Re: [Jmol-users] JmolData.jar jmol-14.6.0_2016.05.24

2016-06-13 Thread Jaime Prilusky 
On 14 Jun 2016, at 3:45 AM, Robert Hanson 
> wrote:

I don't think capture should work from JmolData. Try Jmol.jar

Thank you,
Jaim
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
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Re: [Jmol-users] Load URL

2016-06-13 Thread Otis Rothenberger 
Thanks Bob. I have users load this via my interface, so I decided to simply put 
up a help notice when a user uses this feature while off line. I will have to 
modify my notice based on your note (below) re jsmol.php.

This (JavaScript load local/url command)  is really a neat feature. I almost 
missed it.

As an aside, I set up my wife’s new Windows 10 computer this week. Although my 
stuff is all small molecule, I was pleasantly surprised at my page’s Jmol 
response on Windows Edge. Running locally is another issue entirely, but the 
served page was really good.

Otis


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

> On Jun 13, 2016, at 8:42 PM, Robert Hanson  wrote:
> 
> 
> 
> On Mon, Jun 6, 2016 at 10:25 PM, Otis Rothenberger  > wrote:
> Bob,
> 
> I really like the convenience of the Jmol.loadFileFromDialog(jmolApplet0) 
> feature, but I’d like to be able to trap a URL entry. When I run JSmol 
> locally with no Internet connection, the jsmol.php file is not available for 
> a URL that might need it. I’d like to trap a URL entry gracefully as needed 
> below:
> 
> 1) Model kit running via server - No trap needed.
> 2) Model kit running locally on computer WITH Internet connection: No trap 
> needed.
> 3) Model kit running locally on computer WITH NO Internet connection: Trap 
> needed.
> 
> I detect all three states in my code. Is there a way to trap/check URL entry 
> when code detects condition 3? Running locally with no Internet connection 
> causes the page to hang on a URL entry looking for my jsmol.php file. I could 
> trap condition 3 and turn off the dialog, but I’d like to keep it for local 
> files.
> 
> 
> Otis,
> 
> 
> I think your best bet is to override
> 
> Jmol._loadFileAsynchronously
> 
> 
> adding your own event handlers there. That code is in JSmolCore.js
> 
> Local file loading never goes through JSmol.php. For local file reading, the 
> data is always a byte array, so binary or otherwise, it's all the same.
> 
> 
> Bob
> --
> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
> patterns at an interface-level. Reveals which users, apps, and protocols are 
> consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
> J-Flow, sFlow and other flows. Make informed decisions using capacity 
> planning reports. 
> https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
>  
> 
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net 
> https://lists.sourceforge.net/lists/listinfo/jmol-users 
> 
--
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patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
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Re: [Jmol-users] updating SpectralZoo pages

2016-06-13 Thread Jennifer L. Muzyka 
It is working for me.  It was a cache problem, like Angel and you both 
suggested.

Jennifer



Jennifer Muzyka
H. W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka

From: Robert Hanson 
Sent: Monday, June 13, 2016 8:44 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] updating SpectralZoo pages

Looks good now. Working for you, Jennifer??

Bob
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
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Re: [Jmol-users] JmolData.jar jmol-14.6.0_2016.05.24

2016-06-13 Thread Robert Hanson 
I don't think capture should work from JmolData. Try Jmol.jar

On Mon, Jun 6, 2016 at 12:18 PM, Jaime Prilusky <
jaime.prilu...@weizmann.ac.il> wrote:

> Could it be that command ‘capture’ fails on JmolData.jar from
> jmol-14.6.0_2016.05.24 ?
>
> After loading a model, ‘ capture “file.gif” Y 30 ’ generates a file with
> only GIF89a?? on it.
> On the other side, ‘ write IMAGE 500 500 GIF “file.gif” ‘ works Ok.
>
> Jaim
>
> --
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and protocols
> are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
> ___
> 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
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
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
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Re: [Jmol-users] updating SpectralZoo pages

2016-06-13 Thread Robert Hanson 
Looks good now. Working for you, Jennifer?​

Bob
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
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Re: [Jmol-users] Load URL

2016-06-13 Thread Robert Hanson 
On Mon, Jun 6, 2016 at 10:25 PM, Otis Rothenberger 
wrote:

