Re: [Jmol-users] loop on atom list broken in 13.1.9_dev

[Rolf Huehne]

On 11/27/2012 11:21 PM, Robert Hanson wrote:
> Not seeing that
>
> $ for(var i IN {selected}) {print i.label()}
> H #1
> H #2
> H #3
> H #4
> C #5
> C #6
> C #7
> C #8
> S #9
> $ for(var i IN {selected}) {show i}
> i = ({0})
> i = ({1})
> i = ({2})
> i = ({3})
> i = ({4})
> i = ({5})
> i = ({6})
> i = ({7})
> i = ({8})
>
>
> ??
>
So it looks like it got fixed before the offical release of 13.1.9.
My 13.1.9_dev version was build from SVN on Oct 30 and the official 
release was on Nov 24. Yesterday I couldn't try the latest SVN version 
because there was a problem with a missing regexp library. Today I 
tested the official releases 13.1.8, 13.1.9, 13.0.9 and could also build 
the latest version from SVN. Only in 13.1.8 it didn't work.

Regards,
Rolf


-- 

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Postdoc

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Re: [Jmol-users] JSmol update

[Philip Bays]

Bob:

In the test2 example, I still am getting an error when trying to load the mo 
files.  All that is shown is the file neame.


On Nov 27, 2012, at 9:40 PM, Robert Hanson  wrote:

> http://chemapps.stolaf.edu/jmol/jsmol.zip
> 
> http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
> 
> The top middle link is a test that demonstrates that JSmol successfully 
> implements "threads" -- interrupting a running, looping script to execute a 
> moveTo command and re-entering the script at the right place. 
> 
> Talk about a trick! A good challenge, anyway. Bet you can't guess how it's 
> done
> 
> Bob
> 
> 
> -- 
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
> 
> 
> If nature does not answer first what we want,
> it is better to take what answer we get. 
> 
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> 
> 
> --
> Keep yourself connected to Go Parallel: 
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
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> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

J. Philip Bays
Emeritus Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu





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[Jmol-users] Jmol call function

[smith82]

Dear all,
 
I'd like to ask you for help with my problem.I use jmol for viewing of my 
results, but now I need extend my solution.
In my code I use command jmolButton:
 
jmolButton("model NEXT","Next")
 
I need call some php function and together use "model NEXT", when I push the 
jmolButton.
Can you write me some example how to solve this problem?
 
Thank you for help.
 
Regards
 
Smith
 
 

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Re: [Jmol-users] Jmol call function

[Simone Sturniolo]

I have just started working with JSO, but I can tell you at least that you
can replace the jmol script ("model NEXT") with a Javascript function. You
only have to pass an array [, , ...]
to the jmolButton function. If your function does simple operations which
can be coded in Javascript, that would probably be the best option.
Otherwise - if you have to do operations that are strictly server-side -
maybe it's better to use something like AJAX? I don't really know about
this as it's something I'm working at right now, so anyone's advice is
welcome.
Regards,

Simone


2012/11/28 

> Dear all,
>
> I'd like to ask you for help with my problem.I use jmol for viewing of my
> results, but now I need extend my solution.
> In my code I use command jmolButton:
>
> jmolButton("model NEXT","Next")
>
> I need call some php function and together use "model NEXT", when I push
> the jmolButton.
> Can you write me some example how to solve this problem?
>
> Thank you for help.
>
> Regards
>
> Smith
>
>
>
>
> --
> Keep yourself connected to Go Parallel:
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net
> ___
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> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



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[Jmol-users] JSmol update

[Greeves, Nick]

Looks great, Bob.

One of the issues until now was the JSmol "applet" taking its time to execute a 
command which effectively froze the page on a iPad until the command was 
completed.
This may make that less of a problem. I'll test later. And No, I can't guess 
how it was done.
Being patient is not my forte!
All the best
Nick
--
3D Organic Animations http://www.chemtube3d.com
Tel: +44 (0)151-794-3506 (3500 secretary)



Begin forwarded message:

Message: 2
Date: Tue, 27 Nov 2012 20:40:11 -0600
From: Robert Hanson mailto:hans...@stolaf.edu>>
Subject: [Jmol-users] JSmol update
To: "jmol-users@lists.sourceforge.net"
mailto:jmol-users@lists.sourceforge.net>>
Message-ID:
mailto:CAF_YUvXUu17WdWuTrqkV+Tg4h6n9X63F_h8Paud8RDo=u8_...@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"

http://chemapps.stolaf.edu/jmol/jsmol.zip

http://chemapps.stolaf.edu/jmol/jsmol/test2.htm

The top middle link is a test that demonstrates that JSmol successfully
implements "threads" -- interrupting a running, looping script to execute a
moveTo command and re-entering the script at the right place.

