Re: [Jmol-users] JSmol menu doesn't open in FirstGlance

2014-04-14 Thread Robert Hanson
Try upgrading to Jmol 14.0.


On Sun, Apr 13, 2014 at 5:06 PM, Eric Martz ema...@microbio.umass.eduwrote:

 I cannot seem to get the JSmol menu to open (14.0.4):

 http://firstglance.jmol.org/fg.htm?mol=1d66use=html5

 For comparison, the menu opens just fine with the Java applet:

 http://firstglance.jmol.org/fg.htm?mol=1d66

 I have the same problem with JSmol 14.0.13 in local testing.

 Is JSmol too close to the edge of the window?

 Any suggestions?

 Eric




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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
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Re: [Jmol-users] JSmol menu doesn't open in FirstGlance

2014-04-14 Thread Eric Martz
Hi, Bob,

As stated below, I am already using 14.0.4 in the released version of 
FirstGlance 1.98 (firstglance.jmol.org, uncheck the Java checkbox and 
enter a PDB code).

Also when I use 14.0.13 (running in Firefox from local files) I can't 
get the menu to open.

Regards, Eric

At 4/14/14, Robert Hanson wrote:
Try upgrading to Jmol 14.0.


On Sun, Apr 13, 2014 at 5:06 PM, Eric Martz 
mailto:ema...@microbio.umass.eduema...@microbio.umass.edu wrote:
I cannot seem to get the JSmol menu to open (14.0.4):

http://firstglance.jmol.org/fg.htm?mol=1d66use=html5http://firstglance.jmol.org/fg.htm?mol=1d66use=html5

For comparison, the menu opens just fine with the Java applet:

http://firstglance.jmol.org/fg.htm?mol=1d66http://firstglance.jmol.org/fg.htm?mol=1d66

I have the same problem with JSmol 14.0.13 in local testing.

Is JSmol too close to the edge of the window?

Any suggestions?

Eric



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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

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Re: [Jmol-users] JSmol menu doesn't open in FirstGlance

2014-04-14 Thread Robert Hanson
Right, sorry. Looked at the wrong line:

Jmol Version: 14.0.4 2014-01-05 16:16:
java.vendor: j2s
java.version: JSmol 13.3.9 11/23/2013 10:51:10 PM




On Mon, Apr 14, 2014 at 6:56 PM, Eric Martz ema...@microbio.umass.eduwrote:

 Hi, Bob,

 As stated below, I am already using 14.0.4 in the released version of
 FirstGlance 1.98 (firstglance.jmol.org, uncheck the Java checkbox and
 enter a PDB code).

 Also when I use 14.0.13 (running in Firefox from local files) I can't
 get the menu to open.

 Regards, Eric

 At 4/14/14, Robert Hanson wrote:
 Try upgrading to Jmol 14.0.
 
 
 On Sun, Apr 13, 2014 at 5:06 PM, Eric Martz
 mailto:ema...@microbio.umass.eduema...@microbio.umass.edu wrote:
 I cannot seem to get the JSmol menu to open (14.0.4):
 
 http://firstglance.jmol.org/fg.htm?mol=1d66use=html5
 http://firstglance.jmol.org/fg.htm?mol=1d66use=html5
 
 For comparison, the menu opens just fine with the Java applet:
 
 http://firstglance.jmol.org/fg.htm?mol=1d66
 http://firstglance.jmol.org/fg.htm?mol=1d66
 
 I have the same problem with JSmol 14.0.13 in local testing.
 
 Is JSmol too close to the edge of the window?
 
 Any suggestions?
 
 Eric
 
 
 

 --
 Put Bad Developers to Shame
 Dominate Development with Jenkins Continuous Integration
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 Larson-Anderson Professor of Chemistry
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 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
 

 --
 Learn Graph Databases - Download FREE O'Reilly Book
 Graph Databases is the definitive new guide to graph databases and their
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-- 
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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
--
Learn Graph Databases - Download FREE O'Reilly Book
Graph Databases is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
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Re: [Jmol-users] JSmol menu doesn't open in FirstGlance

2014-04-14 Thread Robert Hanson
Anyway, that's still quite old. We are up to 14.0.13.


