10-16 Thread Angel Herráez

Ok, Rolf, 

> It is aimed at avoiding to waste time for any kind of unwanted rendering 
> for any atom. I might need for example only 'spacefill' with customized 
> radii.

Yes, I understand your intention of saving time or computation. My problem 
was rather with he definition of "no rendering".

> I don't really know if 'Hide all' would help because I don't know what 
> is still done for the hidden atoms.

Right. Hide supresses any visuals, but styles are applied to atoms behind the 
curtain. Not clear if your "waste" is happening or not.


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Re: [Jmol-users] Default rendering changeable?

2015-10-16 Thread Angel Herráez

Rolf, it probably does not affect your problem, but your script is not the best 
example for this. Clearly, changing the vdw property does not take effect 
immediately, only when you issue a spacefill command, so that's not a good 
test

Maybe this:

set defaultLoadScript "set echo top left; echo finished loading; spacefill 1.0 
only;";
load =1deh;

For me, the model does load as 1 angstrom balls. Of course, it may be that it 
first loads with "default rendering" and is later restyled. I donot see any 
changes, the first display is 1A balls.

I am not yet sure what you aim at by "nothing should be rendered"  
spacefill off, wireframe off, cartoons off; ?
hide all ?




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Re: [Jmol-users] All deployed Jmol Java applets are disabled

2015-10-16 Thread Angel Herráez

Argghhh

For me, upgrading to a new version means checking every page that nothing 
is broken or changes when the scripts are run. Yes, that has happened to 
me before and one cannot assume they will run the same (I have 14.3.3 
running in most of my pages -- I thought it was older, so it may not be so 
bad).

Well, being positive, this is going to be a real push for everybody to move up 
to the brand new, shiny Jmol 14.4!!
 :-D

Bob, please make sure to speak to RCSB.


El 15 Oct 2015 a las 23:48, Robert Hanson escribió:
> Not kidding. All deployed Jmol applets are dead. Period. They will report:
·
 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28871 Alcalá de Henares  (Madrid), Spain


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[Jmol-users] Jmol 14.4.0_2015.10.14

2015-10-16 Thread Robert Hanson

I have recompiled Jmol 14.4.0 with a newly signed certificate.

This is important only if your site uses the Jmol Java applet.

This applet will not work again until this update is installed. Your
current applet will fail indicating that its certificate has been revoked.
This fixes that issue. If you want, you may be able to just extract the
jsmol/java directory from Jmol.zip and copy the JAR files to your site to
the same directory. But I recommend you upload the entire package.

You can see proper operation of the Java applet at

http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED

I am very sorry for this inconvenience.

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
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Re: [Jmol-users] Jmol 14.4.0_2015.10.14

2015-10-16 Thread David Hibbitts

Nevermind, had to clear the java cache on my laptop.

On Fri, Oct 16, 2015 at 6:30 AM, David Hibbitts  wrote:

> Hi Robert,
>
> I don't see any updated files on sourceforge, most recent appears to be:
>
> Jmol-14.4.0_2015.10.13-full.tar.gz
> 
>
> Is that the one we should be downloading? I just grabbed that one and
> upgraded my site but am still getting the certificate error.
>
> Thanks,
>
> On Fri, Oct 16, 2015 at 2:04 AM, Robert Hanson  wrote:
>
>> I have recompiled Jmol 14.4.0 with a newly signed certificate.
>>
>> This is important only if your site uses the Jmol Java applet.
>>
>> This applet will not work again until this update is installed. Your
>> current applet will fail indicating that its certificate has been revoked.
>> This fixes that issue. If you want, you may be able to just extract the
>> jsmol/java directory from Jmol.zip and copy the JAR files to your site to
>> the same directory. But I recommend you upload the entire package.
>>
>> You can see proper operation of the Java applet at
>>
>> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
>>
>> I am very sorry for this inconvenience.
>>
>> 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
>>
>>
>>
>> --
>>
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
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Re: [Jmol-users] Jmol 14.4.0_2015.10.14

2015-10-16 Thread David Hibbitts

Hi Robert,

I don't see any updated files on sourceforge, most recent appears to be:

Jmol-14.4.0_2015.10.13-full.tar.gz


Is that the one we should be downloading? I just grabbed that one and
upgraded my site but am still getting the certificate error.