> Bob,
>
> I really like the convenience of the Jmol.loadFileFromDialog(jmolApplet0)
> feature, but I’d like to be able to trap a URL entry. When I run JSmol
> locally with no Internet connection, the jsmol.php file is not available
> for a URL that might need it. I’d like to trap a URL entry gracefully as
> needed below:
>
> 1) Model kit running via server - No trap needed.
> 2) Model kit running locally on computer WITH Internet connection: No trap
> needed.
> 3) Model kit running locally on computer WITH NO Internet connection: Trap
> needed.
>
> I detect all three states in my code. Is there a way to trap/check URL
> entry when code detects condition 3? Running locally with no Internet
> connection causes the page to hang on a URL entry looking for my jsmol.php
> file. I could trap condition 3 and turn off the dialog, but I’d like to
> keep it for local files.
>
>
Otis,


I think your best bet is to override

Jmol._loadFileAsynchronously


adding your own event handlers there. That code is in JSmolCore.js

Local file loading never goes through JSmol.php. For local file reading,
the data is always a byte array, so binary or otherwise, it's all the same.


Bob
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
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Re: [Jmol-users] updating SpectralZoo problems

2016-06-13 Thread Robert Hanson 
ANIM.js is no longer part of Jmol. So what this indicates is that you have
some sort of mix of files. Or more probably your browser cache needs
clearing.

On Fri, Jun 10, 2016 at 10:45 AM, Jennifer L. Muzyka <
jennifer.muz...@centre.edu> wrote:

> Thanks to Eric and Otis and others who have offered suggestions.  I am
> coming to believe that something is indeed wrong with my installation.
> Yesterday I downloaded the zip file from Sourceforge.  Then I copied the
> jsmol folder to the server.  When I try to open the example files (
> http://chemserv.centre.edu/muzyka/spectralzoo/jsmol/supersimple.htm) I
> see the same error messages that I sometimes see with the SpectralZoo file
> -
>
> [Java2Script] The required class file
>
> j2s/J/c/ANIM.js
> could not be loaded. Script error: expected expression, got '<'
>
> data:
>
> 
> 
> 404 Not Found
> 
> Not Found
> The requested URL /muzyka/spectralzoo/jsmol/j2s/J/c/ANIM.js was not
> found on this server.
> 
> Apache/2.4.7 (Ubuntu) Server at chemserv.centre.edu Port
> 80
> 
>
>
> Sure enough, there’s no file name ANIM.js in the c folder.  Is there
> something wrong with my approach to copy the whole directory over?
> Any advice?
> Jennifer
>
>
>
>
> Jennifer Muzyka
> H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
> Centre College
> 600 West Walnut Street
> Danville, KY  40422
>
> jennifer.muz...@centre.edu
> http://web.centre.edu/muzyka
> http://organicers.org
>
> 859-238-5413
> fax 859-236-7925
>
>
>
>
>
>
>
>
> --
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and protocols
> are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
> ___
> 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
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
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
Jmol-users mailing list
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Re: [Jmol-users] updating SpectralZoo problems

2016-06-13 Thread Otis Rothenberger 
Jennifer,

The page hangs for me on the first structure load, BUT if I wait it out, all is 
OK. I missed this point in my initial check. All is well after this initial 
load.

This initial hang, however, is repeated in some subsequent (no cache clearing) 
new sessions. I don’t know that this is a problem, but it mirrors a behavior 
that I’m seeing on my site now that I moved to GoDaddy. Since it’s not related 
to local cache, I’ve been assuming that its related to the GoDaddy Name Server 
DNS software. It’s irritating, but there’s not much I can do about it. I’m 
spoiled because my site was on a high end service that I had to drop because of 
cost/space limitations.

So I think I’m seeing this type of Name Server DNS software delay on your 
page’s initial load on occasion. I just did not catch it at fist because I was 
thinking that the page was already loaded. It was, but that load structure 
button is loading a new page!

Are you using GoDaddy by any chance?

