Re: [Jmol-users] updating SpectralZoo problems

[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.
> 
> 
> --
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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, 
> J-Flow, sFlow and other flows. Make informed decisions using capacity 
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> ___
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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, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
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Re: [Jmol-users] updating SpectralZoo problems

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

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

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

[Jmol-users] updating SpectralZoo problems

[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