Thanks,

On Fri, Oct 16, 2015 at 2:04 AM, Robert Hanson  wrote:

> I have recompiled Jmol 14.4.0 with a newly signed certificate.
>
> This is important only if your site uses the Jmol Java applet.
>
> This applet will not work again until this update is installed. Your
> current applet will fail indicating that its certificate has been revoked.
> This fixes that issue. If you want, you may be able to just extract the
> jsmol/java directory from Jmol.zip and copy the JAR files to your site to
> the same directory. But I recommend you upload the entire package.
>
> You can see proper operation of the Java applet at
>
> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
>
> I am very sorry for this inconvenience.
>
> 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
>
>
>
> --
>
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
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Re: [Jmol-users] Jmol 14.4.0_2015.10.14 - alert boxes

2015-10-16 Thread Otis Rothenberger

Simon,

I was seeing this where the script WAS completing after the alert box was 
dismissed. Bob correctly pointed out that I was running some Bootstrap related 
scripts that imposed JavaScript “use strict.” When I removed this from the 
Bootstrap related scripts, the problem disappeared.

However, like you, I continue to see these alert boxes where the script has an 
error where previous versions of Jmol would have died without the alert. One 
example of this is the following:

Jmol.evaluateVar(jmolApplet0, "'hexane'.find('SMILES','CCC') > 0”)

I know the script is ridiculous, but it happened because of an answer key 
error. Earlier versions of Jmol did not throw an error alert with this script.

To summarize, I was seeing two problems - one seems to be corrected by editing 
“use strict” out of my Bootstrap .js files. The other problem, alert where Jmol 
formerly died without alert, seems to remain.

Otis

--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com

> On Oct 16, 2015, at 7:12 AM, si...@publcif.co.uk wrote:
> 
> Just installed this.
> 
> For some of my pages I now get alerts boxes popping up saying:
> 
>  TypeError: a.equals is not a function try/catch path:
> 0 function (b,d)
>  args[0]=TypeError: a.equals is not a function
>  args[1]=function (){a.instantialize(this,arguments)}
> 1 JS.ScriptEval.executeCommands(a,b)
>  args[0]=false
>  args[1]=true
> 2 JS.ScriptEval.resumeEval(a)
>  args[0]=[JS.ScriptContext object]
> 3 function ()
> 
> This occurs when running a script that renders polyhedra.
> 
> Apart from the fact that a script that has worked for years now seems to fail,
> why does an alert box popup rather than just the messages being  
> written to the console?
> 
> Do I need to set something to turn off alerts in this version of Jmol?
> 
> I'll try to figure out exactly what causes the script to fail, but in  
> the meantime any help with preventing the alert boxes would be  
> appreciated.
> 
> Thanks
> 
> Simon Westrip
> 
> 
> 
> 
> 
> Quoting Robert Hanson :
> 
>> I have recompiled Jmol 14.4.0 with a newly signed certificate.
>> 
>> This is important only if your site uses the Jmol Java applet.
>> 
>> This applet will not work again until this update is installed. Your
>> current applet will fail indicating that its certificate has been revoked.
>> This fixes that issue. If you want, you may be able to just extract the
>> jsmol/java directory from Jmol.zip and copy the JAR files to your site to
>> the same directory. But I recommend you upload the entire package.
>> 
>> You can see proper operation of the Java applet at
>> 
>> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
>> 
>> I am very sorry for this inconvenience.
>> 
>> 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
>> 
> 
> 
> 
> --
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> 




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Re: [Jmol-users] Jmol 14.4.0_2015.10.14

2015-10-16 Thread Rolf Huehne

On 10/16/2015 12:46 PM, David Hibbitts wrote:
> Nevermind, had to clear the java cache on my laptop.
>
But the file 'Jmol-14.4.0_2015.10.13-binary.zip' still has the same MD5 
checksum as the file I donwnloaded yesterday.