Otis

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

> On Jun 13, 2016, at 10:18 AM, Otis Rothenberger  wrote:
> 
> Hi Jennifer,
> 
> I hate to be a "poop," but even with cache clearing this page is still not 
> working for me on Safari or Windows 10 Edge:
> 
> http://chemserv.centre.edu/muzyka/spectralzoo/jsmol/specZoo.php 
> 
> 
> Is this the page that you were referencing in your latest note?
> 
> Otis
> 
> --
> Otis Rothenberger
> o...@chemagic.org 
> http://chemagic.org 
> 
> On Jun 13, 2016, at 9:11 AM, Jennifer L. Muzyka  > wrote:
> 
>> Thanks for Angel and Otis for helping me with the troubleshooting.  After I 
>> cleared my cache, it works for me too!  I’m embarrassed to make such a silly 
>> mistake.  
>> Jennifer
>> 
>> 
>> 
>> 
>> 
>> 
>> Jennifer Muzyka
>> H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
>> Centre College
>> 600 West Walnut Street
>> Danville, KY  40422
>> 
>> jennifer.muz...@centre.edu 
>> http://web.centre.edu/muzyka 
>> http://organicers.org 
>> 
>> 859-238-5413
>> fax 859-236-7925
>> 
>> 
>> 
>> 
>> 
>> 
>>> On Jun 11, 2016, at 6:08 AM, Angel Herráez >> > wrote:
>>> 
>>> Jennifer,
>>> 
>>> Your page
>>> http://chemserv.centre.edu/muzyka/spectralzoo 
>>> 
>>> is mostly functional for me (at least in Firefox Windows7).
>>> 
>>> 1. JSpecViewer loads, and it loads spectra when I click on the buttons.
>>> 
>>> 2. JSmol aldo loads, althoug it is hidden due to the css rule
>>>   #structure { display: none; }
>>> 
>>> 3. The [Show Structure] button is not working because it sends data to a 
>>> structure.htm page that does not exist. I have made a local duplicate of 
>>> your page with the proper structure.htm file and it also works.
>>> 
>>> 
>>> So I believe there is no problem due to upgrading your JSmol version, there 
>>> is no JmolScript problem, even Javascript problems.
>>> You have most likely a mixed up collection of pieces of javascript code 
>>> inherited from previous page.
>>> 
>>> For example,
>>> - you are calling jquery.js twice (at the top and the bottom of your page) 
>>> -- in fact, three times counting the copy included in JSmol.min.js
>>> - you are calling a mixture of JSmol-related js files, which are not needed 
>>> as Otis pointed out
>>> - you are missing or have the wrong path to structure.htm
>>> 
>>> This is my advice:
>>> 
>>> (head section) Leave just these:
>>> 
>>> 
>>> 
>>> 
>>> 
>>> (bottom of body) Remove this line:
>>> 
>>>  
>>> 
>>> Optionally:
>>> 
>>> You can probably remove the jmol_isReady  part, and clean up your Info 
>>> definitions to these:
>>> 
>>> Info = {
>>>   width: 800,
>>>   height: 300,
>>>   color: "#FF",
>>>   serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php 
>>> ",
>>>   disableInitialConsole: true,
>>>   use: "HTML5"
>>> }
>>> var Info2 = {
>>>   width: 200,
>>>   height: 200,
>>>   serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php 
>>> ",
>>>   use: "HTML5",
>>>   j2sPath: "j2s"
>>> }
>>> 
>>> Although not important for your setup, this is the correct function, just 
>>> in case:
>>> 
>>> function cloneJSmol(JSmolObject) {
>>>   var t = JSmolObject._jmolType; //temp
>>>   if ( /_Canvas2D/.test(t) ) { t = 'HTML5'; }
>>>   else if ( /_Canvas3D/.test(t) ) { t = 'WebGL'; }
>>>   else if ( /_Applet/.test(t) ) { t = 'Java'; }
>>>   else { t = null; }
>>>   JSmolCloneData.type = t;
>>>   JSmolCloneData.state = Jmol.getPropertyAsString(JSmolObject, 'stateInfo');
>>>   window.open(' structure.htm','JSmolPopup','resizable,

Re: [Jmol-users] updating SpectralZoo problems

2016-06-13 Thread Jennifer L. Muzyka 
Otis,
That IS the page I was referring to.  I’m happy to have you testing it for me 
on different platforms - I don’t have access to Windows 10 Edge.  What kind of 
errors to you see?

I do have access to Safari, and it works on my Mac running Yosemite.  I haven’t 
tested with mobile Safari.  Please tell me more about what you see so that I 
can address the problems, Otis.
Jennifer








Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Jun 13, 2016, at 10:18 AM, Otis Rothenberger 
> wrote:

Hi Jennifer,

I hate to be a "poop," but even with cache clearing this page is still not 
working for me on Safari or Windows 10 Edge:

http://chemserv.centre.edu/muzyka/spectralzoo/jsmol/specZoo.php

Is this the page that you were referencing in your latest note?

