from:"Jonathan Gutow"

Re: [Jmol-developers] Fwd: [sage-cell] Re: Encoding problems for jsmol context menu

2016-11-09 Thread Jonathan Gutow

Thanks. I have passed it on. I'll let you know it this helps.

Jonathan

On 11/9/16 12:54 PM, Robert Hanson wrote:
>
>
> On Wed, Nov 9, 2016 at 3:13 AM, Angel Herráez  > wrote:
>
> Hi Jonathan
>
> while https://sagecell.sagemath.org/embedded_sagecell.js
>  seems to be
> encoded as "windows-1252"
>
>
> that would do it.
>
>
>
>
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[Jmol-developers] Fwd: [sage-cell] Re: Encoding problems for jsmol context menu

2016-11-08 Thread Jonathan Gutow

Sorry forgot the link

http://netmath.vcrp.de/downloads/Systeme/Sage/SpatX.html

 Forwarded Message 
Subject:Fwd: [sage-cell] Re: Encoding problems for jsmol context menu
Date:   Tue, 8 Nov 2016 19:40:23 -0600
From:   Jonathan Gutow <gu...@uwosh.edu>
To: jmol-developers@lists.sourceforge.net

I've been asked about a problem with character encoding for JSmol
embedded in a page that is served from a different server. The language
encoding seems to work directly on the server, but not when embedded.
The whole intent of the "sage-cell server" is to be able to embed single
interactive symbolic mathematics cells into arbitrary pages; thus it
would be nice to find a way around this problem.

To see the problem set your preferred language to German (de) and go to
this page.
http://netmath.vcrp.de/downloads/Systeme/Sage/SpatX.html

Then click on the Auswerten button. Some calculations will happen and
then a plot in JSmol will appear below. Right-click to actuate the JSmol
menu. You will see that some of the characters are not rendered.

The fix for the problem was not obvious to me.

Any suggestions?

Thanks,
Jonathan

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[Jmol-developers] Do we really want "includemissinghydrogens" set to true by default when calling getproperty moleculeinfo?

2016-11-08 Thread Jonathan Gutow

The reason I ask this question is this setting appears to be why some 
files come up with too many hydrogens in the molecular formula delivered 
as part of moleculeinfo.

The issue is most evident with quantum output files where double bonds 
are not explicitly listed. It also shows up in pdb files where atom 
connectivity does not indicate double bonds. What happens is that extra 
hydrogens that are not in the molecule are added for aromatic carbons 
and other atoms that would formally have double bonds too them. The 
boolean includeMissingHydrogens is hard-coded to True in the call to 
getMolecularFormula made when the command getProperty moleculeinfo is 
issued.

I would argue this is not appropriate unless we know that all formal 
bonds are provided.

What do others think?

Jonathan

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 http://www.uwosh.edu/facstaff/gutow/


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[Jmol-developers] Fwd: [sage-cell] Re: Encoding problems for jsmol context menu

2016-11-08 Thread Jonathan Gutow

I've been asked about a problem with character encoding for JSmol 
embedded in a page that is served from a different server. The language 
encoding seems to work directly on the server, but not when embedded. 
The whole intent of the "sage-cell server" is to be able to embed single 
interactive symbolic mathematics cells into arbitrary pages; thus it 
would be nice to find a way around this problem.

To see the problem set your preferred language to German (de) and go to 
this page.


Then click on the Auswerten button. Some calculations will happen and 
then a plot in JSmol will appear below. Right-click to actuate the JSmol 
menu. You will see that some of the characters are not rendered.

The fix for the problem was not obvious to me.

Any suggestions?

Thanks,
Jonathan


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Re: [Jmol-developers] Escape.e function misidentifying P4 types as T3...

2015-12-31 Thread Jonathan Gutow

Good idea.  It will speed things up slightly.  I will do it.

Jonathan

On Wed, Dec 30, 2015 at 7:52 PM, Robert Hanson <hans...@stolaf.edu> wrote:

> Go ahead the change that Escape.e to Escape.eP4 anyway, and check that in
> if you want.
>
> On Wed, Dec 30, 2015 at 3:02 PM, Jonathan Gutow <gu...@uwosh.edu> wrote:
>
>> I can verify that the reordering fixed the problem.
>>
>> Jonathan
>>
>> On Wed, Dec 30, 2015 at 10:50 AM, Robert Hanson <hans...@stolaf.edu>
>> wrote:
>>
>>> I checked in a new Escape.java, which I guess fixes the problem. Do an
>>> update on that, Jonathan. I guess we could leave the SurfaceTool the way it
>>> is then.
>>>
>>> On Wed, Dec 30, 2015 at 10:46 AM, Robert Hanson <hans...@stolaf.edu>
>>> wrote:
>>>
>>>> In SurfaceTool.java, this:
>>>>
>>>>   cmd.append(" plane ").append(Escape.e(plane))
>>>>
>>>>
>>>> should read:
>>>>
>>>>   cmd.append(" plane ").append(Escape.eP4(plane))
>>>>
>>>> similar with:
>>>>
>>>> .append(Escape.e(slice.leftPlane));
>>>> .append(Escape.e(slice.rightPlane));
>>>>
>>>> and in Escape.java:
>>>>
>>>> if (x instanceof T3)
>>>>   return eP((T3) x);
>>>> if (x instanceof P4)
>>>>   return eP4((P4) x);
>>>>
>>>>
>>>> should read
>>>>
>>>> if (x instanceof P4)
>>>>   return eP4((P4) x);
>>>> if (x instanceof T3)
>>>>   return eP((T3) x);
>>>>
>>>>
>>>> On Tue, Dec 29, 2015 at 7:59 PM, Jonathan Gutow <gu...@uwosh.edu>
>>>> wrote:
>>>>
>>>>> It appears that at line 117 in Escape.java, type P4 objects are being
>>>>> misidentified as type T3.  This means that the value of the "w" subtype is
>>>>> not being returned as part of the returned text vector only "x", "y" and
>>>>> "z".  I noticed this because it breaks the surface tool which uses P4
>>>>> objects to define planes.
>>>>>
>>>>> It is not clear to me why this is happening.  Is P4 type a subtype of
>>>>> T3?
>>>>>
>>>>> Jonathan
>>>>>
>>>>> --
>>>>>Dr. Jonathan H. Gutow
>>>>> Chemistry Department gu...@uwosh.edu
>>>>> UW-OshkoshOffice:
>>>>> 920-424-1326
>>>>> 800 Algoma Boulevard FAX:920-424-2042
>>>>> Oshkosh, WI 54901
>>>>>http://www.uwosh.edu/facstaff/gutow/
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> ___
>>>>> Jmol-developers mailing list
>>>>> Jmol-developers@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Robert M. Hanson
>>>> Larson-Anderson Professor of Chemistry
>>>> Chair, Department 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
>>> Chair, Department 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
>>>
>>>
>>>
>>> --
>>>
>>> ___
>>> Jmol-developers ma

Re: [Jmol-developers] Escape.e function misidentifying P4 types as T3...

2015-12-30 Thread Jonathan Gutow

I wondered about that.  I figured you might know.  Thanks for dealing with
this.

Jonathan

On Wed, Dec 30, 2015 at 10:37 AM, Robert Hanson <hans...@stolaf.edu> wrote:

> It's an ordering issue. Yes, P4 subclasses T4, which subclasses T3. I'll
> fix it.
>
> On Tue, Dec 29, 2015 at 7:59 PM, Jonathan Gutow <gu...@uwosh.edu> wrote:
>
>> It appears that at line 117 in Escape.java, type P4 objects are being
>> misidentified as type T3.  This means that the value of the "w" subtype is
>> not being returned as part of the returned text vector only "x", "y" and
>> "z".  I noticed this because it breaks the surface tool which uses P4
>> objects to define planes.
>>
>> It is not clear to me why this is happening.  Is P4 type a subtype of T3?
>>
>> Jonathan
>>
>> --
>>Dr. Jonathan H. Gutow
>> Chemistry Department gu...@uwosh.edu
>> UW-OshkoshOffice:
>> 920-424-1326
>> 800 Algoma Boulevard FAX:920-424-2042
>> Oshkosh, WI 54901
>>http://www.uwosh.edu/facstaff/gutow/
>>
>>
>> --
>>
>> ___
>> Jmol-developers mailing list
>> Jmol-developers@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department 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
>
>
>
> --
>
> ___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>


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UW-Oshkosh
Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
   http://www.uwosh.edu/facstaff/gutow/
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Re: [Jmol-developers] Escape.e function misidentifying P4 types as T3...

2015-12-30 Thread Jonathan Gutow

I can verify that the reordering fixed the problem.

Jonathan

On Wed, Dec 30, 2015 at 10:50 AM, Robert Hanson <hans...@stolaf.edu> wrote:

> I checked in a new Escape.java, which I guess fixes the problem. Do an
> update on that, Jonathan. I guess we could leave the SurfaceTool the way it
> is then.
>
> On Wed, Dec 30, 2015 at 10:46 AM, Robert Hanson <hans...@stolaf.edu>
> wrote:
>
>> In SurfaceTool.java, this:
>>
>>   cmd.append(" plane ").append(Escape.e(plane))
>>
>>
>> should read:
>>
>>   cmd.append(" plane ").append(Escape.eP4(plane))
>>
>> similar with:
>>
>> .append(Escape.e(slice.leftPlane));
>> .append(Escape.e(slice.rightPlane));
>>
>> and in Escape.java:
>>
>> if (x instanceof T3)
>>   return eP((T3) x);
>> if (x instanceof P4)
>>   return eP4((P4) x);
>>
>>
>> should read
>>
>> if (x instanceof P4)
>>   return eP4((P4) x);
>> if (x instanceof T3)
>>   return eP((T3) x);
>>
>>
>> On Tue, Dec 29, 2015 at 7:59 PM, Jonathan Gutow <gu...@uwosh.edu> wrote:
>>
>>> It appears that at line 117 in Escape.java, type P4 objects are being
>>> misidentified as type T3.  This means that the value of the "w" subtype is
>>> not being returned as part of the returned text vector only "x", "y" and
>>> "z".  I noticed this because it breaks the surface tool which uses P4
>>> objects to define planes.
>>>
>>> It is not clear to me why this is happening.  Is P4 type a subtype of T3?
>>>
>>> Jonathan
>>>
>>> --
>>>Dr. Jonathan H. Gutow
>>> Chemistry Department gu...@uwosh.edu
>>> UW-OshkoshOffice:
>>> 920-424-1326
>>> 800 Algoma Boulevard FAX:920-424-2042
>>> Oshkosh, WI 54901
>>>http://www.uwosh.edu/facstaff/gutow/
>>>
>>>
>>> --
>>>
>>> ___
>>> Jmol-developers mailing list
>>> Jmol-developers@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Department 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
> Chair, Department 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
>
>
>
> --
>
> ___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>


-- 
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Chemistry Department gu...@uwosh.edu
UW-Oshkosh
Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
   http://www.uwosh.edu/facstaff/gutow/
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[Jmol-developers] Escape.e function misidentifying P4 types as T3...

2015-12-29 Thread Jonathan Gutow

It appears that at line 117 in Escape.java, type P4 objects are being
misidentified as type T3.  This means that the value of the "w" subtype is
not being returned as part of the returned text vector only "x", "y" and
"z".  I noticed this because it breaks the surface tool which uses P4
objects to define planes.

It is not clear to me why this is happening.  Is P4 type a subtype of T3?

Jonathan

-- 
   Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh
Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
   http://www.uwosh.edu/facstaff/gutow/
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Re: [Jmol-developers] update on Export To Web

2015-12-20 Thread Jonathan Gutow

Angel,

Go for it.  I wish I had time to work on this some more.  It also appears that 
the surface slicer now needs work (bit rot or a change in the syntax for 
definitions of a plane, I haven't investigated).  I will try to look at what 
ever you produce and may be able to give some advice on the widgets, but that 
is about all I can promise at the moment.

All, keep up the good work.

Jonathan
> On Dec 20, 2015, at 3:49 AM, Angel Herráez  wrote:
> 
> Dear developers, in particular Bob and Jonathan,
> 
> Over the last weeks I was teaching a course where whe learned to produce 
> webpages from Jmol Export to Web.
> As a consequence, I am starting some revision of the page code generated, 
> to be more HTML5-compliant and cleaner in terms of tags (e.g. less table 
> tags, more div's and css)
> I have managed to do a new setup of Eclipse in my computer and so I am 
> again able to locally test my builds of Jmol.
> 
> This message is a warning to avoid any clashes in case some of you may 
> think of changing the source meanwhile. I will discuss with you and commit 
> my changes once I'm satisfied with the result.
> 
> Jonathan, I've noticed that the widgets are not yet implemented in the 
> current 
> (JSmol) version. I am not sure if I will understand your approach and so may 
> or not change that part. Right now I am working just on the html source of 
> the templates.
> 
> Best,
> Angel
> 
> 
> 
> --
> ___
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 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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Re: [Jmol-developers] What is the second Canvas2d for that shows up below the active one when using JSmol?

2014-04-21 Thread Jonathan Gutow

On Mon, Apr 21, 2014 at 6:53 PM, Robert Hanson hans...@stolaf.edu wrote:

I'm sure that some simple element inspection will answer your question.
Send me that if you need to.

On Mon, Apr 21, 2014 at 5:39 PM, Gutow, Jonathan H gu...@uwosh.eduwrote:

At present it is on my development lap top. To test you would have to
set up the whole SAGE server. I will look for a way that it could be
launching twice.

thanks,
Jonathan
On Apr 21, 2014, at 11:38 AM, Robert Hanson hans...@stolaf.edu wrote:

Any chance you can provide a link to an offending page? What did you
learn from inspect element? Is it a duplicate? What is its outerHTML value?
Sounds to me like something is running twice.

On Mon, Apr 21, 2014 at 10:11 AM, Gutow, Jonathan H gu...@uwosh.edu
wrote:
It isn't actually in $(document).ready because the call is triggered by
a watch function that is looking for the div created by AJAX activity. If
the div contains a particular hidden div this is called.

Jonathan
On Apr 21, 2014, at 9:32 AM, Robert Hanson hans...@stolaf.edu wrote:

Looks perfect. And that's in $(document).ready ?

On Sun, Apr 20, 2014 at 9:42 PM, Jonathan Gutow gu...@uwosh.edu
wrote:
These applets are created on the fly on a page that is already in
existence using a call that looks like:

$('#'+jmolDivStr).html(Jmol.getAppletHtml(jmolApplet+appletID,jmolStatus.jmolInfo[appletID]));
*jmolDivStr contains the string name of the div the applet is being
inserted into. This div is created based on an AJAX interaction with the
SageMath server.
*jmolApplet is the string name of the applets
*appletID is the number assigned to the applet
*jmolStatus.jmolInfo[appletID] just points to the jmolInfo data
structure that has been constructed for this particular applet based on
information from the server.

I am using the coverImage feature of applet loading. I see the 2nd
canvas whether or not I defer applet loading.

Does that clarify the situation any? Any other ideas about what I
should look at?

Thanks,
Jonathan

On Sun, Apr 20, 2014 at 9:16 PM, Robert Hanson hans...@stolaf.edu
wrote:
Something's going wrong with your code, but I don't know from this.
Try using Firefox and Inspect Element to see what that object is. My
guess is that you are generating the canvas twice. Are you being sure to
NOT use Jmol.getApplet() within the page and instead are only creating the
applet within $(document).ready(function() {...}) ?