On Mon, Apr 14, 2014 at 7:13 PM, Robert Hanson hans...@stolaf.edu wrote:

 Right, sorry. Looked at the wrong line:

 Jmol Version: 14.0.4 2014-01-05 16:16:
 java.vendor: j2s
 java.version: JSmol 13.3.9 11/23/2013 10:51:10 PM




 On Mon, Apr 14, 2014 at 6:56 PM, Eric Martz ema...@microbio.umass.eduwrote:

 Hi, Bob,

 As stated below, I am already using 14.0.4 in the released version of
 FirstGlance 1.98 (firstglance.jmol.org, uncheck the Java checkbox and
 enter a PDB code).

 Also when I use 14.0.13 (running in Firefox from local files) I can't
 get the menu to open.

 Regards, Eric

 At 4/14/14, Robert Hanson wrote:
 Try upgrading to Jmol 14.0.
 
 
 On Sun, Apr 13, 2014 at 5:06 PM, Eric Martz
 mailto:ema...@microbio.umass.eduema...@microbio.umass.edu wrote:
 I cannot seem to get the JSmol menu to open (14.0.4):
 
 http://firstglance.jmol.org/fg.htm?mol=1d66use=html5
 http://firstglance.jmol.org/fg.htm?mol=1d66use=html5
 
 For comparison, the menu opens just fine with the Java applet:
 
 http://firstglance.jmol.org/fg.htm?mol=1d66
 http://firstglance.jmol.org/fg.htm?mol=1d66
 
 I have the same problem with JSmol 14.0.13 in local testing.
 
 Is JSmol too close to the edge of the window?
 
 Any suggestions?
 
 Eric
 
 
 

 --
 Put Bad Developers to Shame
 Dominate Development with Jenkins Continuous Integration
 Continuously Automate Build, Test  Deployment
 Start a new project now. Try Jenkins in the cloud.
 http://p.sf.net/sfu/13600_Cloudbeeshttp://p.sf.net/sfu/13600_Cloudbees
 ___
 Jmol-users mailing list
 mailto:Jmol-users@lists.sourceforge.net
 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
 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
 

 --
 Learn Graph Databases - Download FREE O'Reilly Book
 Graph Databases is the definitive new guide to graph databases and
 their
 applications. Written by three acclaimed leaders in the field,
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 --
 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




-- 
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
--
Learn Graph Databases - Download FREE O'Reilly Book
Graph Databases is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
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Re: [Jmol-users] JSmol menu doesn't open in FirstGlance

2014-04-14 Thread Robert Hanson
Let's see what we can find here:


jmolApplet0._applet.viewer.global.disablePopupMenu
true

so something happened there. That flag is set in viewer:

  private Object getPopupMenu() {
if (jmolpopup == null) {
  jmolpopup = (allowScripting ? apiPlatform.getMenuPopup(menuStructure,
'j') : null);
  if (jmolpopup == null) {
g.disablePopupMenu = true;
return null;
  }
}
return jmolpopup.jpiGetMenuAsObject();
  }

 The way to debug this, Eric, is:

1) replace JSmol.min.js with js/JSmol.full.js
2) replace j2s/core/core.z.js with js/core.js

Then you can go in and debug it and it will look like something reasonable.
The error is being thrown in a method you will find in core.js:


Clazz_overrideMethod (c$, getMenuPopup,
function (menuStructure, type) {
var c = (type == 'j' ? awtjs2d.JmolJSPopup : awtjs2d.JSModelKitPopup);
var jmolpopup = J.api.Interface.getOption (c);
try {
if (jmolpopup != null) jmolpopup.jpiInitialize (this.vwr, menuStructure);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
c = Exception creating  + c + : + e;
System.out.println (c);
return null;
} else {
throw e;
}
}
return jmolpopup;
}, ~S,~S);



I'm pretty surprised it didn't print anything. Use

jmolApplet0._showInfo(true)

to see System.out.println -- the old Java console






On Mon, Apr 14, 2014 at 7:14 PM, Robert Hanson hans...@stolaf.edu wrote:

 Anyway, that's still quite old. We are up to 14.0.13.


 On Mon, Apr 14, 2014 at 7:13 PM, Robert Hanson hans...@stolaf.edu wrote:

 Right, sorry. Looked at the wrong line:

 Jmol Version: 14.0.4 2014-01-05 16:16:
 java.vendor: j2s
 java.version: JSmol 13.3.9 11/23/2013 10:51:10 PM




 On Mon, Apr 14, 2014 at 6:56 PM, Eric Martz ema...@microbio.umass.eduwrote:

 Hi, Bob,

 As stated below, I am already using 14.0.4 in the released version of
 FirstGlance 1.98 (firstglance.jmol.org, uncheck the Java checkbox and
 enter a PDB code).