Otis

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

On Jun 13, 2016, at 9:11 AM, Jennifer L. Muzyka 
> wrote:

Thanks for Angel and Otis for helping me with the troubleshooting.  After I 
cleared my cache, it works for me too!  I’m embarrassed to make such a silly 
mistake.
Jennifer






Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Jun 11, 2016, at 6:08 AM, Angel Herráez 
> wrote:

Jennifer,

Your page

http://chemserv.centre.edu/muzyka/spectralzoo

is mostly functional for me (at least in Firefox Windows7).

1. JSpecViewer loads, and it loads spectra when I click on the buttons.

2. JSmol aldo loads, althoug it is hidden due to the css rule
  #structure { display: none; }

3. The [Show Structure] button is not working because it sends data to a 
structure.htm page that does not exist. I have made a local duplicate of your 
page with the proper structure.htm file and it also works.


So I believe there is no problem due to upgrading your JSmol version, there is 
no JmolScript problem, even Javascript problems.
You have most likely a mixed up collection of pieces of javascript code 
inherited from previous page.

For example,
- you are calling jquery.js twice (at the top and the bottom of your page) -- 
in fact, three times counting the copy included in JSmol.min.js
- you are calling a mixture of JSmol-related js files, which are not needed as 
Otis pointed out
- you are missing or have the wrong path to structure.htm

This is my advice:

(head section) Leave just these:





(bottom of body) Remove this line:

 

Optionally:

You can probably remove the jmol_isReady  part, and clean up your Info 
definitions to these:

Info = {
  width: 800,
  height: 300,
  color: "#FF",
  serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php;,
  disableInitialConsole: true,
  use: "HTML5"
}
var Info2 = {
  width: 200,
  height: 200,
  serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php;,
  use: "HTML5",
  j2sPath: "j2s"
}

Although not important for your setup, this is the correct function, just in 
case:

function cloneJSmol(JSmolObject) {
  var t = JSmolObject._jmolType; //temp
  if ( /_Canvas2D/.test(t) ) { t = 'HTML5'; }
  else if ( /_Canvas3D/.test(t) ) { t = 'WebGL'; }
  else if ( /_Applet/.test(t) ) { t = 'Java'; }
  else { t = null; }
  JSmolCloneData.type = t;
  JSmolCloneData.state = Jmol.getPropertyAsString(JSmolObject, 'stateInfo');
  window.open(' structure.htm','JSmolPopup','resizable, width=500, height=500');
}



--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. 
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Jmol-users mailing list
Jmol-users@lists.sourceforge.net
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--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed

Re: [Jmol-users] updating SpectralZoo problems

2016-06-13 Thread Otis Rothenberger 
Hi Jennifer,

I hate to be a "poop," but even with cache clearing this page is still not 
working for me on Safari or Windows 10 Edge:

http://chemserv.centre.edu/muzyka/spectralzoo/jsmol/specZoo.php

Is this the page that you were referencing in your latest note?