Bob

On Sun, Apr 20, 2014 at 8:48 PM, Jonathan Gutow gu...@uwosh.edu
wrote:
I'm having issues with the 2nd 2-D canvas that shows up below the
active JSmol blocking access to some of the active components on a web
page. Is this second canvas a place that backup drawing is done. It never
shows anything, but is collecting clicks and a popup menu can be activated
in it. It shows up outside of the boarder of the div within which JSmol is
active. In the DOM this second canvas is listed in the same div as JSmol
is active in.

Did I trigger something bad or am I misusing something?

Thanks,
Jonathan

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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

[Jmol-developers] What is the second Canvas2d for that shows up below the active one when using JSmol?

2014-04-20 Thread Jonathan Gutow

I'm having issues with the 2nd 2-D canvas that shows up below the active
JSmol blocking access to some of the active components on a web page.  Is
this second canvas a place that backup drawing is done.  It never shows
anything, but is collecting clicks and a popup menu can be activated in
it.  It shows up outside of the boarder of the div within which JSmol is
active.  In the DOM this second canvas is listed in the same div as JSmol
is active in.

Did I trigger something bad or am I misusing something?

Thanks,
Jonathan
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Re: [Jmol-developers] What is the second Canvas2d for that shows up below the active one when using JSmol?

2014-04-20 Thread Jonathan Gutow

These applets are created on the fly on a page that is already in existence
using a call that looks like:
 
$('#'+jmolDivStr).html(Jmol.getAppletHtml(jmolApplet+appletID,jmolStatus.jmolInfo[appletID]));
*jmolDivStr contains the string name of the div the applet is being
inserted into.  This div is created based on an AJAX interaction with the
SageMath server.
*jmolApplet is the string name of the applets
*appletID is the number assigned to the applet
*jmolStatus.jmolInfo[appletID] just points to the jmolInfo data structure
that has been constructed for this particular applet based on information
from the server.

I am using the coverImage feature of applet loading.  I see the 2nd canvas
whether or not I defer applet loading.

Does that clarify the situation any?  Any other ideas about what I should
look at?

Thanks,
Jonathan


On Sun, Apr 20, 2014 at 9:16 PM, Robert Hanson hans...@stolaf.edu wrote:

 Something's going wrong with your code, but I don't know from this. Try
 using Firefox and Inspect Element to see what that object is. My guess is
 that you are generating the canvas twice. Are you being sure to NOT use
 Jmol.getApplet() within the page and instead are only creating the applet
 within $(document).ready(function() {...}) ?

 Bob




 On Sun, Apr 20, 2014 at 8:48 PM, Jonathan Gutow gu...@uwosh.edu wrote:

 I'm having issues with the 2nd 2-D canvas that shows up below the active
 JSmol blocking access to some of the active components on a web page.  Is
 this second canvas a place that backup drawing is done.  It never shows
 anything, but is collecting clicks and a popup menu can be activated in
 it.  It shows up outside of the boarder of the div within which JSmol is
 active.  In the DOM this second canvas is listed in the same div as JSmol
 is active in.

 Did I trigger something bad or am I misusing something?

 Thanks,
 Jonathan


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 http://www.stolaf.edu/people/hansonr


 If nature does not answer first what we want,
 it is better to take what answer we get.

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Re: [Jmol-developers] Need advice on collision between jquery and JSmol...

2014-04-13 Thread Jonathan Gutow

Switching to the JSmol.min.nojq.js and putting after I load jquery seems to
have solved the menu and dialog collision problems.  Thank you Angel and
Bob.

Jonathan


On Sat, Apr 12, 2014 at 3:55 PM, Jonathan Gutow gu...@uwosh.edu wrote:

 Bob,

 Thanks.  That makes some sense.  I've actually been in the process of
 updating the Sage stuff to the latest jquery because it was misbehaving, so
 the version should be good.  I will swap to the nojq version of jsmol.

 I'll get back to you with my experience.

 Hypercube...cool.  Something I really wanted to play with but just haven't
 had time to think about.  I would actually like to develop an n-D
 visualization tool, where you can choose which coordinates to visualize
 against...I have thoughts but no time at the moment...

 Jonathan


 On Sat, Apr 12, 2014 at 2:00 PM, Robert Hanson hans...@stolaf.edu wrote:

 Jonathan, good to hear! (Hey, and tell them I am implementing 4D mesh
 rotation... think hypercube!)

 We have no problem on another project (MagresView), so I know it is
 possible.

 1) Make sure your jQuery version is 1.10+ for full MSIE support; 1.7
 should be fine otherwise.
 2) Use Jsmol.min.nojq.js
 3) load jQuery first, including jQuery.ui.menu.js, then the JSmol library.
 4) Make sure the SageMath jquery-ui-1.8.11.custom.css has been generated
 with a proper scope, and, I guess, that Sage is set up do handle that
 properly. See
 http://filamentgroup.com/lab/using_multiple_jquery_ui_themes_on_a_single_page/

 Bob





 On Sat, Apr 12, 2014 at 9:12 AM, Jonathan Gutow gu...@uwosh.edu wrote:

 I'm working with the SageMath package, which uses jquery and jquery-ui
 extensively for its web interface.  I am having trouble embedding JSmol in
 this because there is a collision.  If I load the JSmol js libraries first
 and the the jquery libraries all the SageMath functions work, but the JSmol
 right-click popup menu does not.  If I switch the load order I loose
 anything that uses dialogs in the SageMath interface and then the JSmol
 right-click menu works.

 I haven't been able to figure out which functions are colliding.  I
 think it has to do with the dialog feature, but have no other clues.

 Any suggestions?

 Thanks,
 Jonathan


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[Jmol-developers] Need advice on collision between jquery and JSmol...

2014-04-12 Thread Jonathan Gutow

I'm working with the SageMath package, which uses jquery and jquery-ui
extensively for its web interface.  I am having trouble embedding JSmol in
this because there is a collision.  If I load the JSmol js libraries first
and the the jquery libraries all the SageMath functions work, but the JSmol
right-click popup menu does not.  If I switch the load order I loose
anything that uses dialogs in the SageMath interface and then the JSmol
right-click menu works.

I haven't been able to figure out which functions are colliding.  I think
it has to do with the dialog feature, but have no other clues.

Any suggestions?

Thanks,
Jonathan
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Re: [Jmol-developers] Need advice on collision between jquery and JSmol...

2014-04-12 Thread Jonathan Gutow

I am trying to use the standard jsmol.min.js.  Should I be trying the other?

Jonathan


On Sat, Apr 12, 2014 at 11:45 AM, Herráez Sánchez Ángel 
angel.herr...@uah.es wrote:

  Hi Jonathan


  My knowledge is that the popup menu uses functions copied from jQuery
 UI, but they are embedded into JSmol rather than calling the UI library.
 That might be the origin of the collision. Also the CSS style of the popup
 sometimes get contaminated --something I had on my wishlist.

 I am recently having some trouble with the popup menu, in a page that uses
 jQuery and the jQuery UI accordion: the popup opens but immediately
 closes. Only by some combination of dragging and left clicking I manage to
 keep it open for a while until I can choose a menu entry. Hard to describe.
 It does not happen all the time. I intended to try and isolate the problem
 later on.


  Are you using jsmol-nojq.min.js ?





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Re: [Jmol-developers] Need advice on collision between jquery and JSmol...

2014-04-12 Thread Jonathan Gutow

Bob,

Thanks.  That makes some sense.  I've actually been in the process of
updating the Sage stuff to the latest jquery because it was misbehaving, so
the version should be good.  I will swap to the nojq version of jsmol.

I'll get back to you with my experience.

Hypercube...cool.  Something I really wanted to play with but just haven't
had time to think about.  I would actually like to develop an n-D
visualization tool, where you can choose which coordinates to visualize
against...I have thoughts but no time at the moment...

Jonathan


On Sat, Apr 12, 2014 at 2:00 PM, Robert Hanson hans...@stolaf.edu wrote:

 Jonathan, good to hear! (Hey, and tell them I am implementing 4D mesh
 rotation... think hypercube!)

 We have no problem on another project (MagresView), so I know it is
 possible.

 1) Make sure your jQuery version is 1.10+ for full MSIE support; 1.7
 should be fine otherwise.
 2) Use Jsmol.min.nojq.js
 3) load jQuery first, including jQuery.ui.menu.js, then the JSmol library.
 4) Make sure the SageMath jquery-ui-1.8.11.custom.css has been generated
 with a proper scope, and, I guess, that Sage is set up do handle that
 properly. See
 http://filamentgroup.com/lab/using_multiple_jquery_ui_themes_on_a_single_page/

 Bob





 On Sat, Apr 12, 2014 at 9:12 AM, Jonathan Gutow gu...@uwosh.edu wrote:

 I'm working with the SageMath package, which uses jquery and jquery-ui
 extensively for its web interface.  I am having trouble embedding JSmol in
 this because there is a collision.  If I load the JSmol js libraries first
 and the the jquery libraries all the SageMath functions work, but the JSmol
 right-click popup menu does not.  If I switch the load order I loose
 anything that uses dialogs in the SageMath interface and then the JSmol
 right-click menu works.

 I haven't been able to figure out which functions are colliding.  I think
 it has to do with the dialog feature, but have no other clues.

 Any suggestions?

 Thanks,
 Jonathan


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Re: [Jmol-developers] proposal of a new logo-banner-icon for Jmol + JSmol

2013-05-12 Thread Jonathan Gutow

I like the logos.  Let us know when all the icons are accessible for viewing.

Jonathan
On May 11, 2013, at 2:20 PM, Angel Herráez wrote:

 Dear developers,
 
 Today I fancied some new logos and icons for Jmol and JSmol. 
 I cannot acess my server now, but will upload soon a full set (png, svg, ico, 
 icns, favicon) to one of my webpages so users may download them if they 
 like.
 Meanwhile, I have uploaded a combined J(S)mol logo-banner to the wiki,
 http://wiki.jmol.org/index.php/File:J%28S%29mol_logos13.png
 (also attached here)
 
 I suggest replacing the old Jmol logo in the top-left corner of the wiki with 
 this. Nico, if there's consensus, could you do that replacement? I understand 
 it is a wiki admin operation.
 
 Then I will remove the old icon from the home page and update other wiki 
 pages with the new icons --or links to them. 
 And hopefully I will start some updates aimed for the Jmol.org website to 
 include this and news about JSmol.
 
 Cheers,
 Angel
 
 
 
 
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Re: [Jmol-developers] Problems with new repository build

2013-03-16 Thread Jonathan Gutow

René,

Did Bob's suggestion work for you?  
I had no trouble compiling on my systems, although I seem to have lost the file 
JmolDevelopersGuide.html.  So I agree with Bob that there is no problem with 
the repository.

Jonathan
On Mar 15, 2013, at 12:12 PM, Robert Hanson wrote:

 You need to use Java 7 now.
 
 
 On Fri, Mar 15, 2013 at 5:25 AM, Kanters, Rene rkant...@richmond.edu wrote:
 Hi,
 
 I just moved over to the new repository and after completely cleaning out my 
 old Jmol stuff, Eclipse now can not build the project. I have 100 error and 
 most seem to be related to not being able to resolve things in
 
 org/openscience/jmol/app/surfacetool/SurfaceToolGUI.java (angleUnitsList)
 org/openscience/jmol/app/jmolpanel/GaussianDialog.java (basisBox) 
 RecentFilesDialog.java (fileList) PovrayDialog.java (imageSizeRatioCombo, 
 mosaicPreviewComboEnd, outputFormatCombo)
 org/jmol/export/dialog/Dialog.java (cb)
 org/openscience/jmol/app/webexport/WebPanel.java (instanceList)
 
 I am not sure how to resolve this and get Jmol to compile properly again. Any 
 help is greatly appreciated.
 
 Cheers,
 René
 
 
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Re: [Jmol-developers] Either I misunderstand or JmolData.jar has a problem...

2013-01-26 Thread Jonathan Gutow

I got the same problem with 13.0.12 and I think it may relate specifically to 
loading files that are not .pdb.gz.  I got it to work using a PNGJ scene made 
with 1lcd.pdb, but not one made with a .pmesh file.  I also got some oddities 
with a .xyz file, but haven't reproduced that.  I may have messed up that file..

I will try it with the development version as well.

Jonathan
On Jan 26, 2013, at 1:40 AM, Robert Hanson wrote:

 or maybe even 13.0.12 --- you are several versions back using 13.0.9 (Nov, 
 2012)
 
 
 On Sat, Jan 26, 2013 at 9:35 AM, Robert Hanson hans...@stolaf.edu wrote:
 Can you try that with Jmol 13.1.12 and tell me if that is still a problem? 
 I'm not seeing it:
 
 jmoldata -s plwilliamson.png
 
 JmolData using command options [-s, plwilliamson.png]
 Add -n (NOGRAPHICS) for faster performance if you are not creating images.
 (C) 2012 Jmol Development
 Jmol Version: 13.1.12  2013-01-23 14:58
 java.vendor: Oracle Corporation
 java.version: 1.7.0_10
 os.name: Windows 8
 Access: ALL
 memory: 12.1/95.0
 processors available: 4
 useCommandThread: false
 Executing script from file: plwilliamson.png
 FileManager opening C:\jmol-dev\bobtest\plwilliamson.png
 FileManager opening C:\jmol-dev\bobtest\plwilliamson.png|JmolManifest.txt
 FileManager opening C:\jmol-dev\bobtest\plwilliamson.png
 FileManager opening C:\jmol-dev\bobtest\plwilliamson.png|state.spt
 FileManager opening C:\jmol-dev\bobtest\plwilliamson.png
 
 FileManager.getAtomSetCollectionFromFile(C:/jmol-dev/bobtest/plwilliamson.png|2a
 gv.pdb.gz)
 FileManager opening C:\jmol-dev\bobtest\plwilliamson.png|2agv.pdb.gz
 FileManager opening C:\jmol-dev\bobtest\plwilliamson.png
 The Resolver thinks Pdb
 
 
 Bob
 
 
 -- 
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 St. Olaf College
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 If nature does not answer first what we want,
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 St. Olaf College
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 it is better to take what answer we get. 
 
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Re: [Jmol-developers] use of the OBJECT tag in IE9

2012-06-03 Thread Jonathan Gutow

All works fine with MacOS and Google Chrome (pretty much same as Safari, they 
use the same rendering engine.)

Jonathan
On Jun 3, 2012, at 1:16 PM, Robert Hanson wrote:

 Not studying Macs with this, but it's worth checking anyway. 
 
 Anyone who has a Mac/Safari or Windows/MSIE, please test:
 
 http://chemapps.stolaf.edu/jmol/chemdoodle/sno.htm
 http://chemapps.stolaf.edu/jmol/chemdoodle/sno2.htm
 http://chemapps.stolaf.edu/jmol/chemdoodle/sok.htm
 http://chemapps.stolaf.edu/jmol/chemdoodle/sok2.htm
 http://chemapps.stolaf.edu/jmol/chemdoodle/sok3.htm
 http://chemapps.stolaf.edu/jmol/chemdoodle/sok4.htm
 
 In principle, all of these should show a spinning protein.
 
 I need advise from someone with CSS experience -- what am I doing wrong 
 between sno2.htm and sok4.htm? The only difference there is putting the 
 applet in a table (sno2.htm) or not (sok4.htm). My experience is that MSIE is 
 always right - just very particular. I'm missing something subtle.  
 
 Bob
 
 
 On Sat, Jun 2, 2012 at 11:21 PM, Jaime Prilusky 
 jaime.prilu...@weizmann.ac.il wrote:
 Bob,
 
 Safari 5.1.7 on Mac 10.7.4 shows the empty white square and stays there. 
 No mouse movements nor clicks are enough to elicit any behavior. 
 
 
 
 FireFox 12.0 and Chrome 19.0... on Mac load the applet immediately.
 