So is it compiled already with the new certificate or not?

Unfortunately I can't check it myself because the 'IcedTea-Web Java 
plugin' crashes currently in my Firefox 41.0.2 on Linux and my Chromium 
31.0 doesn't seem to care about the revoked certificate of older versions.

Regards,
Rolf

> On Fri, Oct 16, 2015 at 6:30 AM, David Hibbitts  wrote:
>
>> Hi Robert,
>>
>> I don't see any updated files on sourceforge, most recent appears to be:
>>
>> Jmol-14.4.0_2015.10.13-full.tar.gz
>> 
>>
>> Is that the one we should be downloading? I just grabbed that one and
>> upgraded my site but am still getting the certificate error.
>>
>> Thanks,
>>
>> On Fri, Oct 16, 2015 at 2:04 AM, Robert Hanson  wrote:
>>
>>> I have recompiled Jmol 14.4.0 with a newly signed certificate.
>>>
>>> This is important only if your site uses the Jmol Java applet.
>>>
>>> This applet will not work again until this update is installed. Your
>>> current applet will fail indicating that its certificate has been revoked.
>>> This fixes that issue. If you want, you may be able to just extract the
>>> jsmol/java directory from Jmol.zip and copy the JAR files to your site to
>>> the same directory. But I recommend you upload the entire package.
>>>
>>> You can see proper operation of the Java applet at
>>>
>>> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
>>>
>>> I am very sorry for this inconvenience.
>>>
>>> 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
>>>
>>>
>>>
>>> --
>>>
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>
>
>
> --
>
>
>
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-- 

Rolf Huehne
Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

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

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

VAT No: DE 153 925 464
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Tax Number: 162/141/08228


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Re: [Jmol-users] Jmol 14.4.0_2015.10.14 - alert boxes

2015-10-16 Thread simon

Just installed this.

For some of my pages I now get alerts boxes popping up saying:

  TypeError: a.equals is not a function try/catch path:
0 function (b,d)
  args[0]=TypeError: a.equals is not a function
  args[1]=function (){a.instantialize(this,arguments)}
1 JS.ScriptEval.executeCommands(a,b)
  args[0]=false
  args[1]=true
2 JS.ScriptEval.resumeEval(a)
  args[0]=[JS.ScriptContext object]
3 function ()

This occurs when running a script that renders polyhedra.

Apart from the fact that a script that has worked for years now seems to fail,
why does an alert box popup rather than just the messages being  
written to the console?

Do I need to set something to turn off alerts in this version of Jmol?

I'll try to figure out exactly what causes the script to fail, but in  
the meantime any help with preventing the alert boxes would be  
appreciated.

Thanks

Simon Westrip





Quoting Robert Hanson :

> I have recompiled Jmol 14.4.0 with a newly signed certificate.
>
> This is important only if your site uses the Jmol Java applet.
>
> This applet will not work again until this update is installed. Your
> current applet will fail indicating that its certificate has been revoked.
> This fixes that issue. If you want, you may be able to just extract the
> jsmol/java directory from Jmol.zip and copy the JAR files to your site to
> the same directory. But I recommend you upload the entire package.
>
> You can see proper operation of the Java applet at
>
> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
>
> I am very sorry for this inconvenience.
>
> 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
>



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Re: [Jmol-users] All deployed Jmol Java applets are disabled

2015-10-16 Thread Eric Martz

Are you sure its *irrevocable*, Bob? That's quite unfortunate. As Angel 
says, it will take me some time to verify that current Jmol works in 
FirstGlance. Typically, I find one or more bugs/issues and have to wait 
till they're fixed (in my code or in Jmol) before I release a new 
version. And often I end up releasing with an earlier version of Jmol to 
avoid some problem or other. This means nobody can use FirstGlance with 
Java until I can get all those issues ironed out.