 Also when I use 14.0.13 (running in Firefox from local files) I can't
 get the menu to open.

 Regards, Eric

 At 4/14/14, Robert Hanson wrote:
 Try upgrading to Jmol 14.0.
 
 
 On Sun, Apr 13, 2014 at 5:06 PM, Eric Martz
 mailto:ema...@microbio.umass.eduema...@microbio.umass.edu wrote:
 I cannot seem to get the JSmol menu to open (14.0.4):
 
 http://firstglance.jmol.org/fg.htm?mol=1d66use=html5
 http://firstglance.jmol.org/fg.htm?mol=1d66use=html5
 
 For comparison, the menu opens just fine with the Java applet:
 
 http://firstglance.jmol.org/fg.htm?mol=1d66
 http://firstglance.jmol.org/fg.htm?mol=1d66
 
 I have the same problem with JSmol 14.0.13 in local testing.
 
 Is JSmol too close to the edge of the window?
 
 Any suggestions?
 
 Eric
 
 
 

 --
 Put Bad Developers to Shame
 Dominate Development with Jenkins Continuous Integration
 Continuously Automate Build, Test  Deployment
 Start a new project now. Try Jenkins in the cloud.
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 http://p.sf.net/sfu/13600_Cloudbees
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 mailto:Jmol-users@lists.sourceforge.net
 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
 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
 

 --
 Learn Graph Databases - Download FREE O'Reilly Book
 Graph Databases is the definitive new guide to graph databases and
 their
 applications. Written by three acclaimed leaders in the field,
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 --
 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




 --
 Robert M. Hanson
 Larson-Anderson Professor of 

Re: [Jmol-users] JSmol menu doesn't open in FirstGlance

2014-04-14 Thread Robert Hanson
Eric, make sure you have both newer JSmol.min.js and j2s directory.


On Mon, Apr 14, 2014 at 7:30 PM, Robert Hanson hans...@stolaf.edu wrote:

 Let's see what we can find here:


 jmolApplet0._applet.viewer.global.disablePopupMenu
 true

 so something happened there. That flag is set in viewer:

   private Object getPopupMenu() {
 if (jmolpopup == null) {
   jmolpopup = (allowScripting ?
 apiPlatform.getMenuPopup(menuStructure, 'j') : null);
   if (jmolpopup == null) {
 g.disablePopupMenu = true;
 return null;
   }
 }
 return jmolpopup.jpiGetMenuAsObject();
   }

  The way to debug this, Eric, is:

 1) replace JSmol.min.js with js/JSmol.full.js
 2) replace j2s/core/core.z.js with js/core.js

 Then you can go in and debug it and it will look like something
 reasonable. The error is being thrown in a method you will find in core.js:


 Clazz_overrideMethod (c$, getMenuPopup,
 function (menuStructure, type) {
 var c = (type == 'j' ? awtjs2d.JmolJSPopup : awtjs2d.JSModelKitPopup);
 var jmolpopup = J.api.Interface.getOption (c);
 try {
 if (jmolpopup != null) jmolpopup.jpiInitialize (this.vwr, menuStructure);
 } catch (e) {
 if (Clazz_exceptionOf (e, Exception)) {
 c = Exception creating  + c + : + e;
 System.out.println (c);
 return null;
 } else {
 throw e;
 }
 }
 return jmolpopup;
 }, ~S,~S);



 I'm pretty surprised it didn't print anything. Use

 jmolApplet0._showInfo(true)

 to see System.out.println -- the old Java console






 On Mon, Apr 14, 2014 at 7:14 PM, Robert Hanson hans...@stolaf.edu wrote:

 Anyway, that's still quite old. We are up to 14.0.13.


 On Mon, Apr 14, 2014 at 7:13 PM, Robert Hanson hans...@stolaf.eduwrote:

 Right, sorry. Looked at the wrong line:

 Jmol Version: 14.0.4 2014-01-05 16:16:
 java.vendor: j2s
 java.version: JSmol 13.3.9 11/23/2013 10:51:10 PM




 On Mon, Apr 14, 2014 at 6:56 PM, Eric Martz 
 ema...@microbio.umass.eduwrote:

 Hi, Bob,

 As stated below, I am already using 14.0.4 in the released version of
 FirstGlance 1.98 (firstglance.jmol.org, uncheck the Java checkbox and
 enter a PDB code).