 Jaim
 
 
 On Jun 3, 2012, at 4:34 AM, Robert Hanson wrote:
 
 I use MSIE 9, and I haven't had any problem like that. So I think it's OK. 
 But I am having one odd behavior -- our current set up for JmolCore is 
 making it so that you have to move the mouse over the Jmol applet before 
 Java loads. Strangest thing I've ever seen. I'm trying to track it down.
 
 Q: If you use MSIE 9 (or any other version of MSIE), could you please go to
 
   http://chemapps.stolaf.edu/jmol/chemdoodle/sno2.htm
 
 and tell me if you  see the applet right away (just a black box) or only 
 after you move the mouse over it?
 
 Can you see what's wrong with my code and help me fix it?
 
 Thanks,
 
 Bob
 
 
 On Sat, Jun 2, 2012 at 12:02 PM, Angel Herráez angel.herr...@uah.es wrote:
 Version 9 of MSIE may use the OBJECT tag common to other browsers,
 rather than the class-id based tag characteristic of MSIE6+
 
 Rich Apodaca reports [1] about problems running applets in IE9 with some
 versions of Java, so  I am testing Jmol.js to switch to the HTML-type object
 tag for IE9.
 
 I see that the new JmolCore.js uses the same methods for inserting applets,
 so it will need the same fix-improvement.
 
 If there is no objection I will go for it. (Still have to set-up my SVN 
 commit
 software, new computer, but hopefully will be able to do it this weekend)
 
 [1]
 http://metamolecular.com/blog/2012/05/29/ie9-error-when-pasting-from-che
 mdraw-to-chemwriter-and-a-fix/
 
 
 
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Re: [Jmol-developers] use of the OBJECT tag in IE9

2012-06-03 Thread Jonathan Gutow

OK, I agree...although my experience is things usually work in Safari, Chrome, 
Opera, usually FF, but not MSIE.

So other MacOS tests:
Safari: all work
FF: all work

Linux test with Chrome (nothing else installed at the moment):  all work

Jonathan
On Jun 3, 2012, at 5:25 PM, Robert Hanson wrote:

 no such thing as pretty much in this game! :)
 
 On Sun, Jun 3, 2012 at 5:21 PM, Jonathan Gutow gu...@uwosh.edu wrote:
 All works fine with MacOS and Google Chrome (pretty much same as Safari, they 
 use the same rendering engine.)
 
 Jonathan
 

 Dr. Jonathan H. Gutow
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800 Algoma BoulevardFAX:920-424-2042
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[Jmol-developers] Headless images with JmolData.jar still has problems...

2012-03-29 Thread Jonathan Gutow

I have to see if something happened to my server, but suddenly I am getting 
JmolData.jar looking for a GUI.  This is the error I get:

-
No protocol specified
Exception in thread main java.lang.InternalError: Can't connect to X11
window server using ':0.0' as the value of the DISPLAY variable.
at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method)
at
sun.awt.X11GraphicsEnvironment.access$200(X11GraphicsEnvironment.java:62\
)
at
sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:178)
at java.security.AccessController.doPrivileged(Native Method)
at
sun.awt.X11GraphicsEnvironment.clinit(X11GraphicsEnvironment.jav\
a:142)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:186)
at
java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnviron\
ment.java:82)
at java.awt.image.BufferedImage.createGraphics(BufferedImage.java:1152)
at java.awt.image.BufferedImage.getGraphics(BufferedImage.java:1142)
at org.jmol.awt.Image.getGraphics(Unknown Source)
at org.jmol.awt.Platform.getGraphics(Unknown Source)
at org.jmol.g3d.Platform3D.createInstance(Unknown Source)
at org.jmol.g3d.Graphics3D.init(Graphics3D.java:265)
at org.jmol.viewer.Viewer.init(Viewer.java:290)
at org.jmol.viewer.Viewer.allocateViewer(Viewer.java:384)
at org.jmol.api.JmolViewer.allocateViewer(Unknown Source)
at org.openscience.jmol.app.JmolData.init(JmolData.java:59)
at org.openscience.jmol.app.JmolData.main(JmolData.java:77)

-
This is very strange as the server session this is running in has been running 
as a detached screen session for a couple of days without this problem 
appearing.  It may be possible the screen session was still able to access the 
GUI of the user account the screen session was started in.  I will look into 
that.  If that is the case, we still haven't traced every instance of GUI use 
in JmolData.jar.

Jonathan
 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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Re: [Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?

2012-03-21 Thread Jonathan Gutow

I was able to successfully embed it in the SAGE web server.  Now for lots of 
code cleanup...

Jonathan
On Mar 20, 2012, at 7:43 PM, Robert Hanson wrote:

 OK, so I definitely learned something! 
 
 On Tue, Mar 20, 2012 at 5:48 PM, Jonathan Gutow gu...@uwosh.edu wrote:
 Bob,
 
 You did it!  My preliminary tests show it works.  I have to do some 
 modifications to get it embedded in Sage, but I think it will work fine.
 
 Thanks,
 Jonathan
 
 On Mar 19, 2012, at 9:53 PM, Robert Hanson wrote:
 
 OK, Jonathan. I think I found the problem. Please try what I just checked in 
 -- do a build, and then use jmolData.jar instead of jmol.jar.  
 
 Formerly:
 
 JmolData.jar  -s foo.spt

execute the script foo.spt with absolutely no graphics and no rendering, 
 including no image creation
 
 now:
 
 JmolData.jar -s foo.spt
 
execute the script foo.spt still with rending for image creation, just 
 not for screen display
 
 Jmoldata.jar -n -s foo.spt
 
   as before, now for performance enhancement, no graphics of any kind.
 
 Let's see how that works. 
 
 Bob
 
 
 On Mon, Mar 19, 2012 at 8:30 PM, Robert Hanson hans...@stolaf.edu wrote:
 If awt is not there, you are out of luck. But with the -n flag there is no 
 creation of Display. But there might be a reference to it. Let me see. Based 
 on this discussion: 
 http://java.sun.com/developer/technicalArticles/J2SE/Desktop/headless/  we 
 should be able to do it. 
 
 Bob
 
 
 On Mon, Mar 19, 2012 at 6:06 PM, Jonathan Gutow gu...@uwosh.edu wrote:
 Bob,
 
 Thanks for trying...Your changes definitely reduce the error messages, but 
 the application is still looking for screen dimensions somewhere in the tree 
 after entering JmolPanel.  It is making a call to the awt package. I'm 
 suspicious this is all associated with the allocation of a Display near line 
 242 in JmolPanel.
 
 I've got a solution for Sage, but we should keep picking at this as more 
 people would be able to use Jmol as a server side image generator.  Some 
 people really don't like running a GUI on their servers.
 
 Jonathan
 On Mar 19, 2012, at 3:51 PM, Robert Hanson wrote:
 
 Could be I'm wrong.Try what I just checked in. Be sure to use the 
 
 -ions t.spt
 
 option (silent/no console/no graphics)
 
 You  won't get THAT error. but will it create an image? I used this script:
 
 load $tylenol
 write image 300 300 t.png
 
 
 Bob
 
 
 On Mon, Mar 19, 2012 at 7:55 AM, Gutow, Jonathan H gu...@uwosh.edu wrote:
 I dug a little and agree it would be a significant undertaking to make the 
 image generation work without the GUI.  That said, we might want to put 
 that on a long term to-do list.
 
  
 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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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 Chemistry Departmentgu...@uwosh.edu
 UW-Oshkosh  Office: 920-424-1326
 800 Algoma BoulevardFAX:920-424-2042
 Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow
 
 
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 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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-developers] Do we need to initialize the graphics environment when Jmol is running headless?

2012-03-20 Thread Jonathan Gutow

Bob,

You did it!  My preliminary tests show it works.  I have to do some 
modifications to get it embedded in Sage, but I think it will work fine.

Thanks,
Jonathan
On Mar 19, 2012, at 9:53 PM, Robert Hanson wrote:

 OK, Jonathan. I think I found the problem. Please try what I just checked in 
 -- do a build, and then use jmolData.jar instead of jmol.jar.  
 
 Formerly:
 
 JmolData.jar  -s foo.spt

execute the script foo.spt with absolutely no graphics and no rendering, 
 including no image creation
 
 now:
 
 JmolData.jar -s foo.spt
 
execute the script foo.spt still with rending for image creation, just not 
 for screen display
 
 Jmoldata.jar -n -s foo.spt
 
   as before, now for performance enhancement, no graphics of any kind.
 
 Let's see how that works. 
 
 Bob
 
 
 On Mon, Mar 19, 2012 at 8:30 PM, Robert Hanson hans...@stolaf.edu wrote:
 If awt is not there, you are out of luck. But with the -n flag there is no 
 creation of Display. But there might be a reference to it. Let me see. Based 
 on this discussion: 
 http://java.sun.com/developer/technicalArticles/J2SE/Desktop/headless/  we 
 should be able to do it. 
 
 Bob
 
 
 On Mon, Mar 19, 2012 at 6:06 PM, Jonathan Gutow gu...@uwosh.edu wrote:
 Bob,
 
 Thanks for trying...Your changes definitely reduce the error messages, but 
 the application is still looking for screen dimensions somewhere in the tree 
 after entering JmolPanel.  It is making a call to the awt package. I'm 
 suspicious this is all associated with the allocation of a Display near line 
 242 in JmolPanel.
 
 I've got a solution for Sage, but we should keep picking at this as more 
 people would be able to use Jmol as a server side image generator.  Some 
 people really don't like running a GUI on their servers.
 
 Jonathan
 On Mar 19, 2012, at 3:51 PM, Robert Hanson wrote:
 
 Could be I'm wrong.Try what I just checked in. Be sure to use the 
 
 -ions t.spt
 
 option (silent/no console/no graphics)
 
 You  won't get THAT error. but will it create an image? I used this script:
 
 load $tylenol
 write image 300 300 t.png
 
 
 Bob
 
 
 On Mon, Mar 19, 2012 at 7:55 AM, Gutow, Jonathan H gu...@uwosh.edu wrote:
 I dug a little and agree it would be a significant undertaking to make the 
 image generation work without the GUI.  That said, we might want to put that 
 on a long term to-do list.
 
  
 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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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 https://lists.sourceforge.net/lists/listinfo/jmol-developers
 
 
  Dr. Jonathan H. Gutow
 Chemistry Departmentgu...@uwosh.edu
 UW-Oshkosh  Office: 920-424-1326
 800 Algoma BoulevardFAX:920-424-2042
 Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow
 
 
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 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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
 --
 This SF email is sponsosred by:
 Try Windows Azure free for 90 days Click Here 
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 https://lists.sourceforge.net/lists/listinfo/jmol-developers

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh

Re: [Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?

2012-03-19 Thread Jonathan Gutow

Bob,

Thanks for trying...Your changes definitely reduce the error messages, but the 
application is still looking for screen dimensions somewhere in the tree after 
entering JmolPanel.  It is making a call to the awt package. I'm suspicious 
this is all associated with the allocation of a Display near line 242 in 
JmolPanel.

I've got a solution for Sage, but we should keep picking at this as more people 
would be able to use Jmol as a server side image generator.  Some people really 
don't like running a GUI on their servers.

Jonathan
On Mar 19, 2012, at 3:51 PM, Robert Hanson wrote:

 Could be I'm wrong.Try what I just checked in. Be sure to use the 
 
 -ions t.spt
 
 option (silent/no console/no graphics)
 
 You  won't get THAT error. but will it create an image? I used this script:
 
 load $tylenol
 write image 300 300 t.png
 
 
 Bob
 
 
 On Mon, Mar 19, 2012 at 7:55 AM, Gutow, Jonathan H gu...@uwosh.edu wrote:
 I dug a little and agree it would be a significant undertaking to make the 
 image generation work without the GUI.  That said, we might want to put that 
 on a long term to-do list.
 
  
 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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
 --
 This SF email is sponsosred by:
 Try Windows Azure free for 90 days Click Here 
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 https://lists.sourceforge.net/lists/listinfo/jmol-developers

 Dr. Jonathan H. Gutow
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UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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[Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?

2012-03-17 Thread Jonathan Gutow

I've been working on using 12.0.45 as a server-side static graphics engine for 
the SageMath group.  I've run into the following problem.  The server does not 
run in an X-session, so there is no graphics environment.  This causes an error 
when Jmol is run as Jmol.jar -ionx.  The error seems to imply that we are still 
initializing the look-and-feel, even when there is no GUI.  Is there any reason 
we can't switch this off?  Here's the error:

Exception in thread main java.lang.NoClassDefFoundError: Could not
initialize class sun.awt.X11GraphicsEnvironment
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:186)
at
java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnviron\
ment.java:82)
at sun.awt.X11.XToolkit.clinit(XToolkit.java:112)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:186)
at java.awt.Toolkit$2.run(Toolkit.java:849)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:841)
at
sun.swing.SwingUtilities2$AATextInfo.getAATextInfo(SwingUtilities2.java:\
121)
at
javax.swing.plaf.metal.MetalLookAndFeel.initComponentDefaults(MetalLookA\
ndFeel.java:1564)
at
javax.swing.plaf.basic.BasicLookAndFeel.getDefaults(BasicLookAndFeel.jav\
a:147)
at
javax.swing.plaf.metal.MetalLookAndFeel.getDefaults(MetalLookAndFeel.jav\
a:1599)
at javax.swing.UIManager.setLookAndFeel(UIManager.java:530)
at javax.swing.UIManager.setLookAndFeel(UIManager.java:570)
at javax.swing.UIManager.initializeDefaultLAF(UIManager.java:1320)
at javax.swing.UIManager.initialize(UIManager.java:1407)
at javax.swing.UIManager.maybeInitialize(UIManager.java:1395)
at javax.swing.UIManager.getDefaults(UIManager.java:644)
at javax.swing.UIManager.put(UIManager.java:973)
at org.jmol.export.dialog.Dialog.setupUIManager(Unknown Source)
at org.openscience.jmol.app.jmolpanel.JmolPanel.startJmol(Unknown
Source)
at org.openscience.jmol.app.Jmol.main(Unknown Source)


 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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Re: [Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?

2012-03-17 Thread Jonathan Gutow

Is this because of the try{...} at line 513 of JmolPanel.java?  Shouldn't this 
be inside the preceding if..., which checks to see if the display and splash 
are enabled?

Jonathan
On Mar 17, 2012, at 8:38 AM, Jonathan Gutow wrote:

 I've been working on using 12.0.45 as a server-side static graphics engine 
 for the SageMath group.  I've run into the following problem.  The server 
 does not run in an X-session, so there is no graphics environment.  This 
 causes an error when Jmol is run as Jmol.jar -ionx.  The error seems to imply 
 that we are still initializing the look-and-feel, even when there is no GUI.  
 Is there any reason we can't switch this off?  Here's the error:
 
 Exception in thread main java.lang.NoClassDefFoundError: Could not
 initialize class sun.awt.X11GraphicsEnvironment
   at java.lang.Class.forName0(Native Method)
   at java.lang.Class.forName(Class.java:186)
   at
 java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnviron\
 ment.java:82)
   at sun.awt.X11.XToolkit.clinit(XToolkit.java:112)
   at java.lang.Class.forName0(Native Method)
   at java.lang.Class.forName(Class.java:186)
   at java.awt.Toolkit$2.run(Toolkit.java:849)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:841)
   at
 sun.swing.SwingUtilities2$AATextInfo.getAATextInfo(SwingUtilities2.java:\
 121)
   at
 javax.swing.plaf.metal.MetalLookAndFeel.initComponentDefaults(MetalLookA\
 ndFeel.java:1564)
   at
 javax.swing.plaf.basic.BasicLookAndFeel.getDefaults(BasicLookAndFeel.jav\
 a:147)
   at
 javax.swing.plaf.metal.MetalLookAndFeel.getDefaults(MetalLookAndFeel.jav\
 a:1599)
   at javax.swing.UIManager.setLookAndFeel(UIManager.java:530)
   at javax.swing.UIManager.setLookAndFeel(UIManager.java:570)
   at javax.swing.UIManager.initializeDefaultLAF(UIManager.java:1320)
   at javax.swing.UIManager.initialize(UIManager.java:1407)
   at javax.swing.UIManager.maybeInitialize(UIManager.java:1395)
   at javax.swing.UIManager.getDefaults(UIManager.java:644)
   at javax.swing.UIManager.put(UIManager.java:973)
   at org.jmol.export.dialog.Dialog.setupUIManager(Unknown Source)
   at org.openscience.jmol.app.jmolpanel.JmolPanel.startJmol(Unknown
 Source)
   at org.openscience.jmol.app.Jmol.main(Unknown Source)
 
 
 Dr. Jonathan H. Gutow
 Chemistry Departmentgu...@uwosh.edu
 UW-Oshkosh  Office: 920-424-1326
 800 Algoma BoulevardFAX:920-424-2042
 Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow
 
 
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Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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[Jmol-developers] Is there a reason the ticks on the boundbox are placed along the edges they are?