Talk about a trick! A good challenge, anyway. Bet you can't guess how it's
done

Bob


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Re: [Jmol-users] Jmol call function

[Angel Herráez]

Hello Smith

I have little experience with php, but I will tell you what you can 
do with Javascript and hopefully you can adapt it:

> jmolButton("model NEXT","Next")
> 
> I need call some php function and together use "model NEXT", when I 
> push the jmolButton.
> Can you write me some example how to solve this problem?


Two ways:

 jmolButton("model NEXT; javascript myFunction(a,b,c)","Next")

(you may need quotes around "myFunction(a,b,c)", not sure)

or




That is, either you call the Jmol command from the html (method 2) or 
you call the Javascript from inside JmolScript

Hope it helps,




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Re: [Jmol-users] JSmol update

[Robert Hanson]

Do you think it's your browser?


On Wed, Nov 28, 2012 at 6:26 AM, Philip Bays  wrote:

> Bob:
>
> In the test2 example, I still am getting an error when trying to load the
> mo files.  All that is shown is the file neame.
>
>
> On Nov 27, 2012, at 9:40 PM, Robert Hanson  wrote:
>
> http://chemapps.stolaf.edu/jmol/jsmol.zip
>
> http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
>
> The top middle link is a test that demonstrates that JSmol successfully
> implements "threads" -- interrupting a running, looping script to execute
> a moveTo command and re-entering the script at the right place.
>
> Talk about a trick! A good challenge, anyway. Bet you can't guess how it's
> done
>
> Bob
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
> --
> Keep yourself connected to Go Parallel:
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
>
> http://goparallel.sourceforge.net___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
>
>
>
>
>
>
>
> --
> Keep yourself connected to Go Parallel:
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net
> ___
> 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, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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Re: [Jmol-users] JSmol update

[Robert Hanson]

Ah, by the way, I notice now that I have "multithreading" working, we are
back to needing an operating script queue. Scripts are not being queued
properly if they have any sort of move, moveTo, delay, or (animated) rotate
command in them right now.


On Wed, Nov 28, 2012 at 7:44 AM, Greeves, Nick wrote:

>  Looks great, Bob.
>
>  One of the issues until now was the JSmol "applet" taking its time to
> execute a command which effectively froze the page on a iPad until the
> command was completed.
> This may make that less of a problem. I'll test later. And No, I can't
> guess how it was done.
> Being patient is not my forte!
> All the best
> Nick
> --
> 3D Organic Animations http://www.chemtube3d.com
> Tel: +44 (0)151-794-3506 (3500 secretary)
>
>
>
> Begin forwarded message:
>
> Message: 2
> Date: Tue, 27 Nov 2012 20:40:11 -0600
> From: Robert Hanson 
> Subject: [Jmol-users] JSmol update
> To: "jmol-users@lists.sourceforge.net"
> 
> Message-ID:
> 
> Content-Type: text/plain; charset="iso-8859-1"
>
> http://chemapps.stolaf.edu/jmol/jsmol.zip
>
> http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
>
> The top middle link is a test that demonstrates that JSmol successfully
> implements "threads" -- interrupting a running, looping script to execute a
> moveTo command and re-entering the script at the right place.
>
> Talk about a trick! A good challenge, anyway. Bet you can't guess how it's
> done
>
> Bob
>
>
>
>
> --
> Keep yourself connected to Go Parallel:
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net
> ___
> 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, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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Re: [Jmol-users] JSmol update

[Otis Rothenberger]

Phil,

On Safari 6.0.2, I load the MO files. Are you using Safari?

Otis

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




On Nov 28, 2012, at 12:46 PM, Robert Hanson wrote:

> Do you think it's your browser?
> 
> 
> On Wed, Nov 28, 2012 at 6:26 AM, Philip Bays  wrote:
> Bob:
> 
> In the test2 example, I still am getting an error when trying to load the mo 
> files.  All that is shown is the file neame.
> 
> 
> On Nov 27, 2012, at 9:40 PM, Robert Hanson  wrote:
> 
>> http://chemapps.stolaf.edu/jmol/jsmol.zip
>> 
>> http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
>> 
>> The top middle link is a test that demonstrates that JSmol successfully 
>> implements "threads" -- interrupting a running, looping script to execute a 
>> moveTo command and re-entering the script at the right place. 
>> 
>> Talk about a trick! A good challenge, anyway. Bet you can't guess how it's 
>> done
>> 
>> Bob
>> 
>> 
>> -- 
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>> 
>> 
>> If nature does not answer first what we want,
>> it is better to take what answer we get. 
>> 
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>> 
>> 
>> --
>> Keep yourself connected to Go Parallel: 
>> INSIGHTS What's next for parallel hardware, programming and related areas?
>> Interviews and blogs by thought leaders keep you ahead of the curve.
>> http://goparallel.sourceforge.net___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
> 
> 
> 
> 
> 
> 
> --
> Keep yourself connected to Go Parallel:
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net
> ___
> 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, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
> 
> 
> If nature does not answer first what we want,
> it is better to take what answer we get. 
> 
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> 
> 
> --
> Keep yourself connected to Go Parallel: 
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

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Re: [Jmol-users] R: Re: R: JSmol -- Are we done?

