Re: [Jmol-users] updating SpectralZoo problems

[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 
mailto:osrot...@icloud.com>> 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 
mailto:osrot...@icloud.com>> 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 
mailto:jennifer.muz...@centre.edu>> 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 
mailto:angel.herr...@uah.es>> 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');
}



---

[Jmol-users] minor update

[Robert Hanson]

*Download Jmol-14.6.0_2016.06.14-binary.tar.gz (66.5 MB)
*

Just a few updates here:

Jmol.___JmolVersion="14.6.0_2016.06.14"

bug fix: reading of protein structure for a group that is not in a polymer
causes null pointer exception  (Angel)

bug fix: set hermiteLevel -4 allows hermite during mouse move but not
spinning (Eric)

bug fix: polyhedron faces not generated correctly when positions are very
close together

bug fix: polyhedron face areas not calculated correctly





-- 
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. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users