2012-03-05 Thread Jonathan Gutow

I was wondering if we have a good reason for placing the boundbox ticks along 
the edges we do.  This is not the usual placement for ticks in a righthand 
coordinate system.  Our Z-ticks are in the normal position (edge in quadrants 
with X  Y negative), but the X  Y ticks are not in the normal positions.  
Normal would be X-ticks along the edge in the quadrants with Z  Y negative and 
Y-ticks along the edge in the quadrants with Z negative and X positive.

If nobody has a reason not to I suggest we change to this more standard 
placement or alternatively have the option of using the more normal placement.

Jonathan
 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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Re: [Jmol-developers] Problems in calling Jmol

2011-12-04 Thread Jonathan Gutow

I don't use the jmol.sh script  very often, but one possibility is that the 
memory defaults in it are too small for the virtual machine he is using.  
Another guess is that he is using the IceTea JVM and not the Sun/Oracle JVM.  
IceTea is getting better, but I've still had occasional problems with it.

Jonathan
On Dec 4, 2011, at 12:02 PM, Robert Hanson wrote:

 Hellow, Linux experts? What can you suggest for Moon?
 
 On Sun, Dec 4, 2011 at 12:44 AM, Moon Cheung moon...@gmail.com wrote:
 It has the same problem in running Jmol.sh from the command line.This time 
 Jmol will stop at Creating main window.
 And once the problem occurs, it will occur continuously after i kill the 
 process.
 
 Best Regards
 Moon
 
 
 2011/12/4 Robert Hanson hans...@stolaf.edu
 Does Jmol.sh run generally on your machine from the command line?
 
 On Sat, Dec 3, 2011 at 6:25 AM, Moon Cheung moon...@gmail.com wrote:
 Hi,
 
 When i use system call in c to call Jmol under Linux(the code is 
 (void)system(/opt/QtSDK/Projects/jmol-12.2.7/jmol.sh -s 
 /opt/QtSDK/Projects/testing3.pdb.spt))
 And testing3.pdb.spt is a Rasmol Script in the code.
 There is a problem that the Jmol will stop running at Setting up drag and 
 drop.
 This situation will occur 1 around 5 times.
 What can i do with this situation?
 
 Best Regards,
 Moon
 
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 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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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 data and makes sense of it. IT sense. And common sense.
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 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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-developers] high priority problem

2011-11-02 Thread Jonathan Gutow

I would not be surprised by this as we are using a very old vecmath the last 
time I checked.

Jonathan
On Nov 2, 2011, at 7:28 AM, Egon Willighagen wrote:

 On Wed, Nov 2, 2011 at 1:28 PM, Egon Willighagen
 egon.willigha...@gmail.com wrote:
 On Wed, Nov 2, 2011 at 1:07 PM, Robert Hanson hans...@stolaf.edu wrote:
 We have two independent reports of javax.Point3i problems when Jmol Jar
 files are compiled on a PC and run on a mac. It seems somehow the Poin3i(int
 x, int y, int z) initializer is missing.
 
 It sounds to me that vecmatch is missing from the Jmol jar...
 
 Or that the Mac has another vecmath on the classpath by default, with
 a slightly different API, and earlier on the classpath...
 
 Egon
 
 -- 
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 Postdoctoral Researcher
 Institutet för miljömedicin
 Karolinska Institutet (http://ki.se/imm)
 Homepage: http://egonw.github.com/
 LinkedIn: http://se.linkedin.com/in/egonw
 Blog: http://chem-bla-ics.blogspot.com/
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Re: [Jmol-developers] Mac test

2011-11-02 Thread Jonathan Gutow

Working for me too on MacOS in Chrome.  I think you've got it.

Jonathan
On Nov 2, 2011, at 9:54 AM, Robert Hanson wrote:

 Once more, please. This time:
 
 http://chemapps.stolaf.edu/jmol/docs/examples-12/test3/t.htm
 http://chemapps.stolaf.edu/jmol/docs/examples-12/test3/t-signed.htm
 http://chemapps.stolaf.edu/jmol/docs/examples-12/test3/t2.htm
 
 Bob
 
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Re: [Jmol-developers] Project idea: Jmol-Python API -- Jmol.py

2011-10-30 Thread Jonathan Gutow

Bob,

This looks like a good idea to me.  As I've been working with Sage, which is 
python based, I have some ideas about how that might work.  It might also 
change the way Jmol can be used by Sage, although I'm not sure there is too 
much they would want to change about the way it is used as a 3-D viewer.

This is something I would like to work on.  However,  because of the way the 
Univ. of Wisc. System is going, the only way I am going to get to devote 
adequate time to it, is if I can get funded to work on it.  I also think this 
is a project which I could get some of my CS colleagues interested in.  I'm 
game, but as you've said, we would have to assemble a team and a pretty careful 
plan about how we would start this.  Maybe the first step is to assemble a team 
to write a grant proposal or proposals?  We could target national funding 
agencies (maybe the international collaboration angle as well?) and maybe 
Google Summer of Code grants to fund some students?

Jonathan
On Oct 30, 2011, at 5:27 AM, Robert Hanson wrote:

 What do you think of writing a Python interface to Jmol?
 
 It seems to me a lot of people like to use Python. It's the programming 
 language of the average scientist. Now that we have Jmol set up with a 
 sockets interface (Molecular Playground), why not write an interface that 
 would be the entire JmolViewer interface, but via sockets? And then write a 
 Python (or whatever language) API to go along with it? The Python developer 
 would simply add the Jmol.py toolkit along with Jmol.jar and have instant 
 access to (any number of) viewers, a POV-ray generator, a molecular structure 
 analysis engine, structure and surface file readers, callback mechanisms, a 
 customizable interface (possibly even using the signed applet with a local 
 HTML page), the option to run headless with no visible viewer, etc., etc. 
 
 From a Python viewpoint, it would be just another package. Jmol.py would work 
 something like a database -- you make a connection, configure the connection, 
 make function calls (queries), get results -- and the API would handle all 
 the connectivity via sockets. 
 
 From a Jmol viewpoint, it would look like Jmol just turned into a Python 
 version.
 
 In effect, rather than writing a PyMol plug-in, what Python developer/user 
 would be doing would be writing a Python program with a Jmol plug-in. Heck, 
 we might even be able to write a PyMol-Jmol API that would enable PyMol 
 plug-ins to be directly adaptable to Jmol, but of course with all the added 
 power, breadth, and flexibility of Jmol. Sort of like the way we were able to 
 port virtually all of Rasmol/Chime capability to Jmol and extend that 
 immensely. (But I would consider that a secondary goal.)
 
 Good idea? Anyone want to work on this?  I would definitely want to assemble 
 a team to do this -- I personally have no experience at all with Python. 
 Might even be fundable.
 
 :)
 
 Bob
 
 
 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 If nature does not answer first what we want,
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Re: [Jmol-developers] Packaging 12.2 for Debian/Ubuntu, disabling naga

2011-10-30 Thread Jonathan Gutow

Michael,

I think you now have to wait on NAGA, if this is a hold up.  As anybody can 
download Jmol and run or develop it on Ubuntu as it now stands, I don't see 
this as a pressing issue for the Jmol development team.  Presently, I do most 
of my developing on an Ubuntu machine.

You've done the correct thing by filing a report with NAGA.

Regards,
Jonathan
On Oct 30, 2011, at 2:44 PM, Michael Banck wrote:

 Hi,
 
 I took a look at packaging 12.2 (congrats!) for Debian/Ubuntu, and
 realized it now requires the naga NIO asynchronous sockets
 implementation.  I know you bundle the jar in your release tarball, but
 we have to remove all binary jars and repackage the tarball prior to
 build as per Debian policy and in order to comply with the Debian Free
 Software Guidelines.
 
 Naga has not yet been packaged for Debian, and as neither their
 subversion repository nor their release jarfiles have any
 copyright/license information (the website says MIT), this will likely
 not be accepted into the Debian/Ubuntu repositories for now.  I have
 filed issue http://code.google.com/p/naga/issues/detail?id=12 to that
 effect.
 
 In the meantime, is there maybe a way to disable the need for having
 naga around while building jmol?
 
 
 Best regards,
 
 Michael
 
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Re: [Jmol-developers] Jmol Android suggestions?

2011-10-20 Thread Jonathan Gutow

I'm not familiar with the browser capabilities of Android, but thought that 
java applets within a browser cannot run because the OS is essentially a JVM.  
If this is true, can we think about a way to have the Android Jmol app open in 
parallel to the browser, so that people can at least play with the live 3-D, 
even if they lose much of the web site functionality?

Jonathan
On Oct 20, 2011, at 4:40 PM, Robert Hanson wrote:

 Now that Mario and I have Jmol running on Android, it would be good to get a 
 discussion going as to what to do with it. It's sort of an app and sort of an 
 applet, and it certainly doesn't have to do exactly what the applet or the 
 application do. What do you think would be good? Here is what it does now:
 
 -- user selects DOWNLOAD and indicates a PDB ID or other keyword
-- list of PDB structures related to that query
   -- user picks one; Jmol displays with cartoons only; color structure
 
 -- user selects OPEN and indicates a file on the tablet
-- file is loaded as above
 
 -- user selects one of a few standard styles
   -- model is rendered that way
 
 But that's just a starting point. What else do we want it to do?
 
 Bob
 
 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 If nature does not answer first what we want,
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Re: [Jmol-developers] (no subject)

2011-10-13 Thread Jonathan Gutow

Hmm...I was under the impression that Bob already checked that you have the 
proper commit permissions.  
Other ideas:
Has something happened to your SourceForge Login (try logging in on the web 
site in a browser)?
You Eclipse is corrupted (try installing a whole new copy).

Now I'm completely out of ideas.  Anyone else?

Jonathan
On Oct 13, 2011, at 12:19 PM, Mario Kosmiskas wrote:

 I'm using Eclipse for all SVN operations. I created a new workspace and 
 checked out the projects. Commits give the same error - 403 Forbidden.
 
 Can you check if I have check in rights?
 
 
 From: Jonathan Gutow [gu...@uwosh.edu]
 Sent: Wednesday, October 12, 2011 8:24 AM
 To: jmol-developers@lists.sourceforge.net
 Subject: Re: [Jmol-developers] (no subject)
 
 This looks like an issue with commit rights or a bad path in his SVN records. 
  Checking it out again should fix the bad path.  Good luck.
 
 Jonathan
 On Oct 12, 2011, at 9:51 AM, Robert Hanson wrote:
 
 Mario,
 
 First, try that again. I tried team  cleanup to see if that somehow 
 clears up a lock or something.
 Second, try checking  in just  one single file, not the whole thing.  
 (Uncheck all except one.)
 Third, just create a new text file in a directory and try committing that.
 Fourth, try checking the project out as another project with a different 
 name, changing one thing, and checking it back in. Just to see if that works.
 
 
 passing this to Jmol-developers, because someone might have an idea.
 
 
 
 On Wed, Oct 12, 2011 at 8:53 AM, Mario Kosmiskas mar...@uw.edu wrote:
 Just tried to check in, still getting an error
 
 
 (Commit operation failed. 403 Forbidden)
 
 
 --
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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
 --
 All the data continuously generated in your IT infrastructure contains a
 definitive record of customers, application performance, security
 threats, fraudulent activity and more. Splunk takes this data and makes
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 800 Algoma Boulevard FAX:920-424-2042
 Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow
 
 
 
 
 
 
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Re: [Jmol-developers] (no subject)

2011-10-12 Thread Jonathan Gutow

This looks like an issue with commit rights or a bad path in his SVN records.  
Checking it out again should fix the bad path.  Good luck.

Jonathan
On Oct 12, 2011, at 9:51 AM, Robert Hanson wrote:

 Mario,
 
 First, try that again. I tried team  cleanup to see if that somehow clears 
 up a lock or something. 
 Second, try checking  in just  one single file, not the whole thing.  
 (Uncheck all except one.)
 Third, just create a new text file in a directory and try committing that. 
 Fourth, try checking the project out as another project with a different 
 name, changing one thing, and checking it back in. Just to see if that works. 
 
 
 passing this to Jmol-developers, because someone might have an idea. 
 
 
 
 On Wed, Oct 12, 2011 at 8:53 AM, Mario Kosmiskas mar...@uw.edu wrote:
 Just tried to check in, still getting an error
 
  
 (Commit operation failed. 403 Forbidden)
 
 
 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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
 --
 All the data continuously generated in your IT infrastructure contains a
 definitive record of customers, application performance, security
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 http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-developers] (no subject)

2011-10-11 Thread Jonathan Gutow

Yeah!  Looks good!
Jonathan
On Oct 11, 2011, at 9:12 AM, Robert Hanson wrote:

 Mario -- Got it!  http://stolaf.edu/people/hansonr/jmol/test/success.png
 
 On Tue, Oct 11, 2011 at 8:52 AM, Robert Hanson hans...@stolaf.edu wrote:
 Happy day! OK -- off to other things. Now it is in your hands for a while -- 
 it successfully loads and displays caffeine.xyz from the web. -- or at least 
 I thought it did. Now I went to get an image of it (that I DID see!) and it 
 won't display.
 
 I'm a little worried about the threading -- I'm not sure viewer.repaint() 
 should be continuing on to Viewer.renderScreenImage() in the same thread. I'm 
 pretty surprised that works, actually. I would have thought it would 
 deadlock. In Jmol the way it works is that Jmol just sends an update me 
 message to the system, and then that thread comes back through with an 
 update() request. We might want to set up our own thread for updateCanvas().
 
 
 
 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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
 --
 All the data continuously generated in your IT infrastructure contains a
 definitive record of customers, application performance, security
 threats, fraudulent activity and more. Splunk takes this data and makes
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 ___
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800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-developers] translations lost due to refactoring?

2011-09-29 Thread Jonathan Gutow

Uh-Oh!  This does not sound good.  Unfortunately, I have no idea what happened.

Jonathan
On Sep 29, 2011, at 1:10 PM, Angel Herráez wrote:

 There is a huge number of phrases that are now untranslated in the current 
 .PO files, I guess 
 this is a consequence of the recent refactoring. But many of them were 
 already translated 
 before.
 
 Why have they been lost?
 It's going to be quite a task to retranslate them all
 
 
 
 
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Re: [Jmol-developers] serious refactoring of Jmol

2011-09-27 Thread Jonathan Gutow

This looks cool...I'm going to see if I can convince my School to set something 
up.