[Angel Herráez]

Pino, 
I suggest to first be sure that you clear your browser cache -- js 
files remain there and you might be seeing the effect of a mixture of 
old and new files



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Re: [Jmol-users] JSmol update

[Philip Bays]

Otis:

I am using Safari, Firefox, and Camino (with which I have never used for JSmol 
until just now).   I am getting an "unrecognized file type" error in all of 
them.  I have not cleared the Safari cache because I do not see how to do it.   
It used to be in the Safari drop down menu.   I do not see it there now or in 
the preferences??  A get the same message with the signed and unsigned Java 
applets as well.

Phil

On Nov 28, 2012, at 1:09 PM, Otis Rothenberger  wrote:

> Phil,
> 
> On Safari 6.0.2, I load the MO files. Are you using Safari?
> 
> Otis
> 
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
> 
> 
> 
> 
> On Nov 28, 2012, at 12:46 PM, Robert Hanson wrote:
> 
>> Do you think it's your browser?
>> 
>> 
>> On Wed, Nov 28, 2012 at 6:26 AM, Philip Bays  wrote:
>> Bob:
>> 
>> In the test2 example, I still am getting an error when trying to load the mo 
>> files.  All that is shown is the file neame.
>> 
>> 
>> On Nov 27, 2012, at 9:40 PM, Robert Hanson  wrote:
>> 
>>> http://chemapps.stolaf.edu/jmol/jsmol.zip
>>> 
>>> http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
>>> 
>>> The top middle link is a test that demonstrates that JSmol successfully 
>>> implements "threads" -- interrupting a running, looping script to execute a 
>>> moveTo command and re-entering the script at the right place. 
>>> 
>>> Talk about a trick! A good challenge, anyway. Bet you can't guess how it's 
>>> done
>>> 
>>> Bob
>>> 
>>> 
>>> -- 
>>> Robert M. Hanson
>>> Larson-Anderson Professor of Chemistry
>>> Chair, Chemistry Department
>>> St. Olaf College
>>> Northfield, MN
>>> http://www.stolaf.edu/people/hansonr
>>> 
>>> 
>>> If nature does not answer first what we want,
>>> it is better to take what answer we get. 
>>> 
>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>> 
>>> 
>>> --
>>> Keep yourself connected to Go Parallel: 
>>> INSIGHTS What's next for parallel hardware, programming and related areas?
>>> Interviews and blogs by thought leaders keep you ahead of the curve.
>>> http://goparallel.sourceforge.net___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> 
>> J. Philip Bays
>> Emeritus Professor of Chemistry
>> Department of Chemistry and Physics
>> Saint Mary's College
>> Notre Dame, IN 46556
>> pb...@saintmarys.edu
>> 
>> 
>> 
>> 
>> 
>> 
>> --
>> Keep yourself connected to Go Parallel:
>> INSIGHTS What's next for parallel hardware, programming and related areas?
>> Interviews and blogs by thought leaders keep you ahead of the curve.
>> http://goparallel.sourceforge.net
>> ___
>> 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, Chemistry Department
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>> 
>> 
>> If nature does not answer first what we want,
>> it is better to take what answer we get. 
>> 
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>> 
>> 
>> --
>> Keep yourself connected to Go Parallel: 
>> INSIGHTS What's next for parallel hardware, programming and related areas?
>> Interviews and blogs by thought leaders keep you ahead of the curve.
>> http://goparallel.sourceforge.net___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> --
> Keep yourself connected to Go Parallel: 
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

J. Philip Bays
Emeritus Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu





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[Jmol-users] R: Re: R: Re: R: JSmol -- Are we done?

[pino.stricc...@libero.it]

Angel, i cleared the cache. Now the applet seems to load but when i load a 
molecule i receive format non recognized error. No javascript error in console 
(firefox or google chrome). Could be a problem of Jquery libraries that are 
different? a conflict? 
Pino

>Messaggio originale
>Da: angel.herr...@uah.es
>Data: 28/11/2012 19.20
>A: "pino.stricc...@libero.it", 
>Ogg: Re: [Jmol-users] R: Re:  R: JSmol -- Are we done?
>
>Pino, 
>I suggest to first be sure that you clear your browser cache -- js 
>files remain there and you might be seeing the effect of a mixture of 
>old and new files
>
>
>

>--
>Keep yourself connected to Go Parallel: 
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>___
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>https://lists.sourceforge.net/lists/listinfo/jmol-users
>



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Re: [Jmol-users] R: Re: R: Re: R: JSmol -- Are we done?