Otis

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

> On Jun 13, 2016, at 9:11 AM, Jennifer L. Muzyka  
> wrote:
> 
> Thanks for Angel and Otis for helping me with the troubleshooting.  After I 
> cleared my cache, it works for me too!  I’m embarrassed to make such a silly 
> mistake.  
> Jennifer
> 
> 
> 
> 
> 
> 
> Jennifer Muzyka
> H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
> Centre College
> 600 West Walnut Street
> Danville, KY  40422
> 
> jennifer.muz...@centre.edu
> http://web.centre.edu/muzyka
> http://organicers.org
> 
> 859-238-5413
> fax 859-236-7925
> 
> 
> 
> 
> 
> 
>> On Jun 11, 2016, at 6:08 AM, Angel Herráez  wrote:
>> 
>> Jennifer,
>> 
>> Your page
>> http://chemserv.centre.edu/muzyka/spectralzoo
>> is mostly functional for me (at least in Firefox Windows7).
>> 
>> 1. JSpecViewer loads, and it loads spectra when I click on the buttons.
>> 
>> 2. JSmol aldo loads, althoug it is hidden due to the css rule
>>   #structure { display: none; }
>> 
>> 3. The [Show Structure] button is not working because it sends data to a 
>> structure.htm page that does not exist. I have made a local duplicate of 
>> your page with the proper structure.htm file and it also works.
>> 
>> 
>> So I believe there is no problem due to upgrading your JSmol version, there 
>> is no JmolScript problem, even Javascript problems.
>> You have most likely a mixed up collection of pieces of javascript code 
>> inherited from previous page.
>> 
>> For example,
>> - you are calling jquery.js twice (at the top and the bottom of your page) 
>> -- in fact, three times counting the copy included in JSmol.min.js
>> - you are calling a mixture of JSmol-related js files, which are not needed 
>> as Otis pointed out
>> - you are missing or have the wrong path to structure.htm
>> 
>> This is my advice:
>> 
>> (head section) Leave just these:
>> 
>> 
>> 
>> 
>> 
>> (bottom of body) Remove this line:
>> 
>>  
>> 
>> Optionally:
>> 
>> You can probably remove the jmol_isReady  part, and clean up your Info 
>> definitions to these:
>> 
>> Info = {
>>   width: 800,
>>   height: 300,
>>   color: "#FF",
>>   serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php;,
>>   disableInitialConsole: true,
>>   use: "HTML5"
>> }
>> var Info2 = {
>>   width: 200,
>>   height: 200,
>>   serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php;,
>>   use: "HTML5",
>>   j2sPath: "j2s"
>> }
>> 
>> Although not important for your setup, this is the correct function, just in 
>> case:
>> 
>> function cloneJSmol(JSmolObject) {
>>   var t = JSmolObject._jmolType; //temp
>>   if ( /_Canvas2D/.test(t) ) { t = 'HTML5'; }
>>   else if ( /_Canvas3D/.test(t) ) { t = 'WebGL'; }
>>   else if ( /_Applet/.test(t) ) { t = 'Java'; }
>>   else { t = null; }
>>   JSmolCloneData.type = t;
>>   JSmolCloneData.state = Jmol.getPropertyAsString(JSmolObject, 'stateInfo');
>>   window.open(' structure.htm','JSmolPopup','resizable, width=500, 
>> height=500');
>> }
>> 
>> 
>>   
>> --
>> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
>> patterns at an interface-level. Reveals which users, apps, and protocols are 
>> consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
>> J-Flow, sFlow and other flows. Make informed decisions using capacity 
>> planning reports. 
>> https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> --
> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
> patterns at an interface-level. Reveals which users, apps, and protocols are 
> consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
> J-Flow, sFlow and other flows. Make informed decisions using capacity 
> planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity

Re: [Jmol-users] updating SpectralZoo problems

2016-06-13 Thread Jennifer L. Muzyka 
Thanks for Angel and Otis for helping me with the troubleshooting.  After I 
cleared my cache, it works for me too!  I’m embarrassed to make such a silly 
mistake.
Jennifer






Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Jun 11, 2016, at 6:08 AM, Angel Herráez 
> wrote:

Jennifer,

Your page

http://chemserv.centre.edu/muzyka/spectralzoo

is mostly functional for me (at least in Firefox Windows7).

1. JSpecViewer loads, and it loads spectra when I click on the buttons.

2. JSmol aldo loads, althoug it is hidden due to the css rule
  #structure { display: none; }

3. The [Show Structure] button is not working because it sends data to a 
structure.htm page that does not exist. I have made a local duplicate of your 
page with the proper structure.htm file and it also works.


So I believe there is no problem due to upgrading your JSmol version, there is 
no JmolScript problem, even Javascript problems.
You have most likely a mixed up collection of pieces of javascript code 
inherited from previous page.

For example,
- you are calling jquery.js twice (at the top and the bottom of your page) -- 
in fact, three times counting the copy included in JSmol.min.js
- you are calling a mixture of JSmol-related js files, which are not needed as 
Otis pointed out
- you are missing or have the wrong path to structure.htm

This is my advice:

(head section) Leave just these:





(bottom of body) Remove this line:

 

Optionally:

You can probably remove the jmol_isReady  part, and clean up your Info 
definitions to these:

Info = {
  width: 800,
  height: 300,
  color: "#FF",
  serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php;,
  disableInitialConsole: true,
  use: "HTML5"
}
var Info2 = {
  width: 200,
  height: 200,
  serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php;,
  use: "HTML5",
  j2sPath: "j2s"
}

Although not important for your setup, this is the correct function, just in 
case:

function cloneJSmol(JSmolObject) {
  var t = JSmolObject._jmolType; //temp
  if ( /_Canvas2D/.test(t) ) { t = 'HTML5'; }
  else if ( /_Canvas3D/.test(t) ) { t = 'WebGL'; }
  else if ( /_Applet/.test(t) ) { t = 'Java'; }
  else { t = null; }
  JSmolCloneData.type = t;
  JSmolCloneData.state = Jmol.getPropertyAsString(JSmolObject, 'stateInfo');
  window.open(' structure.htm','JSmolPopup','resizable, width=500, height=500');
}



--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. 
https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users