Jonathan
On Sep 27, 2011, at 10:55 AM, Robert Hanson wrote:

 Over the past few days I've been doing some major refactoring of Jmol 12. The 
 changes should be transparent, but the overall effect should be significant. 
 
 All core java.awt and java.swing references are now made from within 
 org.jmol.awt  or org.jmol.export (where all the file dialogs are). 
 org.jmol.console, org.jmol.modelkit, and org.jmol.viewer.MouseManager14.java 
 (now Mouse.java) have all been moved into org.jmol.awt. This is in 
 preparation for Mario Kosmiskas integrating his Jmol Android and NET apps 
 into core Jmol. Both Android and NET will be separate Java/C## projects 
 (within the Jmol Sourceforge project) that link to the Jmol project, so 
 developers not interested in those won't need the Android SDK.
 
 In addition, I've been working with Adam Williams at U-Mass Amherst on adding 
 JSON-protocol NIO socket and kiosk capability to the Jmol app. What this 
 means is that you will be able to start Jmol in kiosk mode, which basically 
 makes the application look like the applet (an undecorated black square) that 
 can be projected onto a wall. By specifying a port number on the Jmol command 
 line, you will be able to communicate with Jmol via that port essentially 
 like applets communicate with each other using SYNC commands. Adam has 
 written a Kinect-driven host that takes this Jmol app as its client. Jmol 
 listens asynchronously on the port for raw mouse motions, script commands, 
 and SYNC messages using a simple JSON protocol, and reports back to the host 
 when a script has completed. Adam has installed this at U-Mass Amherst as the 
 Molecular Playground http://molecularPlayground.org and we are currently 
 installing a version of this at St. Olaf. 
 
 So maybe the theme for the week is from small to large -- Jmol on cell 
 phones and in public spaces.
 
 Bob
 
 
 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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
 --
 All the data continuously generated in your IT infrastructure contains a
 definitive record of customers, application performance, security
 threats, fraudulent activity and more. Splunk takes this data and makes
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Re: [Jmol-developers] Idea for on-the-fly unsigned to signed applet switching...

2011-09-23 Thread Jonathan Gutow

Once you've got the state, all I did was make a little function that toggles 
the setting to use the signed applet in Jmol.js.  You could do it from outside 
Jmol.js, but I think that is a bad programming habit.  Here's the function I 
added to Jmol.js in the form of a patch.

@@ -139,6 +139,10 @@
   _jmol.params.doTranslate = ''+TF;
 }
 
+function jmolToSigned(){
+_jmolGetJarFilename(true);
+}
+
 function _jmolGetJarFilename(fileNameOrFlag) {
   _jmol.archivePath =
 (typeof(fileNameOrFlag) == string  ? fileNameOrFlag : (fileNameOrFlag ?  
JmolAppletSigned : JmolApplet) + 0.jar);


On Sep 23, 2011, at 4:24 AM, Robert Hanson wrote:

 var state = jmolGetPropertyAsString(stateInfo)
 ...
 jmolScript(state)
 
 
 2011/9/23 Angel Herráez angel.herr...@uah.es
 Jonathan, I'm trying to use this idea of replacing the applet with
 the signed vesion on request.
 Coud you share the scripts you use for retrieving the state and
 applying ti again after the applet has been replaced? I'm stuck
 trying   jmolEvaluate('state'),   show state,  print state...
 
 Thanks a lot,
 Angel
 
 
 
 
 
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Re: [Jmol-developers] Jmol for Android

2011-09-19 Thread Jonathan Gutow

I would like to second Bob's Fantastic! We've talked about this before, but
haven't had anybody with the time to pursue it. This is wonderful!

Since I'm guilty of some of the Swing portions of the Jmol code, I can say I
think Bob is right about where the is Swing. Everything I am aware of that is
not in the list below is part of the application.

Jonathan
On Sep 19, 2011, at 6:06 PM, Robert Hanson wrote:

Here's where I see Swing being used outside of Jmol.jar (the application):

org.jmol.applet.AppletConsole
org.jmol.export.dialog
org.jmol.modelkit.ModelKit
org.jmol.multitouch.JmolMultiTouchClientAdapter
org.jmol.popup.JmolPopup
viewer.StatusManager (prompt command display)

Not too bad, really. Most of these would not be implemented on a mobile
device anyway, or would in any case need a different implementation
altogether. In fact, I think all of those except the prompt command are
implemented safely using class loaders -- meaning there are no direct
references to them anywhere in the code. That means they all use interfaces
and can all be simply overlaid with other packages or ignored entirely.

Where can we find this android app to try it out?

Got anything for the iPhone? :)

By the way, JmolData is a core library that has no UI. (And no graphics!)

Bob

On Mon, Sep 19, 2011 at 5:50 PM, Robert Hanson hans...@stolaf.edu wrote:
Mario,

Fantastic!

You might be interested in knowing that a few years back Jmol was completely
compatible with non-Swing applications, but we opted for integrating Swing
completely when we moved to Java 1.6 (sorry about that!). Let's get your work
onto SourceForge as an android branch and see what we can do with it. We need
to have some way of keeping these in sync -- a few months is a LONG time in
this business, and you certainly don't want to miss out on cool new features.
I think the best way to manage this would be a package similar to the
application package org.openscience:

org.jmol (core + applet)
org.openscience (Java app, with Swing)
org.jmol-android (android app)

We can talk about how to modify org.jmol to retain compatibility.

Bob

On Mon, Sep 19, 2011 at 3:51 PM, Mario Kosmiskas mar...@uw.edu wrote:
I was interested in making Jmol work on Android and spent some time
refactoring the code. The challenge was to isolate the graphics toolkit since
Android doesn't support Swing.

By removing the dependency on Swing I was able to successfully create a
simple Jmol Android App. The app is capable of loading models and user
interaction (rotate and zoom) via the touch panel (although I haven't
implemented pinch-zoom yet). I tried a variety of molecules from PDB.org
without problems. Some screenshots:

https://skydrive.live.com/redir.aspx?cid=38307cadfc15224bpage=playresid=38307CADFC15224B!105authkey=aMGRb02VYIs%24

The refactoring turned out to not be extensive in terms of number of modified
files but required the separation of the Swing Frames into their own project.
That effectively created a core Jmol library which doesn't have any UI. The
existing Swing Frames and applets are built on top of it, as well as the
Android app.

To further test the library I compiled it with IKVM into a .NET DLL. That
allowed me to create a native Windows executable written in C#, no JVM
required. It could make it easier for people to integrate Jmol into a variety
of other projects.

I worked off of a trunk snapshot a few months old. I would be glad to discuss
my changes if there is interest in integrating them.

Mario

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--
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http://www.stolaf.edu/people/hansonr
phone: 507-786-3107

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Re: [Jmol-developers] CRYSTAL Input writer for Jmol

2011-09-08 Thread Jonathan Gutow

Dan,

Welcome and thanks for helping out.

Jonathan
On Sep 7, 2011, at 4:36 PM, Robert Hanson wrote:

 OK, Dan. You are authorized as a developer who can check code in. Welcome!
 
 All: Dan has offered to help write a CRYSTAL09 input tab for the application. 
 Others may be joining him from the Dovesi group in Turin. This will probably 
 require some adaptations to CRYSTAL as well, so we will want to work closely 
 with that group. (Not sure who exactly will be our point person for that.) 
 
 Dan, please work with the 
 https://jmol.svn.sourceforge.net/svnroot/jmol/branches/crystal-input/Jmol  
 branch.
 
 I've created there a class that is the same as the Gaussian page as a 
 starting point for you. Have fun! Any questions should be directed to Jmol 
 Developers jmol-developers@lists.sourceforge.net, where others can chime 
 in with suggestions and comments. 
 
 Bob
 
 
 On Tue, Sep 6, 2011 at 2:44 PM, Daniel Jones danieljone...@gmail.com wrote:
 Hi Bob,
 
 I'm set up on SourceForge, I've used my personal email, unfortunately I don't 
 know how much longer I'll be at NAG.  Post doc contracts have an unfortunate 
 habit of ending.
 
 My sourceforge username is drdanjones.
 
 
 Thanks and kind regards,
 Dan
 
 Great! We have some ideas, I think, about round tripping the code so that 
 one can use the output as a basis for another input. 
 
 First thing to do is get yourself set up as a Jmol developer. Then I will 
 create a branch for you to work on. You can do anything with that you want 
 and not worry about wrecking anything. Once you have something, or if you are 
 stuck, let me know, I will check out your code and see what I can do. You 
 will need Eclipse + SVN. The Jmol Wiki for developers can guide you. I always 
 have trouble with getting that going the first time, but give it a try. So:
 
 1) Get a SourceForge ID name.
 2) Let me know you have done that. 
 3) Download Eclipse and get SVN set up. 
 4) See if you can check out the branch that I will set up called Jmol_crystal.
 
  
 
 On Mon, Sep 5, 2011 at 8:55 AM, Daniel Jones daniel.jo...@nag.co.uk wrote:
 Hi Bob,
 
 I really enjoyed your talk today.  Gave me a few ideas about new ways 
 to
 use Jmol.
 
 You mentioned you would like someone to write a module to write 
 CRYSTAL
 input files.  I'd be interested in giving it a go.  I haven't written
 any Java for a while, but there is a little rattling around the back 
 of
 my brain!
 
 Is there a good place to start?  Can I download the source from
 somewhere and just start hacking?  I guess it will be similar in many
 ways to the same functionality for Gaussian.
 
 Thanks and kind regards,
 Dan
 
 
 
 
 The Numerical Algorithms Group Ltd is a company registered in England
 and Wales with company number 1249803. The registered office is:
 Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.
 
 This e-mail has been scanned for all viruses by Star. The service is
 powered by MessageLabs.
 
 
 
 
 
 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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
 
 
 
 This e-mail has been scanned for all viruses by Star.
 
 
 
 
 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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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[Jmol-developers] Wow...the faster surface rendering is much faster!!!

2011-08-04 Thread Jonathan Gutow

Bob,

I'm impressed.  The faster surface rendering is much faster! what did you do?

Jonathan
 Dr. Jonathan H. Gutow
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[Jmol-developers] Something as of revision 15924 has broken mo command...

2011-08-03 Thread Jonathan Gutow

The mo command now sends Jmol into limbo.Not sure what happened.

Jonathan
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Re: [Jmol-developers] Refactoring ideas for cleaner code

2011-08-02 Thread Jonathan Gutow

This sounds like a good idea.  I would really like to see a way of making this 
clearer to read for future programmers as well.  If this is going to undergo a 
major refactoring we should put some thought into organizing the constants in a 
way that makes it easy to find those you are interested in, without have a good 
idea what they are called.  I think we just need to categorize them more 
carefully.

Jonathan
On Aug 2, 2011, at 1:03 PM, Nicolas Vervelle wrote:

 Hi,
 
 Looking at JmolConstants, I think we could refactor it to have much cleaner 
 code in Jmol.
 I think especially about the list of constants.
 Since we are now using Java 5 code, what do you think about using Enum ?
 
 For example, replacing all the CALLBACK_xxx constants and callbackNames[] by 
 an proper Enum in its own file ?
 And then only using the Enums in the rest of the code.
 I think it will be cleaner and a lot better for type safety.
 
 Nico
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[Jmol-developers] question about viewer.getProperty(..) call...

2011-07-14 Thread Jonathan Gutow

I think this is for Bob.

Inorder to create a ghost isosurface (or any other shape), I need to duplicate 
the shape and change some of the rendering parameters.  The cleanest way seems 
to be to make a copy of the command that created the surface and change just 
the name and relevant rendering parameters.  This way the new surface is added 
to the Jmol state in the normal way.  So, I was investigating what I can get 
back using the viewer.getProperty() call.

I used a call like:  Object shapeInfo = viewer.getProperty(Object, 
ShapeInfo, null);  

I gather this is just a little more general than using calls to 
viewer.getShapeProperty.

Anyway, my question is this.  The returned object is missing the Jmol State 
version of the isosurface recreation command, is there another way using some 
version of these getProperty calls to access this?  The title appears to 
have the basic (user entered) command, but I would prefer to work with the Jmol 
State version, because they are more complete and I believe will reduce the 
chances of having to update my code if defaults or parameters change.

Thanks,
Jonathan

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Re: [Jmol-developers] question about viewer.getProperty(..) call...

2011-07-14 Thread Jonathan Gutow

I just thought of something that might help...Is there a way to ask for just 
the state of an object?

Ideally for me what would be very clean would be to be able to call for a list 
of all shapes in the Jmol State and then iterate through that list asking for 
the Jmol State command(s) that create each shape.

Jonathan


On Jul 14, 2011, at 9:34 AM, Jonathan Gutow wrote:

 I think this is for Bob.
 
 Inorder to create a ghost isosurface (or any other shape), I need to 
 duplicate the shape and change some of the rendering parameters.  The 
 cleanest way seems to be to make a copy of the command that created the 
 surface and change just the name and relevant rendering parameters.  This way 
 the new surface is added to the Jmol state in the normal way.  So, I was 
 investigating what I can get back using the viewer.getProperty() call.
 
 I used a call like:  Object shapeInfo = viewer.getProperty(Object, 
 ShapeInfo, null);  
 
 I gather this is just a little more general than using calls to 
 viewer.getShapeProperty.
 
 Anyway, my question is this.  The returned object is missing the Jmol State 
 version of the isosurface recreation command, is there another way using some 
 version of these getProperty calls to access this?  The title appears to 
 have the basic (user entered) command, but I would prefer to work with the 
 Jmol State version, because they are more complete and I believe will reduce 
 the chances of having to update my code if defaults or parameters change.
 
 Thanks,
 Jonathan
 
 Dr. Jonathan H. Gutow
 Chemistry Departmentgu...@uwosh.edu
 UW-Oshkosh  Office: 920-424-1326
 800 Algoma BoulevardFAX:920-424-2042
 Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow
 
 
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[Jmol-developers] Another option for getting the data I need...

2011-07-14 Thread Jonathan Gutow

Based on what I can find in the code here are my options:

1) Modify getShapeProperty to include a getStateCmd option.  Sounds simple, but 
I find this access method strange as it duplicates methodologies built into the 
programming language.  Isn't it easier to define public getter functions within 
objects or make objects publicly readable? This has the additional advantage 
that if getters have javadoc attached to them it is much easier to figure out 
what the things you are looking for are called.  

2) My present preference (lacking public getter functions) is to use the 
viewer.getShapeManager() function to grab the list of shapes and pick the data 
I want out of the data structure.  Of course, when the data structure is 
changed my functions will break.

3) Add public getter functions to ShapeManager.  It looks like it might have to 
be abstract for both of the things I am most interested in (stateCmd and 
boundBoxCorners), because different shapes have different info.  A prime 
example is drawn polygons for which I will need to check all the vertices to 
define the boundbox as that does not appear in the data structure.

I think options 2  3 are something Bob is trying to avoid.  Bob, can you 
explain why?

Any thoughts?

Jonathan
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Re: [Jmol-developers] Question about coordinates in Jmol

2011-07-05 Thread Jonathan Gutow


On Jul 2, 2011, at 2:36 AM, Robert Hanson wrote:

 Yes, the bounding box is in molecular coordinates. So except for the ghosting 
 -- which I actually do think is done best by displaying two surfaces -- 
 that's no problem with the applet, because you can just deliver it any way 
 you want to. I suggest doing them in two different frames, but you wouldn't 
 have to do that. 
Great!  That's the info I need.  One less possibility for changing coordinates 
to worry about.
 
 So the isosurface slab plane does precisely what you are looking for. 
 Both  slab and depth are possible. 
 Also, you might want to play around with zshading. That can produce a very 
 nice effect.
 