[Angel Herráez]

No idea

But my server was giving me trouble serving some pdb and mol files. Maybe 
it's related. I could fix that by renaming to .pdb.txt or .mol.txt (this was 
with a 
former version  of JSmol, I have not checked lately)
The error was in the form of garbage characters in red font inside the JSmol 
panel


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Re: [Jmol-users] JSmol update

[Robert Hanson]

the file that would be causing that error is

http://chemapps.stolaf.edu/jmol/jsmol/JSmolCore.js

or it's a problem with how JSmolCore determines whether your system can
read binary files directly.

Look in that file for

// JSmolCore.js -- Jmol core capability  11/28/2012 1:56:34 PM

at the top to see that you have the latest, then try the page again.

Does sound like a caching issue.

Bob



On Wed, Nov 28, 2012 at 1:04 PM, Philip Bays  wrote:

> Otis:
>
> I am using Safari, Firefox, and Camino (with which I have never used for
> JSmol until just now).   I am getting an "unrecognized file type" error in
> all of them.  I have not cleared the Safari cache because I do not see how
> to do it.   It used to be in the Safari drop down menu.   I do not see it
> there now or in the preferences??  A get the same message with the signed
> and unsigned Java applets as well.
>
> Phil
>
> On Nov 28, 2012, at 1:09 PM, Otis Rothenberger 
> wrote:
>
> Phil,
>
> On Safari 6.0.2, I load the MO files. Are you using Safari?
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Nov 28, 2012, at 12:46 PM, Robert Hanson wrote:
>
> Do you think it's your browser?
>
>
> On Wed, Nov 28, 2012 at 6:26 AM, Philip Bays  wrote:
>
>> Bob:
>>
>> In the test2 example, I still am getting an error when trying to load the
>> mo files.  All that is shown is the file neame.
>>
>>
>> On Nov 27, 2012, at 9:40 PM, Robert Hanson  wrote:
>>
>> http://chemapps.stolaf.edu/jmol/jsmol.zip
>>
>> http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
>>
>> The top middle link is a test that demonstrates that JSmol successfully
>> implements "threads" -- interrupting a running, looping script to execute
>> a moveTo command and re-entering the script at the right place.
>>
>> Talk about a trick! A good challenge, anyway. Bet you can't guess how
>> it's done
>>
>> Bob
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>>
>> --
>> Keep yourself connected to Go Parallel:
>> INSIGHTS What's next for parallel hardware, programming and related areas?
>> Interviews and blogs by thought leaders keep you ahead of the curve.
>>
>> http://goparallel.sourceforge.net___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>  J. Philip Bays
>> Emeritus Professor of Chemistry
>> Department of Chemistry and Physics
>> Saint Mary's College
>> Notre Dame, IN 46556
>> pb...@saintmarys.edu
>>
>>
>>
>>
>>
>>
>>
>> --
>> Keep yourself connected to Go Parallel:
>> INSIGHTS What's next for parallel hardware, programming and related areas?
>> Interviews and blogs by thought leaders keep you ahead of the curve.
>> http://goparallel.sourceforge.net
>> ___
>> 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, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
> --
> Keep yourself connected to Go Parallel:
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
>
> http://goparallel.sourceforge.net___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
> --
> Keep yourself connected to Go Parallel:
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
>
> http://goparallel.sourceforge.net___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
>
>
>
>
>
>
>
> --
> Keep yourself connected to Go Pa

Re: [Jmol-users] JSmol update

[Otis Rothenberger]

Phil,

In the Preferences/Advanced menu, check "Show develop menu in menu bar." There 
is an Empty Caches and a Disable Caches selection in the resulting Develop menu 
item. In the Safari menu selection there is also a Reset Safari... selection. 
They keep changing stuff like this to irritate us!

I'll try other browsers on Mac to see if I see the problem there.

Otis


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




On Nov 28, 2012, at 2:04 PM, Philip Bays wrote:

> Otis:
> 
> I am using Safari, Firefox, and Camino (with which I have never used for 
> JSmol until just now).   I am getting an "unrecognized file type" error in 
> all of them.  I have not cleared the Safari cache because I do not see how to 
> do it.   It used to be in the Safari drop down menu.   I do not see it there 
> now or in the preferences??  A get the same message with the signed and 
> unsigned Java applets as well.
> 
> Phil
> 
> On Nov 28, 2012, at 1:09 PM, Otis Rothenberger  wrote:
> 
>> Phil,
>> 
>> On Safari 6.0.2, I load the MO files. Are you using Safari?
>> 
>> Otis
>> 
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>> 
>> 
>> 
>> 
>> On Nov 28, 2012, at 12:46 PM, Robert Hanson wrote:
>> 
>>> Do you think it's your browser?
>>> 
>>> 
>>> On Wed, Nov 28, 2012 at 6:26 AM, Philip Bays  wrote:
>>> Bob:
>>> 
>>> In the test2 example, I still am getting an error when trying to load the 
>>> mo files.  All that is shown is the file neame.
>>> 
>>> 
>>> On Nov 27, 2012, at 9:40 PM, Robert Hanson  wrote:
>>> 
 http://chemapps.stolaf.edu/jmol/jsmol.zip
 
 http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
 
 The top middle link is a test that demonstrates that JSmol successfully 
 implements "threads" -- interrupting a running, looping script to execute 
 a moveTo command and re-entering the script at the right place. 
 
