Re: [Jmol-users] updating SpectralZoo pages

2016-06-09 Thread Otis Rothenberger 
Hi Again Jennifer,

I spent some time looking at your code. You have a lot going on with JQuery, 
JQuery UI widgets, and Bootstrap. I think I see other possible conflicts in 
addition to the possible unquote attribute issue. You are loading your own 
version of JQuery (along with the UI Widgets). You are, however, using 
JSmol.min.js. If you’re going to load your own JQuery, you may need to use 
JSmol.min.nojq.js - not JSmol.min.js. Since I load JQuery and Bootstrap, I use  
JSmol.min.nojq.js.

The possible nojq issue aside for a minute, Bob or Angel may need to jump in on 
this next point, but I THINK there is redundancy in these lines:













Unless there is something funky going on in the page that I don’t understand, 
JSmol.min.js OR JSmol.min.nojq.js is the only JSmol file that you need to call 
directly.

The docs page that Eric references is important, but I think your basic problem 
is installation. In solving the problem, this page may be equally important:

http://wiki.jmol.org/index.php/Jmol_JavaScript_Object

Worth a Try Suggestion:

Since you are calling the JQuery UI files along with a number of Bootstrap 
files, try:




in place of the

Re: [Jmol-users] updating SpectralZoo pages

2016-06-09 Thread Otis Rothenberger 
Jennifer,

Although you do not have to quote attributes in HTML5, there are reports of 
issues when quotes are not used. Note your JSmol id below:



Before you start an exhaustive problem search, why don’t you just try quoting 
that id to make sure that your not experiencing an issue with this unquoted id?

I’ll keep looking at your page code, but it looks to me like JSmol is loading, 
but id=jsvdiv is not getting its HTML.

Otis


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

> On Jun 9, 2016, at 3:30 PM, Jennifer L. Muzyka  
> wrote:
> 
> We recently got a new server to host the SpectralZoo 
> (http://chemserv.centre.edu/muzyka/spectralzoo 
> ), with new versions of PHP 
> and MySQL.  Some of my SpectralZoo scripts broke, so I thought it might be 
> time to upgrade the Jmol (actually JSmol) that I’m using on the site.  I see 
> even more errors, and I’m stumped about how to solve them.  It looks like I 
> was previously using a version of Jmol from 11/2013.  Can someone point me to 
> something to read to help me sort out the changes so that I can manage the 
> troubleshooting?  (Clearly I have been away from programming for too long…..) 
>  I would appreciate any advice you can offer or articles you can point me 
> towards.  Thanks.
> 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___
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Re: [Jmol-users] updating SpectralZoo pages

2016-06-09 Thread Eric Martz 
New versions of JSmol are supposed to be backwards compatible. There are 
very few intentional changes that require changes in the JSmol command 
scripts, generally quite minor.


It would be good to "set debugscript on" and see where the errors occur.

If you are still stumped, copy the error reports into an email and maybe 
someone on this list will have a suggestion.


If you have loops in your JSmol commands (for or while), I think some 
older syntaxes may not work. Check the manual.


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

Good luck! -Eric


On 6/9/16 3:30 PM, Jennifer L. Muzyka wrote:
We recently got a new server to host the SpectralZoo 
(http://chemserv.centre.edu/muzyka/spectralzoo), with new versions of 
PHP and MySQL.  Some of my SpectralZoo scripts broke, so I thought it 
might be time to upgrade the Jmol (actually JSmol) that I’m using on 
the site.  I see even more errors, and I’m stumped about how to solve 
them.  It looks like I was previously using a version of Jmol from 
11/2013.  Can someone point me to something to read to help me sort 
out the changes so that I can manage the troubleshooting?  (Clearly I 
have been away from programming for too long…..)  I would appreciate 
any advice you can offer or articles you can point me towards.  Thanks.

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 pages

2016-06-09 Thread Jennifer L. Muzyka 
We recently got a new server to host the SpectralZoo 
(http://chemserv.centre.edu/muzyka/spectralzoo), with new versions of PHP and 
MySQL.  Some of my SpectralZoo scripts broke, so I thought it might be time to 
upgrade the Jmol (actually JSmol) that I’m using on the site.  I see even more 
errors, and I’m stumped about how to solve them.  It looks like I was 
previously using a version of Jmol from 11/2013.  Can someone point me to 
something to read to help me sort out the changes so that I can manage the 
troubleshooting?  (Clearly I have been away from programming for too long…..)  
I would appreciate any advice you can offer or articles you can point me 
towards.  Thanks.
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

Re: [Jmol-users] How to change the boundary of cells in Jmol?

2016-06-09 Thread Angel Herráez 
Hello Vincent

Try reading these:

http://chemapps.stolaf.edu/jmol/docs/#loadcrystallographicoptions

http://chemapps.stolaf.edu/jmol/docs/#unitcell

> Recently I try to visualize a periodic cell in Jmol, but it seems that 
> the boundaries of the cell is 
> automatically set to be from 0 to 1 in every direction. How can I change 
> the settings, like, to 
> show the cell in (-0.5, 0.5) in x,y,z direction?


--
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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[Jmol-users] How to change the boundary of cells in Jmol?

2016-06-09 Thread Song, Wenshen 
Hello!

Recently I try to visualize a periodic cell in Jmol, but it seems that the 
boundaries of the cell is automatically set to be from 0 to 1 in every 
direction. How can I change the settings, like,  to show the cell in (-0.5, 
0.5) in x,y,z direction?

Thanks!

Yours,
Vincent

--
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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