 Also when I use 14.0.13 (running in Firefox from local files) I can't
 get the menu to open.

 Regards, Eric

 At 4/14/14, Robert Hanson wrote:
 Try upgrading to Jmol 14.0.
 
 
 On Sun, Apr 13, 2014 at 5:06 PM, Eric Martz
 mailto:ema...@microbio.umass.eduema...@microbio.umass.edu wrote:
 I cannot seem to get the JSmol menu to open (14.0.4):
 
 http://firstglance.jmol.org/fg.htm?mol=1d66use=html5
 http://firstglance.jmol.org/fg.htm?mol=1d66use=html5
 
 For comparison, the menu opens just fine with the Java applet:
 
 http://firstglance.jmol.org/fg.htm?mol=1d66
 http://firstglance.jmol.org/fg.htm?mol=1d66
 
 I have the same problem with JSmol 14.0.13 in local testing.
 
 Is JSmol too close to the edge of the window?
 
 Any suggestions?
 
 Eric
 
 
 

 --
 Put Bad Developers to Shame
 Dominate Development with Jenkins Continuous Integration
 Continuously Automate Build, Test  Deployment
 Start a new project now. Try Jenkins in the cloud.
 http://p.sf.net/sfu/13600_Cloudbees
 http://p.sf.net/sfu/13600_Cloudbees
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 Jmol-users mailing list
 mailto:Jmol-users@lists.sourceforge.net
 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
 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
 

 --
 Learn Graph Databases - Download FREE O'Reilly Book
 Graph Databases is the definitive new guide to graph databases and
 their
 applications. Written by three acclaimed leaders in the field,
 this first edition is now available. Download your free book today!
 http://p.sf.net/sfu/NeoTech
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 https://lists.sourceforge.net/lists/listinfo/jmol-users



 --
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 applications. Written by three acclaimed leaders in the field,
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 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr


 If nature does not answer 

[Jmol-users] JSmol menu doesn't open in FirstGlance

2014-04-13 Thread Eric Martz
I cannot seem to get the JSmol menu to open (14.0.4):

http://firstglance.jmol.org/fg.htm?mol=1d66use=html5

For comparison, the menu opens just fine with the Java applet:

http://firstglance.jmol.org/fg.htm?mol=1d66

I have the same problem with JSmol 14.0.13 in local testing.

Is JSmol too close to the edge of the window?

Any suggestions?

Eric



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[Jmol-users] JSmol menu doesn't open

2014-01-07 Thread Eric Martz
I cannot seem to get the JSmol menu to open in 14.0.3 e.g.

http://firstglance.jmol.org/fg.htm?mol=1d66use=html5

Any suggestions?

Eric




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Re: [Jmol-users] JSmol menu doesn't open

2014-01-07 Thread Jaime Prilusky
Are you in any way disabling or capturing events from mouse right-click ?

Jaim

On Jan 7, 2014, at 5:56 PM, Eric Martz ema...@microbio.umass.edu wrote:

 I cannot seem to get the JSmol menu to open in 14.0.3 e.g.
 
 http://firstglance.jmol.org/fg.htm?mol=1d66use=html5
 
 Any suggestions?
 
 Eric
 
 
 
 
 --
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 organizations don't have a clear picture of how application performance 
 affects their revenue. With AppDynamics, you get 100% visibility into your 
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Re: [Jmol-users] JSmol menu doesn't open (+ request for benchmark times)

2014-01-07 Thread Rzepa, Henry S

On 7 Jan 2014, at 16:58, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote:

 Are you in any way disabling or capturing events from mouse right-click ?
 
 Jaim


14.0.3 JSmol,  I cannot get  the script command menu to produce a menu, eg 
http://www.ch.ic.ac.uk/local/organic/conf/

Might this be related?

PS I have done some simple graphical benchmarks  ( 
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Tablet:tablet#Tested_Devices ), 
testing the rotation of a simple rendered animated, anti-aliased model. 

The Java speed is  ~37 seconds (deriving from spin 10;  which would nominally 
take  36 seconds), whilst various tablet devices can take up to 350 seconds 
(2nd gen iPad Mini).  If there are any owners of tablets not on the current 
(small) list that can report back a benchmark,  I would be very grateful. 



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