 Talk about a trick! A good challenge, anyway. Bet you can't guess how it's 
 done
 
 Bob
 
 
 -- 
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
 If nature does not answer first what we want,
 it is better to take what answer we get. 
 
 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
 
 
 --
 Keep yourself connected to Go Parallel: 
 INSIGHTS What's next for parallel hardware, programming and related areas?
 Interviews and blogs by thought leaders keep you ahead of the curve.
 http://goparallel.sourceforge.net___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users
>>> 
>>> J. Philip Bays
>>> Emeritus Professor of Chemistry
>>> Department of Chemistry and Physics
>>> Saint Mary's College
>>> Notre Dame, IN 46556
>>> pb...@saintmarys.edu
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> --
>>> Keep yourself connected to Go Parallel:
>>> INSIGHTS What's next for parallel hardware, programming and related areas?
>>> Interviews and blogs by thought leaders keep you ahead of the curve.
>>> http://goparallel.sourceforge.net
>>> ___
>>> 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, Chemistry Department
>>> St. Olaf College
>>> Northfield, MN
>>> http://www.stolaf.edu/people/hansonr
>>> 
>>> 
>>> If nature does not answer first what we want,
>>> it is better to take what answer we get. 
>>> 
>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>> 
>>> 
>>> --
>>> Keep yourself connected to Go Parallel: 
>>> INSIGHTS What's next for parallel hardware, programming and related areas?
>>> Interviews and blogs by thought leaders keep you ahead of the curve.
>>> http://goparallel.sourceforge.net___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> 
>> --
>> Keep yourself connected to Go Parallel: 
>> INSIGHTS What's next for parallel hardware, programming and related areas?
>> Interviews and blogs by thought leaders keep you ahead of the curve.
>> http://goparallel.sourceforge.net___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> J. Philip Bays
> Emeritus

Re: [Jmol-users] R: Re: R: Re: R: JSmol -- Are we done?

[Jeff Hansen]

I just checked some more.  Now when I load using the HTML5 option in the first 
column then try to thread test, I get the non-recognized format error.  The mo 
homo SQUARED and mo DENSITY also give the non-recognized format error.  If I 
click on the WebGL load link the thread test does not give the non-recognized 
format error but the script doesn't appear to work correctly either.  The 
molecule moves slowly and stops periodically but nothing else is observed.  The 
mo homo SQUARED and mo DENSITY links do not give the non-recognized format 
error but no molecule is displayed either, at least not in the several minutes 
I waited.



***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***


On Nov 28, 2012, at 2:33 PM, pino.stricc...@libero.it wrote:

> Angel, i cleared the cache. Now the applet seems to load but when i load a 
> molecule i receive format non recognized error. No javascript error in 
> console 
> (firefox or google chrome). Could be a problem of Jquery libraries that are 
> different? a conflict? 
> Pino
> 
>> Messaggio originale
>> Da: angel.herr...@uah.es
>> Data: 28/11/2012 19.20
>> A: "pino.stricc...@libero.it",  sourceforge.net>
>> Ogg: Re: [Jmol-users] R: Re:  R: JSmol -- Are we done?
>> 
>> Pino, 
>> I suggest to first be sure that you clear your browser cache -- js 
>> files remain there and you might be seeing the effect of a mixture of 
>> old and new files
>> 
>> 
>> 
> 
>> --
>> Keep yourself connected to Go Parallel: 
>> INSIGHTS What's next for parallel hardware, programming and related areas?
>> Interviews and blogs by thought leaders keep you ahead of the curve.
>> http://goparallel.sourceforge.net
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> 
> 
> 
> 
> --
> Keep yourself connected to Go Parallel: 
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users


--
Keep yourself connected to Go Parallel: 
INSIGHTS What's next for parallel hardware, programming and related areas?
Interviews and blogs by thought leaders keep you ahead of the curve.
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___
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Re: [Jmol-users] R: Re: R: Re: R: JSmol -- Are we done?

[Jeff Hansen]

I'm seeing the same thing.  I just did a system update to 10.7.5 then updated 
Safari to 6.0.2.  I emptied the cache (Developer menu - turn on in Advanced tab 
of Preferences).  I can load the caffeine molecule using HTML5.  When I try to 
do the MO examples in the middle of the middle column I get the non-recognized 
format error.