Well glory be to JSmol/HTML5 which will keep FirstGlance operational 
meanwhile!


On 10/16/15 12:48 AM, Robert Hanson wrote:
Well, it turns out that, following the instructions of an 
inexperienced representative from GoDaddy (where Jmol's secure signed 
certificate is managed) I just disabled permanently and irrevokably 
all standing Jmol Java applets.


Not kidding. *All deployed Jmol applets are dead*. Period. They will 
report:


Inline image 1


JSmol *JavaScript installations are not affected* (because they are 
not "signed").


Standalone Jmol JAR files are not affected (I am pretty sure).


In short, this is a mandatory upgrade for any site using Jmol or 
JSpecView.

All Integrated-Graphics signed Java applet installations must upgrade.

I am compiling now.

And it was such a good 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



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[Jmol-users] Unsigned Jmol Java applets still work

2015-10-16 Thread Eric Martz

Curiously, very old websites that still use unsigned Jmol java applets 
still work, despite the certificate for newer signed Jmol being revoked.

For example, the tutorials on Hemoglobin, Antibody, and MHC at 
http://molviz.org. These still work in Firefox on OS 10.10.5 Yosemite. 
An alert complains, but seems harmless, and sometimes you have to give 
permission more than once for the applet to run, but basically, after 
you get the unsigned applet configured to work, these still work with 
only minor fussiness.

Instructions for getting unsigned applets to work are included here:
http://proteopedia.org/w/Installing_and_enabling_Java

-Eric

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Re: [Jmol-users] Unsigned Jmol Java applets still work

2015-10-16 Thread Rolf Huehne

On 10/16/2015 04:53 PM, Eric Martz wrote:
> Curiously, very old websites that still use unsigned Jmol java applets
> still work, despite the certificate for newer signed Jmol being revoked.
>
It would be strange if they wouldn't. If there is no cerificate check as 
with the old unsigned Jmol applets, then revocation of a certificate 
should not have any effect.

Regards,
Rolf

-- 

Rolf Huehne
Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

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

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Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Burkhard Zinner

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


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Re: [Jmol-users] Jmol 14.4.0_2015.10.14 - alert boxes

2015-10-16 Thread simon

Otis:

In my case its the "alert where Jmol formerly died without alert"  
problem you describe.

I can live with alerts for failing scripts (i.e. they shouldn't fail  
in the first place if I do my job properly),
but it is now clear that its not just one of my scripts that is  
failing with Jmol 14.4 (though they worked with previous versions).

Looks like it may take some time to identify exactly where the problems are...

Thanks for the info anyway.

Cheers

Simon


Quoting Otis Rothenberger :