  
 
  By the way, you asked about the possibility of duplicating an isosurface so 
  there was a translucent shadow. Since rendering is a two-pass system, a 
  better way
 I like your idea and have sent a comment in a separate message.
 
 
 However, the problem then  is that you really don't have full control over 
 the two colors. Having two surfaces should display just as fast -- actually, 
 faster, because you don't have to switch colors in between passes. If we did 
 the ghost thing, we would have to run through all the colixes and reset them 
 on the fly. Could be done but not trivially. Also, this will not 
 reproduce in PovRAY, I think. (Have to think about that; maybe it will.)
OK, I'll stick with making a duplicate surface.  Send me any brainwaves you 
have on doing this efficiently.  For now, I intend to use the original creation 
command and just switch to translucent mesh for the display mode.

Jonathan

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Re: [Jmol-developers] Question about coordinates in Jmol

2011-06-30 Thread Jonathan Gutow

Last comment first.
On Jun 30, 2011, at 1:10 AM, Robert Hanson wrote:

 By the way, you asked about the possibility of duplicating an isosurface so 
 there was a translucent shadow. Since rendering is a two-pass system, a 
 better way...
 
 ... to do that might be to set a flag to render the translucent pass without 
 slab and the opaque one with. Something on that order would be way preferable 
 to creating a whole new object just for that. 
 
 That might be good.  It certainly would help with memory.  The only issue I 
see with this option is need for another separate control of the ghost 
rendering (mostly I think mesh versus fill and level of transparency).  What 
people have been doing is rendering two surfaces one opaque and slabbed and 
then a ghost unslabbed.  In playing around with orbitals and cavities where you 
may want to see the inside surfaces of the slice through the ghost, I've found 
that the ghost settings that seems to work best are a transparecy of ~200 and 
mesh nofill.  However, most of the SageMath people have been using filled.  The 
math people also have a tendency to use a different color for the ghost.  I'm 
partial to the same surface color rendering/mapping as the slabbed region.

 Dr. Jonathan H. Gutow
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Re: [Jmol-developers] Question about coordinates in Jmol

2011-06-30 Thread Jonathan Gutow

I try to answer your questions below.  In summary, now that you've changed the 
isosurface slab command so that it can be done after the surface is defined I 
am mostly concerned with building a GUI that is intuitive enough that people 
don't have to understand the details of the isosurface and slab commands to 
look at a section through the displayed object.  My first goal is to get this 
working well for isosurfaces, but I don't think it will be hard to extend it to 
do everything.

On Jun 30, 2011, at 1:07 AM, Robert Hanson wrote:

 well, the molecular coordinates are just the molecular coordinates. This 
 slicing is by them, right? Not the screen coordinates? There are three 
 coordinate systems:
 
  -- molecular coordinates
  -- relation of those by rotation to the original view (the orientation 
 quaternion/matrix)
  -- translation of that into screen coordinates (the transformation matrix)
 
 I'd sure like to hear more about what the specs are going to be on this 
 slice command. Before you go too far, Jonathan, can you remind us of what 
 exactly it is going to do?
 
 Q: Are we slicing in molecular coordinates (like isosurface slab plane... and 
 slab plane...) or screen coordinates (like slab/depth and isosurface slab 
 nnn)? 
The first draft will be slicing in molecular coordinates, although I think some 
people might also like a GUI for slab/depth like behavior.
 
 Q: Does the slab change when you rotate the model, or is it fixed? (Basically 
 the same as the previous question.)
People wanted to be able to look at the slice from different angles so that's 
why molecular coordinates.
 
 Q: What functionality does this add that does not already exist in the other 
 commands?
Other than a ghost feature, which presently requires building a duplicate 
surface, I cannot think of anything. 

Anyway, the issue is that people want the ability to specify the slice in a way 
that is logical relative to the view.  Tentatively, I am going to make the 
controls relative to the origin of the boundingbox.  If they are relative to 
the view orientation, things change on rotation and translation.  I think that 
would be confusing.  I think there should also be an option to do everything 
relative to the absolute coordinates (molecular).  I'll just set a switch.  So 
I am still at my original question, which is will the boundbox coordinates 
always be parallel to the molecular coordinates?
 
 There is no point in adding a new command unless it makes *scripting* far 
 easier. This sounds a lot more like a GUI thing -- which would use the 
 already-existent commands, possibly with a few modifications to suit.
I agree.  Initially as I began looking at what Jmol could do, I thought it 
would help.  Now I'm not sure.  
 
 It seems to me a popup window is a nice idea -- at least for the application. 
 Not convinced with respect to the applet -- we don't do that, so far, except 
 with the signed applet for file read/write. A good dialog can take lots and 
 lots of code to produce and work with. If possible, with the applet, we 
 should do that in JavaScript, not Java. (My opinion.)
I agree for another usability reason as well.  When you have more than one 
applet on a page it is difficult to tell which one the pop-ups go with.  A 
javascript tool that is anchored on the page in the vicinity of the applet is 
much easier to understand.  That is one of the reasons, I thought about a 
special command.  The idea being that the smaller the scripts that have to be 
passed the better the potential for speed.  
 
 By the way, you asked about the possibility of duplicating an isosurface so 
 there was a translucent shadow. Since rendering is a two-pass system, a 
 better way 
I like your idea and have sent a comment in a separate message.

Jonathan

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Re: [Jmol-developers] update of CARBOHYDRATE atom set definition

2011-06-29 Thread Jonathan Gutow

I vote for bug-fix and inclusion in 12.0

Jonathan
On Jun 29, 2011, at 1:35 PM, Angel Herráez wrote:

 Dear developers,
 
 I have committed code that updates the definition of the 'carbohydrate' atom 
 set. This is 
 based on a list of residue IDs (provided by Eric some time ago).
 
 While working with some glycans in glycoproteins, I have found out a few 
 common residues 
 (N-acetyl-galactosamine and sialic acid) that were not included in the set, 
 so I have added 
 them in the list.
 
 While doing that, I reviewed the whole list against the PDB Ligand Expo 
 site, http://ligand-
 expo.rcsb.org/ld-search.html  and found out 
 - that some listed residue IDs are now deprecated from the PDB. I have still 
 left them in the 
 list but have separated them and included a comment (in case we want to 
 remove them in 
 future)
 - that two listed residue IDs were not carbohydrates (maybe a typo), so I 
 have removed them
 
 The list will now be documented at http://wiki.jmol.org/index.php/AtomSets
 
 
 Now my question:
 I'd like to introduce this change too in the 12.0.x series. Do you think it 
 qualifies as a bug fix 
 and so it can go there, or is it a change in behaviour and it should only go 
 in the 12.1.x?
 
 Thanks for your views
 Angel
 
 
 
 
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[Jmol-developers] Question about coordinates in Jmol

2011-06-29 Thread Jonathan Gutow

As I am working on figuring out what I have to track for a GUI to control 
slabbing/slicing, I have encountered the issue that the coordinate system for 
the molecule and the viewing space are not always the same.  Do I have to worry 
about relative rotations of these axes or just the offset of the center?  All 
the examples I've found so far have the origins translated versus each other, 
but no relative rotations.  I'm also trolling the code, but if somebody knows 
the answer that will save me time.

Thanks,
Jonathan

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Re: [Jmol-developers] inline script incompatible with loading several files

2011-06-27 Thread Jonathan Gutow

I guess I wasn't aware of the option to load files  I always would have 
done the load...; load append... approach.  That said I cannot think of a 
reason the behavior should be set up to be different.  I vote for the same 
behavior in both cases.

Jonathan
On Jun 26, 2011, at 10:20 AM, Angel Herráez wrote:

 Dear developers,
 
 I am finding that loading several files in one command ignores the inline 
 script in those files.
 
 This is the test case:
 2 pdb files (small molecules)
 each has a REMARK jmolscript: etc.
 
 If I load both using load files ..., the inline scripts are ignored
 If I load using load ...; load append ..., the inline scripts are applied 
 correctly
 
 Jmol 12.0.44, app and applet; same in 12.1.30 app
 
 Sample files are attached 
 
 
 The following section of this message contains a file attachment
 prepared for transmission using the Internet MIME message format.
 If you are using Pegasus Mail, or any other MIME-compliant system,
 you should be able to save it or view it from within your mailer.
 If you cannot, please ask your system administrator for assistance.
 
    File information ---
 File:  molec.zip
 Date:  26 Jun 2011, 17:16
 Size:  2959 bytes.
 Type:  ZIP-archive
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Re: [Jmol-developers] Idea for on-the-fly unsigned to signed applet switching...

2011-06-18 Thread Jonathan Gutow

Sorry, I've been in transit for about the last 16 hours and didn't get all 
these messages in order.  Below are my comments based on testing.
On Jun 18, 2011, at 10:55 AM, Robert Hanson wrote:

 There you go - that's it! #2. Just use the code at 
 http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolPopup.htm
 
 I think it's as easy as opening that page from the original with the ?SIGNED 
 option on the command line.
That's a possibility.  However the popup window is not as intuitive as just 
having the applet switch over.  My testing suggests switching applets as needed 
is not a problem.
 
 
 Bob
 
 
 2011/6/18 Angel Herráez angel.herr...@uah.es
 Hi Jonathan
 
 I have not strong confidence on this, but I will drop a couple of comments
 
 1. I'd guess that changing the archive parameter on the fly will need 
 thorough cross-browser
 evaluation.  Do your Sage pages have a single JmolApplet in them? Otherwise, 
 the shift will
 not work. As I recall, combination of signed and unsigned applets in the same 
 page is not
 possible --but maybe that's a limitation impose by the current design of 
 Jmol.js, using a
 single jmolInitialize() call.
I've found  no problems using a mixture of signed and unsigned applets on a 
page, although I do have to keep track of which is which.  I have controls that 
require a signed applet check and switch to a signed applet if necessary.
 

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
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[Jmol-developers] Idea for on-the-fly unsigned to signed applet switching...

2011-06-17 Thread Jonathan Gutow

I've had some requests here at Sage Days to switch from the unsigned to the 
signed applet when the user asks to do a download of the view they've made on 
the page.


To be able to continue using Jmol.js, I came up with the following idea.
1) Unload the unsigned applet saving its state in Javascript (I already do this 
for memory management in Sage as people often open up lots of Jmols).
2) Call new public function in Jmol.js that sets the _jmol.archive to 
JmolAppletSigned0.jar (Maybe call it jmolToSigned).
3) Reload the Jmol applet using normal Jmol.js calls.  At that point the user 
will get the warnings associated with the signed applet, but should be 
expecting it.


Does anybody see a problem with this idea?


Jonathan
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Re: [Jmol-developers] mo display project

2011-03-11 Thread Jonathan Gutow

I built something simpler than Bob's idea and have wanted to make something 
like what Bob suggests.  However, I've simply not had time.  I think it is a 
good idea.  

As to Spartan Student, my impression from trying a demo they sent me is that 
other than the nice molecule building interface it is rather crippled.  I've 
given up on the commercial software for teaching quantum.  I uses GAMESS for 
the computation engine and then depending on what you want to do you can use 
wxMacMolPlt or Avogadro for building the molecules.  For the most part I then 
have the students use Jmol to look at the results (although they can also use 
wxMacMolPlt).  With some more tweaking, it might be possible to use the Jmol 
builder to generate input for GAMESS as well.  An important point is that I get 
them to look at the raw output to find some numbers as well.  This seems to 
give them a better sense of the kind of information the computations generate, 
than looking a pretty pictures.

Jonathan
On Mar 11, 2011, at 7:43 AM, Angel Herráez wrote:

 Hi Bob
 I agree that sounds much more intuitive and informative.
 
 If I remember well, Jonathan had a page of the sort before he started 
 working on Export to Web
 
 
 
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Re: [Jmol-developers] [ jmol-Feature Requests-3202918 ] Radical curly arrows

2011-03-08 Thread Jonathan Gutow

Would 3-D arrows with only the half of the arrow-head on the outside  
of the arc work?  That's the only way I can imagine doing it in 3D  
that could be well defined.  The problem with this is there would be  
some orientations where the arrowhead would be hard to see.

Jonathan
On Mar 8, 2011, at 6:08 AM, SourceForge.net wrote:

 Feature Requests item #3202918, was opened at 2011-03-08 12:08
 Message generated for change (Tracker Item Submitted) made by  
 ngreeves84
 You can respond by visiting:
 https://sourceforge.net/tracker/?func=detailatid=379136aid=3202918group_id=23629

 Please note that this message will contain a full copy of the  
 comment thread,
 including the initial issue submission, for this request,
 not just the latest update.
 Category: Interface Improvements
 Group: None
 Status: Open
 Priority: 5
 Private: No
 Submitted By: Nick Greeves (ngreeves84)
 Assigned to: Bob Hanson (hansonr)
 Summary: Radical curly arrows

 Initial Comment:
 We have had 3D curly arrows for normal two-electron reactions for  
 some time and they work well.
 http://chemapps.stolaf.edu/jmol/docs/examples-11/draw.htm

 I notice that there has been almost no discussion on this list about  
 radical reactions that involve unpaired electrons and are  
 conventionally represented by curly arrows with half a head  
 sometimes called fishhook arrows.
 http://chemistry2.csudh.edu/rpendarvis/Radicals.html#homolyt

 We are working on representing radical reactions and would like to  
 be able to show the mechanisms in 3D with fishhook curly arrows.  
 Could this be done in Jmol ?


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Re: [Jmol-developers] Still trying to trace why a state script doesn't quite get the orientation right...

2011-02-04 Thread Jonathan Gutow

OK, that makes sense and is easy to do.  I'm already using callbacks  
to make sure Jmol is properly loaded before I do other things.   
Thanks!  Maybe I will have time this weekend.  I'll let  you know.

Jonathan
On Feb 3, 2011, at 9:41 PM, Robert Hanson wrote:

 Ah, hah! Well, that's it then. When you pass a script in the applet  
 tag, it becomes a parameter of the object/applet tag. Those  
 parameters do not preserve line endings -- just like HTML. This was  
 the original reason that Miguel thought it would be difficult to  
 build a model from a scripted model file when I asked him about that  
 in my first question to him. Wow, my first interaction with Jmol!

 So the proper way to do this is to make the script a callback that  
 will notify the page that the applet is now ready for loading, and  
 then to send that script using jmolScript().

 Voila!

 Bob

 On Thu, Feb 3, 2011 at 7:38 PM, Jonathan Gutow gu...@uwosh.edu  
 wrote:

 On Feb 3, 2011, at 2:52 PM, Robert Hanson wrote:


 On Wed, Feb 2, 2011 at 12:56 PM, Jonathan Gutow gu...@uwosh.edu  
 wrote:

 Cool.  What conference exactly?

 http://www.icsti.org/spip.php?rubrique49

 
  I did slip that semicolon in somewhere along the way there. So if
  this is your problem, maybe somehow your JavaScript is stripping  
 all
  the newline characters. Not a good idea. Are you perhaps splitting
  on \n and forgetting to put that back in? Something's amiss
  there I don't think it's a problem inside Jmol.
 That's an idea.  I don't remember doing that, but I only recently  
 came
 back to this code after about 4 months off...I'll check.  It makes
 some sense because what we actually want to do is store the script as
 a hidden div in the page, which can get saved on the server and thus
 restore user changes across openings of the page.  This  means that I
 did have some massaging to make it work OK in a div.  I think I
 replaced all the \n with br/.  The idea being that they would then
 be replaced with \n before passing back to the applet.  I'm pretty
 sure I didn't strip the \n from the backup string version, but I will
 check.