***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***


On Nov 28, 2012, at 2:33 PM, pino.stricc...@libero.it wrote:

> Angel, i cleared the cache. Now the applet seems to load but when i load a 
> molecule i receive format non recognized error. No javascript error in 
> console 
> (firefox or google chrome). Could be a problem of Jquery libraries that are 
> different? a conflict? 
> Pino
> 
>> Messaggio originale
>> Da: angel.herr...@uah.es
>> Data: 28/11/2012 19.20
>> A: "pino.stricc...@libero.it",  sourceforge.net>
>> Ogg: Re: [Jmol-users] R: Re:  R: JSmol -- Are we done?
>> 
>> Pino, 
>> I suggest to first be sure that you clear your browser cache -- js 
>> files remain there and you might be seeing the effect of a mixture of 
>> old and new files
>> 
>> 
>> 
> 
>> --
>> Keep yourself connected to Go Parallel: 
>> INSIGHTS What's next for parallel hardware, programming and related areas?
>> Interviews and blogs by thought leaders keep you ahead of the curve.
>> http://goparallel.sourceforge.net
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> 
> 
> 
> 
> --
> Keep yourself connected to Go Parallel: 
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users


--
Keep yourself connected to Go Parallel: 
INSIGHTS What's next for parallel hardware, programming and related areas?
Interviews and blogs by thought leaders keep you ahead of the curve.
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___
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Re: [Jmol-users] JSmol update

[Otis Rothenberger]

Phil,

My bad. I missed the MO HOMO SQUARED and MO DENSITY links. They are not loading 
with Jmol or HTML5.

Otis


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




On Nov 28, 2012, at 3:01 PM, Otis Rothenberger wrote:

> Phil,
> 
> In the Preferences/Advanced menu, check "Show develop menu in menu bar." 
> There is an Empty Caches and a Disable Caches selection in the resulting 
> Develop menu item. In the Safari menu selection there is also a Reset 
> Safari... selection. They keep changing stuff like this to irritate us!
> 
> I'll try other browsers on Mac to see if I see the problem there.
> 
> Otis
> 
> 

--
Keep yourself connected to Go Parallel: 
INSIGHTS What's next for parallel hardware, programming and related areas?
Interviews and blogs by thought leaders keep you ahead of the curve.
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Jmol-users@lists.sourceforge.net
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Re: [Jmol-users] JSmol update

[Otis Rothenberger]

Bob and Phil,

I think the relevant smol file is missing from this directory:

http://chemapps.stolaf.edu/jmol/jsmol/

Otis


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




On Nov 28, 2012, at 3:30 PM, Otis Rothenberger wrote:

> Phil,
> 
> My bad. I missed the MO HOMO SQUARED and MO DENSITY links. They are not 
> loading with Jmol or HTML5.
> 
> Otis
> 
> 
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
> 
> 
> 
> 
> On Nov 28, 2012, at 3:01 PM, Otis Rothenberger wrote:
> 
>> Phil,
>> 
>> In the Preferences/Advanced menu, check "Show develop menu in menu bar." 
>> There is an Empty Caches and a Disable Caches selection in the resulting 
>> Develop menu item. In the Safari menu selection there is also a Reset 
>> Safari... selection. They keep changing stuff like this to irritate us!
>> 
>> I'll try other browsers on Mac to see if I see the problem there.
>> 
>> Otis
>> 
>> 
> 
> --
> Keep yourself connected to Go Parallel: 
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

--
Keep yourself connected to Go Parallel: 
INSIGHTS What's next for parallel hardware, programming and related areas?
Interviews and blogs by thought leaders keep you ahead of the curve.
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Jmol-users mailing list
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Re: [Jmol-users] JSmol update

[Philip Bays]

Last Saturday we were in the midst of looking at the Firefox error message 
showing up in both Firefox Safari.   At that time I also mentioned this issue.  
 In the next iteration of Bob's uploads, the Firefox error was corrected and 
the MO's loaded.  Bob: whatever you did then needs to be done again:-)

Phil


On Nov 28, 2012, at 3:49 PM, Otis Rothenberger  wrote:

> Bob and Phil,
> 
> I think the relevant smol file is missing from this directory:
> 
> http://chemapps.stolaf.edu/jmol/jsmol/
> 
> Otis
> 
> 
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
> 
> 
> 
> 
> On Nov 28, 2012, at 3:30 PM, Otis Rothenberger wrote:
> 
>> Phil,
>> 
>> My bad. I missed the MO HOMO SQUARED and MO DENSITY links. They are not 
>> loading with Jmol or HTML5.
>> 
>> Otis
>> 
>> 
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>> 
>> 
>> 
>> 
>> On Nov 28, 2012, at 3:01 PM, Otis Rothenberger wrote:
>> 
>>> Phil,
>>> 
>>> In the Preferences/Advanced menu, check "Show develop menu in menu bar." 
>>> There is an Empty Caches and a Disable Caches selection in the resulting 
>>> Develop menu item. In the Safari menu selection there is also a Reset 
>>> Safari... selection. They keep changing stuff like this to irritate us!
>>> 
>>> I'll try other browsers on Mac to see if I see the problem there.
>>> 
>>> Otis
>>> 
>>> 
>> 
>> --
>> Keep yourself connected to Go Parallel: 
>> INSIGHTS What's next for parallel hardware, programming and related areas?
>> Interviews and blogs by thought leaders keep you ahead of the curve.
>> http://goparallel.sourceforge.net___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> --
> Keep yourself connected to Go Parallel: 
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

J. Philip Bays
Emeritus Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu





--
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Re: [Jmol-users] JSmol update

[Robert Hanson]

yes, of course! Try now. Note that the "density" one is not the sort of
thing to have on a web site -- this has to calculate the orbitals for ALL
occupied orbitals. You would really do this off line, create the JVXL file,
and then call that up if it were on line.

Bob



On Wed, Nov 28, 2012 at 2:30 PM, Otis Rothenberger wrote:

> Phil,
>
> My bad. I missed the MO HOMO SQUARED and MO DENSITY links. They are not
> loading with Jmol or HTML5.
>
> Otis
>
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Nov 28, 2012, at 3:01 PM, Otis Rothenberger wrote:
>
> Phil,
>
> In the Preferences/Advanced menu, check "Show develop menu in menu bar."
> There is an Empty Caches and a Disable Caches selection in the resulting
> Develop menu item. In the Safari menu selection there is also a Reset
> Safari... selection. They keep changing stuff like this to irritate us!
>
> I'll try other browsers on Mac to see if I see the problem there.
>
> Otis
>
>
>
>
>
> --
> Keep yourself connected to Go Parallel:
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net
> ___
> 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, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Keep yourself connected to Go Parallel: 
INSIGHTS What's next for parallel hardware, programming and related areas?
Interviews and blogs by thought leaders keep you ahead of the curve.
http://goparallel.sourceforge.net___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] JSmol update

[Jeff Hansen]

Working for me now although the behavior is still different for HTML5 vs. 
WebGL.  The thread test for WebGL doesn't work right for me in Safari and the 
mo links give meshes that I can't see through in WebGL while with HTML5 I can 
see through them.


***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***


On Nov 28, 2012, at 4:53 PM, Robert Hanson wrote:

> yes, of course! Try now. Note that the "density" one is not the sort of thing 
> to have on a web site -- this has to calculate the orbitals for ALL occupied 
> orbitals. You would really do this off line, create the JVXL file, and then 
> call that up if it were on line.
> 
> Bob
> 
> 
> 
> On Wed, Nov 28, 2012 at 2:30 PM, Otis Rothenberger  
> wrote:
> Phil,
> 
> My bad. I missed the MO HOMO SQUARED and MO DENSITY links. They are not 
> loading with Jmol or HTML5.
> 
> Otis
> 
> 
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
> 
> 
> 
> 
> On Nov 28, 2012, at 3:01 PM, Otis Rothenberger wrote:
> 
>> Phil,
>> 
>> In the Preferences/Advanced menu, check "Show develop menu in menu bar." 
>> There is an Empty Caches and a Disable Caches selection in the resulting 
>> Develop menu item. In the Safari menu selection there is also a Reset 
>> Safari... selection. They keep changing stuff like this to irritate us!
>> 
>> I'll try other browsers on Mac to see if I see the problem there.
>> 
>> Otis
>> 
>> 
> 
> 
> --
> Keep yourself connected to Go Parallel:
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net
> ___
> 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, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
> 
> 
> If nature does not answer first what we want,
> it is better to take what answer we get. 
> 
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> 
> 
> --
> Keep yourself connected to Go Parallel: 
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

--
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Interviews and blogs by thought leaders keep you ahead of the curve.
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Re: [Jmol-users] JSmol update

[Otis Rothenberger]

Bob,

OK, now it works, but there's another problem on the page. I believe the script 
on the  MO DENSITY link might be wrong. While it loads in HTML5 mode, it does 
not display the MO in JAVA mode unless I enter:

>mo  homo DENSITY

The link script that loads the model does not id an MO.

If I'm correct, why does it display in HTML5 mode?

