subject:"\[Jmol\-users\] updating SpectralZoo problems"

Re: [Jmol-users] updating SpectralZoo problems

2016-06-15 Thread Jennifer L. Muzyka

Otis,
I’m not using GoDaddy.  My stuff is all hosted at Centre College.  The 
SpectralZoo and ReactionZoo are on a server by themselves, so sometimes weird 
stuff happens to that server and ITS is less likely to find out about it 
because most it’s off the beaten path.
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 10:59 AM, Otis Rothenberger 
> wrote:

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('

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

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. 
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

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. 
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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 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

2016-06-11 Thread Angel Herráez

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
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Re: [Jmol-users] updating SpectralZoo problems

2016-06-10 Thread Otis Rothenberger

Jennifer,

In the jsmol folder, Bob has this file:

jsv_mol.htm

It’s probably the original of the file link in my previous email. This one is 
slightly more commented, and one comment explains the short list of js files vs 
the long list of js files.

Otis



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

> On Jun 10, 2016, at 5:41 PM, Angel Herráez  wrote:
> 
> Dear Jennifer 
> 
> That page
> 
>> (http://chemserv.centre.edu/muzyka/spectralzoo/jsmol/supersimple.htm) I see 
>> the same error 
> 
> is working fine for me now (Firefox under Win7). No errors.
> Caffeine (default) loads ok, and I also entered some other name at the 
> textbox and it was loaded ok.
> 
> Try clearing your browser cache. Maybe some mixture of old and new files is 
> affecting you.
> 
> Or are you trying ot load some other molecule?
> 
> I see no hint that such ANIM.js file exists in Jmol distribution fileset.
> 
> 
> --
> 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

Re: [Jmol-users] updating SpectralZoo problems

2016-06-10 Thread Angel Herráez

Dear Jennifer 

That page

> (http://chemserv.centre.edu/muzyka/spectralzoo/jsmol/supersimple.htm) I see 
> the same error 

is working fine for me now (Firefox under Win7). No errors.
Caffeine (default) loads ok, and I also entered some other name at the 
textbox and it was loaded ok.

Try clearing your browser cache. Maybe some mixture of old and new files is 
affecting you.

Or are you trying ot load some other molecule?

I see no hint that such ANIM.js file exists in Jmol distribution fileset.


--
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

Re: [Jmol-users] updating SpectralZoo problems

2016-06-10 Thread Otis Rothenberger

Jennifer,

This is a super simple page at Robert Lancashire's site:

http://wwwchem.uwimona.edu.jm/spectra/jsmol/demos/vinylpyrrolidinone.html 

It’s not carrying the weight of all of the JQuery/Bootstrap code on your page, 
so the bare bones of getting the load set up is clear, strangely interesting, 
but clear. Some observations on this point:

1) The relevant js load is simply:

2) Both JSmol and JSV Info definitions have the j2sPath reference. You only 
have this with JSmol Info definition.

3) Now it gets really interesting, strange but interesting! The code is not 
lengthy, so check it out on the page. First note that he is using 
Jmol.setAppletSync([jsvApplet, jmolApplet], ["load ../data/vinylpyrr.jdx", ""], 
true); Bob discusses this here:

https://sourceforge.net/p/jmol/mailman/message/31421841/ 

Second, he is using a Javascript construct that concatenates the above and the 
Info variable declarations with a self-invoking anonymous function. Wild guess 
here: He’s doing this because he’s not using JQuery This following example 
code is a variation of the Lancashire code that DOES use JQuery, but it also 
uses the self-invoking anonymous function. I do not know why; I’m just 
reporting what I found!

http://cgit.drupalcode.org/molecule/tree/jsmol/testjsv_mol.htm?id=47b902360e3d8ab55304fb362cad55fd48529607

Anyway, the above use of JQuery loads both applets as follows:

$(document).ready(function() {
 $("#jmoldiv").html(Jmol.getAppletHtml("jmolApplet0", MInfo));
 $("#jsvdiv").html(Jmol.getJSVAppletHtml("jsvApplet0",SInfo));
});

This suggests timing is important.

I hope this helps! It has certainly been instructive on my end.

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

> On Jun 10, 2016, at 2:19 PM, Otis Rothenberger  wrote:
> 
> Jennifer,
> 
> I don’t know. Maybe with the JSpecView connection you need all those script 
> loads. I can see that  src="js/JSmolJSV.js"> would be needed, but I don’t understand the 
> need for some of the others.
> 
> The thing is that this is not loading:
> 
> jmolApplet2 = Jmol.getApplet('jmolApplet2', Info2);
> Jmol.script(jmolApplet2,'load files/structure/triClEthane.PDB’);
> 
> I wonder if you need one of the Jmol ready functions to load this if JSV is 
> in the picture?? StOlaf server is down right now. I’ll look into this later 
> and get back to you.
> 
> Otis
> 

--
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
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Re: [Jmol-users] updating SpectralZoo problems

2016-06-10 Thread Otis Rothenberger

Jennifer,

I don’t know. Maybe with the JSpecView connection you need all those script 
loads. I can see that  would be needed, but I don’t understand the need 
for some of the others.

The thing is that this is not loading:

jmolApplet2 = Jmol.getApplet('jmolApplet2', Info2);
Jmol.script(jmolApplet2,'load files/structure/triClEthane.PDB’);

I wonder if you need one of the Jmol ready functions to load this if JSV is in 
the picture?? StOlaf server is down right now. I’ll look into this later and 
get back to you.

Otis

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

> On Jun 10, 2016, at 11:45 AM, Jennifer L. Muzyka  
> 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

--
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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[Jmol-users] updating SpectralZoo problems

2016-06-10 Thread Jennifer L. Muzyka

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

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