> Simon,
>
> I was seeing this where the script WAS completing after the alert  
> box was dismissed. Bob correctly pointed out that I was running some  
> Bootstrap related scripts that imposed JavaScript ?use strict.? When  
> I removed this from the Bootstrap related scripts, the problem  
> disappeared.
>
> However, like you, I continue to see these alert boxes where the  
> script has an error where previous versions of Jmol would have died  
> without the alert. One example of this is the following:
>
> Jmol.evaluateVar(jmolApplet0, "'hexane'.find('SMILES','CCC') > 0?)
>
> I know the script is ridiculous, but it happened because of an  
> answer key error. Earlier versions of Jmol did not throw an error  
> alert with this script.
>
> To summarize, I was seeing two problems - one seems to be corrected  
> by editing ?use strict? out of my Bootstrap .js files. The other  
> problem, alert where Jmol formerly died without alert, seems to  
> remain.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>> On Oct 16, 2015, at 7:12 AM, si...@publcif.co.uk wrote:
>>
>> Just installed this.
>>
>> For some of my pages I now get alerts boxes popping up saying:
>>
>>  TypeError: a.equals is not a function try/catch path:
>> 0 function (b,d)
>>  args[0]=TypeError: a.equals is not a function
>>  args[1]=function (){a.instantialize(this,arguments)}
>> 1 JS.ScriptEval.executeCommands(a,b)
>>  args[0]=false
>>  args[1]=true
>> 2 JS.ScriptEval.resumeEval(a)
>>  args[0]=[JS.ScriptContext object]
>> 3 function ()
>>
>> This occurs when running a script that renders polyhedra.
>>
>> Apart from the fact that a script that has worked for years now  
>> seems to fail,
>> why does an alert box popup rather than just the messages being
>> written to the console?
>>
>> Do I need to set something to turn off alerts in this version of Jmol?
>>
>> I'll try to figure out exactly what causes the script to fail, but in
>> the meantime any help with preventing the alert boxes would be
>> appreciated.
>>
>> Thanks
>>
>> Simon Westrip
>>
>>
>>
>>
>>
>> Quoting Robert Hanson :
>>
>>> I have recompiled Jmol 14.4.0 with a newly signed certificate.
>>>
>>> This is important only if your site uses the Jmol Java applet.
>>>
>>> This applet will not work again until this update is installed. Your
>>> current applet will fail indicating that its certificate has been revoked.
>>> This fixes that issue. If you want, you may be able to just extract the
>>> jsmol/java directory from Jmol.zip and copy the JAR files to your site to
>>> the same directory. But I recommend you upload the entire package.
>>>
>>> You can see proper operation of the Java applet at
>>>
>>> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
>>>
>>> I am very sorry for this inconvenience.
>>>
>>> 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
>>>
>>
>>
>>
>> --
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>>
>>
>
>
>
>
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Re: [Jmol-users] Default rendering changeable?

2015-10-16 Thread Rolf Huehne

On 10/16/2015 06:52 AM, Robert Hanson wrote:
> You should be able to use
>
> set defaultLoadScript
>
> to override any initial rendering. Pretty sure that executes prior to any
> rendering.
> 
It doesn't look like it is executed prior to the default rendering (1) 
and it also doesn't replace default rendering (2).

If (1) were true, then the atoms should be rendered larger in the 
example below.
If (2) were true, then nothing should be rendered at all.

 Example --
set defaultLoadScript "echo top left 'finished loading'; {all}.vdw=1.0;";
load =1deh;
---

But the atoms are rendered and atom size is based on the standard van 
der Waals radii.

Only after "spacefill auto" the new van der Waals radii are applied.

Regards,
Rolf

-- 

Rolf Huehne
Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

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

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

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

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Re: [Jmol-users] Jmol 14.4.0_2015.10.14 - alert boxes - polyhedra

Re: [Jmol-users] Default rendering changeable?

Re: [Jmol-users] Default rendering changeable?

Re: [Jmol-users] Default rendering changeable?

Re: [Jmol-users] All deployed Jmol Java applets are disabled

[Jmol-users] Jmol 14.4.0_2015.10.14

Re: [Jmol-users] Jmol 14.4.0_2015.10.14

Re: [Jmol-users] Jmol 14.4.0_2015.10.14

Re: [Jmol-users] Jmol 14.4.0_2015.10.14 - alert boxes

Re: [Jmol-users] Jmol 14.4.0_2015.10.14

Re: [Jmol-users] Jmol 14.4.0_2015.10.14 - alert boxes

Re: [Jmol-users] All deployed Jmol Java applets are disabled

[Jmol-users] Unsigned Jmol Java applets still work

Re: [Jmol-users] Unsigned Jmol Java applets still work

Re: [Jmol-users] Jmol 14.4.0_2015.10.14 - alert boxes

Re: [Jmol-users] Default rendering changeable?

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