Otis


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




On Nov 28, 2012, at 4:53 PM, Robert Hanson wrote:

> yes, of course! Try now. Note that the "density" one is not the sort of thing 
> to have on a web site -- this has to calculate the orbitals for ALL occupied 
> orbitals. You would really do this off line, create the JVXL file, and then 
> call that up if it were on line.
> 
> Bob
> 
> 
> 
> On Wed, Nov 28, 2012 at 2:30 PM, Otis Rothenberger  
> wrote:
> Phil,
> 
> My bad. I missed the MO HOMO SQUARED and MO DENSITY links. They are not 
> loading with Jmol or HTML5.
> 
> Otis
> 
> 
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
> 
> 
> 
> 
> On Nov 28, 2012, at 3:01 PM, Otis Rothenberger wrote:
> 
>> Phil,
>> 
>> In the Preferences/Advanced menu, check "Show develop menu in menu bar." 
>> There is an Empty Caches and a Disable Caches selection in the resulting 
>> Develop menu item. In the Safari menu selection there is also a Reset 
>> Safari... selection. They keep changing stuff like this to irritate us!
>> 
>> I'll try other browsers on Mac to see if I see the problem there.
>> 
>> Otis
>> 
>> 
> 
> 
> --
> Keep yourself connected to Go Parallel:
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> 
> 
> 
> -- 
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
> 
> 
> If nature does not answer first what we want,
> it is better to take what answer we get. 
> 
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> 
> 
> --
> Keep yourself connected to Go Parallel: 
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

--
Keep yourself connected to Go Parallel: 
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[Jmol-users] Fwd: R: Re: R: Re: R: JSmol -- Are we done?

[Robert Hanson]

-- Forwarded message --
From: Robert Hanson 
Date: Wed, Nov 28, 2012 at 6:02 PM
Subject: Re: [Jmol-users] R: Re: R: Re: R: JSmol -- Are we done?
To: "jmol-users@lists.sourceforge.net" 


It's a problem with Safari not being able to load binary files, I think, or
my not properly handling that when it does. I can reproduce this on my
MacBook Pro.




On Wed, Nov 28, 2012 at 2:12 PM, Jeff Hansen  wrote:

> I just checked some more.  Now when I load using the HTML5 option in the
> first column then try to thread test, I get the non-recognized format
> error.  The mo homo SQUARED and mo DENSITY also give the non-recognized
> format error.  If I click on the WebGL load link the thread test does not
> give the non-recognized format error but the script doesn't appear to work
> correctly either.  The molecule moves slowly and stops periodically but
> nothing else is observed.  The mo homo SQUARED and mo DENSITY links do not
> give the non-recognized format error but no molecule is displayed either,
> at least not in the several minutes I waited.
>
>
>
> ***
> Jeff Hansen
> Department of Chemistry and Biochemistry
> DePauw University
> 602 S. College Ave.
> Greencastle, IN 46135
> jhan...@depauw.edu
> ***
>
>
> On Nov 28, 2012, at 2:33 PM, pino.stricc...@libero.it wrote:
>
> > Angel, i cleared the cache. Now the applet seems to load but when i load
> a
> > molecule i receive format non recognized error. No javascript error in
> console
> > (firefox or google chrome). Could be a problem of Jquery libraries that
> are
> > different? a conflict?
> > Pino
> >
> >> Messaggio originale
> >> Da: angel.herr...@uah.es
> >> Data: 28/11/2012 19.20
> >> A: "pino.stricc...@libero.it",
>  > sourceforge.net>
> >> Ogg: Re: [Jmol-users] R: Re:  R: JSmol -- Are we done?
> >>
> >> Pino,
> >> I suggest to first be sure that you clear your browser cache -- js
> >> files remain there and you might be seeing the effect of a mixture of
> >> old and new files
> >>
> >>
> >>
> >
> >>
> --
> >> Keep yourself connected to Go Parallel:
> >> INSIGHTS What's next for parallel hardware, programming and related
> areas?
> >> Interviews and blogs by thought leaders keep you ahead of the curve.
> >> http://goparallel.sourceforge.net
> >> ___
> >> Jmol-users mailing list
> >> Jmol-users@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/jmol-users
> >>
> >
> >
> >
> >
> --
> > Keep yourself connected to Go Parallel:
> > INSIGHTS What's next for parallel hardware, programming and related
> areas?
> > Interviews and blogs by thought leaders keep you ahead of the curve.
> > http://goparallel.sourceforge.net
> > ___
> > Jmol-users mailing list
> > Jmol-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
> --
> Keep yourself connected to Go Parallel:
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net
> ___
> 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, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900





-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Keep yourself connected to Go Parallel: 
VERIFY Test and improve your parallel project with help from experts 
and peers. http://goparallel.sourceforge.net___
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Re: [Jmol-users] R: Re: R: Re: R: JSmol -- Are we done?

[Robert Hanson]

got it. -- required modifications to JSmoljQuery.js and JSmolCore.js

Safari should be reading binary files properly now.
http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?USE=HTML5 -- "water.xyz.gz"
or "mo homo SQUARED" links in HTML5




-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Keep yourself connected to Go Parallel: 
VERIFY Test and improve your parallel project with help from experts 
and peers. http://goparallel.sourceforge.net___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users