 That'll do it. I'm sure that's it. The save orientation command  
 does not check to see how many parameters there are, so that next  
 moveto was simply being included on the line of the previous save  
 command. I think if you had used
 That doesn't appear to be it.  I can see all the \n in the string  
 using firebug.  I'll keep poking around, but putting the semicolon  
 back in fixed the problem.  I haven't got time right now, but remind  
 me where the script is broken into pieces (Tokens?) and I will try  
 to give it a gander.  Maybe another pair of eyes will find what is  
 going on.

 One clue is that the faulty script string worked fine if I pasted it  
 into the script console of the applet.  The problem only occurred  
 when the string was passed as the script in a call to  
 jmolApplet([width,height], scriptStr, AppletID).

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Re: [Jmol-developers] Still trying to trace why a state script doesn't quite get the orientation right...

2011-02-04 Thread Jonathan Gutow


On Feb 4, 2011, at 9:01 AM, Angel Herráez wrote:

 I'm rather surprised about the last posts in this thread. Up to now,
 I had the knowledge that the safest way to avoid timing problems
 was to put the script in the jmolAplet call and not in a jmolScript.
 Now it seems there are situations where the other is better (plus the
 callback, of course).
I think it depends what you are doing.  If  you can be sure that your  
script contains semi-colons at the end of every line the JmolApplet  
call should work fine.  That's the other safety feature I am  
considering rather than the callback + JmolScript.  I can strip all \n  
and add a semi-colon in their place if they do not exist.

 Jonathan, just a note. I cannot give details now (this is sort of an
 accumulated perception), but my troubles with line endings have
 always been less if using a textarea to hold the data. So maybe your
 hidden DIV could instead be a hidden TEXTAREA and you need less
 massaging and have less trouble.
 I think that the browsers handle better the newlines in textareas.
 At least this is what I reached when experimenting with passing model
 data between the 2D drawing applet (JChemPaint or others) and the 3D
 viewing applet (Jmol).
Thanks for the idea.  I'll give it a try.

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
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Re: [Jmol-developers] Still trying to trace why a state script doesn't quite get the orientation right...

2011-02-02 Thread Jonathan Gutow

Bob,

Now that SourceForge is semi-functional again and we have a snow day  
here in Oshkosh, I got an updated copy of Jmol.
Jmol 12.0.30 seems to work fine.  Did you change anything in the  
script engine between 12.0.28 and 12.0.30?  I didn't see a note about  
fixing the misplaced semicolon, although I see it is correct now.

Jonathan
On Jan 30, 2011, at 7:20 PM, Robert Hanson wrote:

 Jonathan, can you send me one of those zip files?

 On Sat, Jan 29, 2011 at 8:39 PM, Jonathan Gutow gu...@uwosh.edu  
 wrote:
 I'm looking for suggestions of things to look for.  Within the SAGE  
 math package I use a state script generated by the applet that I  
 have saved as a string to recreate the view the user had in a  
 previous applet in a new one.  The problem is that everything but  
 the final moveto of the _set PerspectiveState() call is being  
 executed properly when I pass this string to the applet.  If I copy  
 the string into the console of an active applet everything works  
 exactly as expected.  Passing the string as the script when the  
 applet is initialized doesn't work.  Any ideas what I should look  
 for?  I'm using 12.0.28 and this worked with all the 11.X versions.   
 I haven't tried backtracking the 12.X versions.  Do I need to do  
 this?  I don't think the misplaced semi-colons Bob and I discussed  
 earlier are the problem.

 Jonathan
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 -- 
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 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107


 If nature does not answer first what we want,
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 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-developers] Still trying to trace why a state script doesn't quite get the orientation right...

2011-02-02 Thread Jonathan Gutow


On Feb 2, 2011, at 11:57 AM, Robert Hanson wrote:

 Jonathan,

 'bout time you guys got some serious snow.
Actually, we probably overreacted.  Most of the snow went south.   
Milwaukee, Madison and places between here and there are apparently  
buried.  We've just got a lot of blowing snow.  That said, it looks  
great.

 We missed it here. Break between January interim and Spring  
 semester. Hey, Monday I get to go out to Microsoft Research and give  
 a talk about Jmol. Fun, eh? (Not to Microsoft -- they're just  
 providing the space for a conference on publishing.)
Cool.  What conference exactly?

 I did slip that semicolon in somewhere along the way there. So if  
 this is your problem, maybe somehow your JavaScript is stripping all  
 the newline characters. Not a good idea. Are you perhaps splitting  
 on \n and forgetting to put that back in? Something's amiss  
 there I don't think it's a problem inside Jmol.
That's an idea.  I don't remember doing that, but I only recently came  
back to this code after about 4 months off...I'll check.  It makes  
some sense because what we actually want to do is store the script as  
a hidden div in the page, which can get saved on the server and thus  
restore user changes across openings of the page.  This  means that I  
did have some massaging to make it work OK in a div.  I think I  
replaced all the \n with br/.  The idea being that they would then  
be replaced with \n before passing back to the applet.  I'm pretty  
sure I didn't strip the \n from the backup string version, but I will  
check.

Jonathan

 Bob


 On Wed, Feb 2, 2011 at 11:43 AM, Jonathan Gutow gu...@uwosh.edu  
 wrote:
 Bob,

 Now that SourceForge is semi-functional again and we have a snow day
 here in Oshkosh, I got an updated copy of Jmol.
 Jmol 12.0.30 seems to work fine.  Did you change anything in the
 script engine between 12.0.28 and 12.0.30?  I didn't see a note about
 fixing the misplaced semicolon, although I see it is correct now.

 Jonathan
 On Jan 30, 2011, at 7:20 PM, Robert Hanson wrote:

  Jonathan, can you send me one of those zip files?
 
  On Sat, Jan 29, 2011 at 8:39 PM, Jonathan Gutow gu...@uwosh.edu
  wrote:
  I'm looking for suggestions of things to look for.  Within the SAGE
  math package I use a state script generated by the applet that I
  have saved as a string to recreate the view the user had in a
  previous applet in a new one.  The problem is that everything but
  the final moveto of the _set PerspectiveState() call is being
  executed properly when I pass this string to the applet.  If I copy
  the string into the console of an active applet everything works
  exactly as expected.  Passing the string as the script when the
  applet is initialized doesn't work.  Any ideas what I should look
  for?  I'm using 12.0.28 and this worked with all the 11.X versions.
  I haven't tried backtracking the 12.X versions.  Do I need to do
  this?  I don't think the misplaced semi-colons Bob and I discussed
  earlier are the problem.
 
  Jonathan
  Dr. Jonathan H. Gutow
  Chemistry Departmentgu...@uwosh.edu
  UW-Oshkosh  Office:
  920-424-1326
  800 Algoma BoulevardFAX:920-424-2042
  Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow
 
 
   
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  --
  Robert M. Hanson
  Professor of Chemistry
  St. Olaf College
  1520 St. Olaf Ave.
  Northfield, MN 55057
  http://www.stolaf.edu/people/hansonr
  phone: 507-786-3107
 
 
  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-developers] Jmol applet not running in Chrome 8.0.552

2011-01-29 Thread Jonathan Gutow

Angel,

I agree my FF failure seems to be a one off.  I restarted FF and all three 
pages now work with FF 3.6.13 and MacOSX 10.6.6.  I will get and check a recent 
version of Chrome later today.  I have to take advantage of the warm (22 F, -6 
C) weather to do some tree trimming, so it will be a few hours.

Jonathan
On Jan 29, 2011, at 11:15 AM, Angel Herráez wrote:

 On 28 Jan 2011 at 21:20, Jonathan Gutow wrote:
 c. Set Mac/Firefox to do the same as other Firefoxes  (Anyone knows of any 
 problems with 
 Mac/Firefox that make the applet tag more adequate than the object tag?)
 Just tested this.  Your version 2 page does not work with FF 3.6+  MacOS 
 10.6. No Jmol appears in the first box. Apparently, MacOS FF does do 
 something different.  I will also test some of the other combinations this 
 weekend.
 
 Actually, this makes little sense. Box #1 is generated by Jmol.js; in page 
 v.2, this is either an 
 applet tag or a revised object tag, both of which are tested in boxes #2 and 
 #3 which 
 apparetly display ok
 So I'm inclined to think that Jonathan's test failed on #1 was coincidental. 
 Otherwise, it's 
 some failure in my Jmol_new.js
 
 I have move forward to a more extensive redesign of Jmol.js and that is now 
 set as page v.3
 http://biomodel.uah.es/angel/Jmol/test/test-object-tags-3.htm
 
 where Jmol.js will insert the revised object tag for almost any browser 
 (change applies to 
 Mac/Firefox, Mac/Opera)
 I have tested this v.3 on Macs using an online service at  browsercam.com  
 (yes, they run 
 Java on their browsers!) and all display fine in Mac 10.4 or 10.5, Firefox, 
 Safari or Opera
 
 So I think I'm going ahead with these changes to be put into the next 
 releases of 12.0 and 
 12.1   I am also doing some review of the Browser Check page at the Jmol 
 website, along 
 similar lines and also to include better identification of browsers.
 
 Real browser reports are still welcome!
 
 
 
 
 
 
 
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Re: [Jmol-developers] Jmol applet not running in Chrome 8.0.552

2011-01-29 Thread Jonathan Gutow

Latest Chrome is working for me on MacOS X with version three page, but not 
version 1.

Jonathan
On Jan 29, 2011, at 11:15 AM, Angel Herráez wrote:

 On 28 Jan 2011 at 21:20, Jonathan Gutow wrote:
 c. Set Mac/Firefox to do the same as other Firefoxes  (Anyone knows of any 
 problems with 
 Mac/Firefox that make the applet tag more adequate than the object tag?)
 Just tested this.  Your version 2 page does not work with FF 3.6+  MacOS 
 10.6. No Jmol appears in the first box. Apparently, MacOS FF does do 
 something different.  I will also test some of the other combinations this 
 weekend.
 
 Actually, this makes little sense. Box #1 is generated by Jmol.js; in page 
 v.2, this is either an 
 applet tag or a revised object tag, both of which are tested in boxes #2 and 
 #3 which 
 apparetly display ok
 So I'm inclined to think that Jonathan's test failed on #1 was coincidental. 
 Otherwise, it's 
 some failure in my Jmol_new.js
 
 I have move forward to a more extensive redesign of Jmol.js and that is now 
 set as page v.3
 http://biomodel.uah.es/angel/Jmol/test/test-object-tags-3.htm
 
 where Jmol.js will insert the revised object tag for almost any browser 
 (change applies to 
 Mac/Firefox, Mac/Opera)
 I have tested this v.3 on Macs using an online service at  browsercam.com  
 (yes, they run 
 Java on their browsers!) and all display fine in Mac 10.4 or 10.5, Firefox, 
 Safari or Opera
 
 So I think I'm going ahead with these changes to be put into the next 
 releases of 12.0 and 
 12.1   I am also doing some review of the Browser Check page at the Jmol 
 website, along 
 similar lines and also to include better identification of browsers.
 
 Real browser reports are still welcome!
 
 
 
 
 
 
 
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Re: [Jmol-developers] Jmol applet not running in Chrome 8.0.552

2011-01-29 Thread Jonathan Gutow

Linux testing:

Version 3 page
Chromium-OK
Epiphany-OK
FF-OK
Midori-OK
NetSurf-No good-appears not to support javascript
SeaMonky-OK
Conkeror-OK
Drooble-No good-again may not support javascript at all.

This looks pretty good to me.

Jonathan
On Jan 29, 2011, at 11:15 AM, Angel Herráez wrote:

 On 28 Jan 2011 at 21:20, Jonathan Gutow wrote:
 c. Set Mac/Firefox to do the same as other Firefoxes  (Anyone knows of any 
 problems with 
 Mac/Firefox that make the applet tag more adequate than the object tag?)
 Just tested this.  Your version 2 page does not work with FF 3.6+  MacOS 
 10.6. No Jmol appears in the first box. Apparently, MacOS FF does do 
 something different.  I will also test some of the other combinations this 
 weekend.
 
 Actually, this makes little sense. Box #1 is generated by Jmol.js; in page 
 v.2, this is either an 
 applet tag or a revised object tag, both of which are tested in boxes #2 and 
 #3 which 
 apparetly display ok
 So I'm inclined to think that Jonathan's test failed on #1 was coincidental. 
 Otherwise, it's 
 some failure in my Jmol_new.js
 
 I have move forward to a more extensive redesign of Jmol.js and that is now 
 set as page v.3
 http://biomodel.uah.es/angel/Jmol/test/test-object-tags-3.htm
 
 where Jmol.js will insert the revised object tag for almost any browser 
 (change applies to 
 Mac/Firefox, Mac/Opera)
 I have tested this v.3 on Macs using an online service at  browsercam.com  
 (yes, they run 
 Java on their browsers!) and all display fine in Mac 10.4 or 10.5, Firefox, 
 Safari or Opera
 
 So I think I'm going ahead with these changes to be put into the next 
 releases of 12.0 and 
 12.1   I am also doing some review of the Browser Check page at the Jmol 
 website, along 
 similar lines and also to include better identification of browsers.
 
 Real browser reports are still welcome!
 
 
 
 
 
 
 
 --
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 ___
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800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
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[Jmol-developers] Still trying to trace why a state script doesn't quite get the orientation right...

2011-01-29 Thread Jonathan Gutow

I'm looking for suggestions of things to look for.  Within the SAGE math 
package I use a state script generated by the applet that I have saved as a 
string to recreate the view the user had in a previous applet in a new one.  
The problem is that everything but the final moveto of the _set 
PerspectiveState() call is being executed properly when I pass this string to 
the applet.  If I copy the string into the console of an active applet 
everything works exactly as expected.  Passing the string as the script when 
the applet is initialized doesn't work.  Any ideas what I should look for?  I'm 
using 12.0.28 and this worked with all the 11.X versions.  I haven't tried 
backtracking the 12.X versions.  Do I need to do this?  I don't think the 
misplaced semi-colons Bob and I discussed earlier are the problem.

Jonathan
 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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Re: [Jmol-developers] Jmol applet not running in Chrome 8.0.552

2011-01-28 Thread Jonathan Gutow

Angel,

I found one problem with your proposal. See below.

Jonathan
On Jan 28, 2011, at 2:28 PM, Angel Herráez wrote:

 Thanks, Oliver, for the report
 
 Pending further testing, this is my interpretation so far:
 
 1.
 This is not an issue with browser handling of the applet tag, but with the 
 object tag (I stand 
 corrected here on my previous comment, after re-reading my own conclusions 
 left in the wiki 
 page last month :-) )
 
 2.
 There is a discussion on the web and many reports of websites suddenly 
 failing due to 
 Chrome's ~recent change of behavior over the object tag
 http://code.google.com/p/chromium/issues/detail?id=62076
 which they say (a) will not be reversed --considered a spec, not a bug, (b) 
 will propagate to 
 Safari as it is updated
 
 The issue is with object tags using a   classid='java:   parameter. The cure 
 is to remove this 
 parameter (apparently the removal does not damage other browsers)
 
 3.
 The reason the problem is only seen in Macs is due to the old browser 
 sniffing code in 
 Jmol.js --which incidentally I discovered last December, don't really 
 remember why--
 * So that Mac/Chrome is read as Mac/Safari and both get an object tag.
 * While Win/Safari and Win/Chrome are not detected and so get (as a fallback) 
 an applet 
 tag.
 * Win/Firefox and Linux/Firefox get object, but Mac/Firefox is set to use 
 applet (don't know 
 why). None of them give trouble.
 More details at the Wiki, 
 http://wiki.jmol.org/index.php/Jmol_Applet/Browser_Support
 
 4. 
 My proposal (partially implemented in my v.2 page modified Jmol.js, which I 
 would propagate 
 to the official Jmol.js and the browser testing page in the Jmol website):
 a. Chrome is detected before Safari (although maybe that's not necessary). Or 
 better, reduce 
 browser sniffing to the (old) exceptions that were known not to work and 
 leave most as 
 feature detection.
 b. Both Chrome and Safari will get the object tag, irrespective of the OS, as 
 other modern 
 browsers are getting.
 c. Set Mac/Firefox to do the same as other Firefoxes  (Anyone knows of any 
 problems with 
 Mac/Firefox that make the applet tag more adequate than the object tag?)
Just tested this.  Your version 2 page does not work with FF 3.6+  MacOS 10.6. 
No Jmol appears in the first box. Apparently, MacOS FF does do something 
different.  I will also test some of the other combinations this weekend.

Jonathan
 d. Most importantly, adopt the new syntax for the object tag, so avoiding the 
 problem seen in 
 Mac/Chrome and a future problem in Mac/Safari
 
 
 
 
 
 
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800 Algoma BoulevardFAX:920-424-2042
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[Jmol-developers] Need to double check the orientation in the state script of 12.0.28...

2011-01-22 Thread Jonathan Gutow

Bob,

I think you are the one who needs to double check this.  If I save a state 
script and reload it in 12.0.28, I seem to get the object in a different 
orientation. It looks like things are still in the state script.  Is the 
orientation not being read properly?

Jonthan
 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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Re: [Jmol-developers] location of code for What's new

2011-01-21 Thread Jonathan Gutow

Angel,

I did a grep on the src tree.  Try some of the following:

1) org/openscience/jmol/app/jmolpanel/WhatsNewDialog.java
2) org/openscience/jmol/app/jmolpanel/Properties/Jmol.properties

Jonathan
On Jan 21, 2011, at 1:16 PM, Angel Herráez wrote:

 Li An-Bang has brought to my attention that
  And,I notice, the Jmol logo in What's new doesn't display  
 correctly.

 I am trying to find the location of the html template for that panel.
 Jmol.properties says

 # Resources for the What's New dialog box
 #
 WhatsNew.changeLogURL=org/openscience/jmol/Data/ChangeLog.html

 But the   org/openscience/jmol/Data/   folder does not exist!
 I have been unable to find any other instance of the word changelog

 Any clues?
 Thanks





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Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-developers] [Jmol-users] Language about Jmol Web Page Maker

2011-01-02 Thread Jonathan Gutow

An-Bang,

I believe I have fixed the translation in widgets problem.  Please try  
version 12.1.30_dev the latest development release.  In case you are  
not set up to do a compile, I have put up a compiled version here:

http://www.uwosh.edu/faculty_staff/gutow/jmol-12.1.30_dev-binary.zip

Thanks for the feedback.

Jonathan

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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[Jmol-developers] I've found the problem with languages like chinese and widgets in web export...

2010-12-26 Thread Jonathan Gutow

I've found the problem with the widgets and translations in webexport.  For 
characters that require a lot of bits we have to use escape codes to force the 
html to always work.  I will fix this but don't have a good network connection 
to upload the corrections while travelling.  I hope to get network access in a 
couple of days.  
 
For those interested we need to make sure that any html generated by a widget 
uses the GT.escapehtml calls, in addition to the GT._ calls to do the 
translation.  The GT.escapehtml converts long characters into escaped 
characters that don't get mangled by the generic encoding.
 
We probably still need to try switching all the pages to UTF-8.
 
Jonathan
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Re: [Jmol-developers] [Jmol-users] Language about Jmol Web Page Maker

2010-12-20 Thread Jonathan Gutow

Nico,

Thanks.  I think this may solve the problem, but I'll look more  
carefully over break.  Some of the translations using the GT system  
are working some are not.  There are a couple of layers used to  
interpret this stuff, so it might be that we lose the encoding when  
passing strings at some point.

Jonathan
On Dec 20, 2010, at 12:05 PM, Nicolas Vervelle wrote:

 Hi Angel,

 For the problem compiling Jmol with the new language menu, I only  
 modified build.xml to tell the Java compiler that the source files  
 were encoded in UTF8 (otherwise, it was deciding alone what the  
 encoding was).

 I believe Java Strings are quite agnostic about the encoding.
 It's only when you write them to files or other things that the  
 encoding can be a problem.
 Some String methods allow you to specify what encoding is used to  
 write or read a String.
 So you can force what encoding is used to write to the file.

 I suggest using an encoding that allows a lot of languages.
 UTF8 seems a good choice.

 Nico


 2010/12/18 Angel Herráez angel.herr...@uah.es
 (This is mostly for Jonathan bu I'm putting here for future  
 reference and also if someone else
 has ideas. It follows from a report in jmol-users that pages  
 generated from Export to Web
 display Chinese text worng in the widgets)

 Jonathan, my first impression:

 The problem is only in the part of the page that comes from the  
 widgets.

 Widget texts like Spin on/off come to widgets.java from the GT  
 system (so they will be
 translated correct) and get inserted into the generated html page by  
 E2W.

 The page has a codepage attribute, but it is getting the wrong  
 characters. So I think it must
 be the java code that has to impose say UTF8 encoding on whatever it  
 is producing.

 This is something similar to the issue with languages in popup menu  
 that Nico updated
 yesterday. Initially, the names were coming in wrong characters.

 I think that even if ISO is apparently working fine, we'd be safer  
 shiftng to UTF8 for all the
 products of E2W. I am looking fot the code that Nico has used to  
 impose a certain codepage
 on certain java files






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Re: [Jmol-developers] [ jmol-Feature Requests-3128416 ] Android support

2010-12-05 Thread Jonathan Gutow

I have done some investigation on this.  I do not believe it is possible 
without changes to Android for us to develop and applet version of Jmol that 
will work within the Android browsers.  That said, an Android App version of 
Jmol is feasible, but will require some work as Android uses a different set of 
GUI primitives than the SWING and AWT Java tools that Jmol uses.  I think this 
is a worthy effort, but maybe we need some support (Google?).

Jonathan
On Dec 5, 2010, at 4:18 PM, SourceForge.net wrote:

 Feature Requests item #3128416, was opened at 2010-12-05 22:18
 Message generated for change (Tracker Item Submitted) made by nobody
 You can respond by visiting: 
 https://sourceforge.net/tracker/?func=detailatid=379136aid=3128416group_id=23629
 
 Please note that this message will contain a full copy of the comment thread,
 including the initial issue submission, for this request,
 not just the latest update.
 Category: None
 Group: None
 Status: Open
 Priority: 5
 Private: No
 Submitted By: Nobody/Anonymous (nobody)
 Assigned to: Nobody/Anonymous (nobody)
 Summary: Android support
 
 Initial Comment:
 Many software packages that have incorporated Jmol can already run on 
 Android, but Jmol does NOT work on Android so their functionality is limited. 
  The Sage mathematics package can be run natively on Android, or accessed via 
 web app notebooks just by pointing a browser to a Sage notebook server.  
 However, all of the Sage 3D displays are based on Jmol, which does not work 
 as an applet in the Android web browser.  Having Jmol as both a standalone 
 app on Android and a browser based applet would greatly enhance the use of 
 Android for scientific programming and visualization.
 
 --
 
 You can respond by visiting: 
 https://sourceforge.net/tracker/?func=detailatid=379136aid=3128416group_id=23629
 
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Re: [Jmol-developers] Ideas for Jmol extension for MediaWiki

2010-11-23 Thread Jonathan Gutow

Nico,

Bob can give you the details, but I think both things you suggest are  
possible.  However, I see one big problem:  in general I do not think  
we should default to opening a live Jmol in the wiki.  A static  
picture which can then become a live Jmol is more appropriate.  I  
think you want behavior more like the Jmol pop-in implemented by the  
export-to-web function.  An example page is here:
http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/Export_to_web_tutorial.shtml

You can use the code in this page which is based on a template made by  
Angel.  Note since this page was generated we have updated things to  
perform better.  You would probably be best off generating a new page  
in Jmol and lifting the code from that.

Jonathan
On Nov 23, 2010, at 1:08 PM, Nicolas Vervelle wrote:

 Hi,

 I have started working again on the extension to include Jmol in  
 Wikipedia.

 The current extension is not as simple as some Wikipedia people  
 would like (see this bugzilla report).
 One idea there is that a Media handler for molecular files should be  
 developed (so that an image could be displayed automatically when  
 going on the page of a CML file). It's interesting but seems  
 complicated.

 I have an other idea that could be not really hard to develop but  
 would enable to show a lot of molecules easily.
 But I need more infos on what Jmol is currently capable (I have lost  
 track and since I am no chimist at all that's difficult to follow).
 The idea is to use a simple tag with only an identifier inside to  
 choose the molecule.
 What do you think of the ideas below ?

 Can Jmol show a molecule having just a SMILES string ?
 If so, what are the commands that need to be executed ?
 I think we could add a syntax for Wikipedia where a user would  
 simply have to add something like smiles/smiles to display  
 the molecule in Jmol.

 Also, can Jmol retrieve a molecular file using only an identifier  
 (like getting the molecule on the pdb database) ?
 What are the options and the commands ?
 That would allow the same kind of addition : pdb/pdb to  
 display a molecule from the pdb database.

 Nico
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Re: [Jmol-developers] Wiki is down and has been since this weekend...Can someone fix?

2010-11-21 Thread Jonathan Gutow

Nico,

Thank  you for your efforts!  I've never maintained a wiki, but do maintain 
some CMS sites.  I'm sure that was a lot of work.

Thank you.

Jonathan
On Nov 21, 2010, at 6:08 AM, Egon Willighagen wrote:

 On Sun, Nov 21, 2010 at 1:01 PM, Nicolas Vervelle nverve...@gmail.com wrote:
 I had problems with all the files (images, molecular files, ...)
 I had to delete all the images and upload them again manually.
 Please, check if there are mistakes.
 I still have to take care of the molecular files.
 
 I am happy you got it solved... thanx for this work; I know how much
 time it costs, and how little reward it typically gives, as people
 take these things for granted...
 
 Nico++
 
 Egon
 
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[Jmol-developers] Wiki is down and has been since this weekend...Can someone fix?

2010-11-16 Thread Jonathan Gutow

The wiki is down and appears to have been this way since the weekend.   
On all my machines I am getting the following error messages.  This is  
not good for our public relations.  Can someone fix this?  Where are  
we hosting this anyway?

Jonathan

error messages---
Warning: Cannot modify header information - headers already sent by  
(output started at /public_html/mediawiki_1_14_0/includes/ 
DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/ 
WebResponse.php on line 16

Warning: Cannot modify header information - headers already sent by  
(output started at /public_html/mediawiki_1_14_0/includes/ 
DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/ 
WebResponse.php on line 16

Warning: Cannot modify header information - headers already sent by  
(output started at /public_html/mediawiki_1_14_0/includes/ 
DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/ 
WebResponse.php on line 16

Warning: Cannot modify header information - headers already sent by  
(output started at /public_html/mediawiki_1_14_0/includes/ 
DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/ 
WebResponse.php on line 16

Warning: Cannot modify header information - headers already sent by  
(output started at /public_html/mediawiki_1_14_0/includes/ 
DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/ 
WebResponse.php on line 16

Warning: Cannot modify header information - headers already sent by  
(output started at /public_html/mediawiki_1_14_0/includes/ 
DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/ 
WebResponse.php on line 16

Warning: Cannot modify header information - headers already sent by  
(output started at /public_html/mediawiki_1_14_0/includes/ 
DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/ 
WebResponse.php on line 16

Warning: Cannot modify header information - headers already sent by  
(output started at /public_html/mediawiki_1_14_0/includes/ 
DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/ 
WebResponse.php on line 16
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Re: [Jmol-developers] Wiki is down and has been since this weekend...Can someone fix?

2010-11-16 Thread Jonathan Gutow

Nico,

I don't have much time and know next to nothing about maintaining a  
wiki, but would really like to see the wiki stay up and be reliable.   
What about setting up some mirrors?  Could we use the sourceforge wiki  
services?

Jonathan
On Nov 16, 2010, at 3:27 PM, Nicolas Vervelle wrote:

 Hi,

 I tried to change the configuration this weekend (allowing uploading  
 pdb files), but something went wrong (I don't know what).
 I have changed LocalSettings.php and includes/DefaultSettings.php.
 I tried to go back to the original configuration, but without any  
 useful result.

 I don't have much time available right now, so I didn't manage to  
 fix it :( Hope to have time this weekend.
 Any help would be appreciated.

 I was thinking of trying to upgrade to latest MediaWiki (1.16.0),  
 but I need some free time to do this.

 Nico

 PS: Wiki is hosted on sivit.fr, but I doubt the hosting has anything  
 to do with the problem


 On Tue, Nov 16, 2010 at 10:21 PM, Jonathan Gutow gu...@uwosh.edu  
 wrote:
 The wiki is down and appears to have been this way since the weekend.
 On all my machines I am getting the following error messages.  This is
 not good for our public relations.  Can someone fix this?  Where are
 we hosting this anyway?

 Jonathan

 error messages---
 Warning: Cannot modify header information - headers already sent by
 (output started at /public_html/mediawiki_1_14_0/includes/
 DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/
 WebResponse.php on line 16

 Warning: Cannot modify header information - headers already sent by
 (output started at /public_html/mediawiki_1_14_0/includes/
 DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/
 WebResponse.php on line 16

 Warning: Cannot modify header information - headers already sent by
 (output started at /public_html/mediawiki_1_14_0/includes/
 DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/
 WebResponse.php on line 16

 Warning: Cannot modify header information - headers already sent by
 (output started at /public_html/mediawiki_1_14_0/includes/
 DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/
 WebResponse.php on line 16

 Warning: Cannot modify header information - headers already sent by
 (output started at /public_html/mediawiki_1_14_0/includes/
 DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/
 WebResponse.php on line 16

 Warning: Cannot modify header information - headers already sent by
 (output started at /public_html/mediawiki_1_14_0/includes/
 DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/
 WebResponse.php on line 16

 Warning: Cannot modify header information - headers already sent by
 (output started at /public_html/mediawiki_1_14_0/includes/
 DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/
 WebResponse.php on line 16

 Warning: Cannot modify header information - headers already sent by
 (output started at /public_html/mediawiki_1_14_0/includes/
 DefaultSettings.php:1) in /public_html/mediawiki_1_14_0/includes/
 WebResponse.php on line 16
 --
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 Chemistry Department gu...@uwosh.edu
 UW-Oshkosh   Office: 
 920-424-1326
 800 Algoma Boulevard FAX:920-424-2042
 Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-developers] WebExport static?

2010-11-13 Thread Jonathan Gutow

I cannot recall a reason for them being static.  I do recall we had some issues 
that required us to make sure that some things were protected.  I may have time 
to look at the code this afternoon.  Any module in particular?

Jonathan
On Nov 12, 2010, at 7:36 PM, Robert Hanson wrote:

 Jonathan, Angel? Do either of you know why there are so many static fields in 
 WebExport? I'd like to make them nonstatic.
 
 -- 
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 St. Olaf College
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Re: [Jmol-developers] WebExport static?

2010-11-13 Thread Jonathan Gutow

Bob,

I think these are a holdover from when we were trying to maintain the ability 
of webexport to run separately.  It is now so dependent on direct connections 
to the rest of Jmol that I do not think it can run without Jmol.  Thus I will 
put on my list (maybe for January) the removal of all the code left over from 
when it was a standalone entity.

Jonathan
On Nov 13, 2010, at 1:18 PM, Robert Hanson wrote:

 WebExport is the one. I've carefully gone through all the other Jmol code and 
 made sure that there are no static references to anything but constants. This 
 is important from a threading point of view. I think it's OK as it is, but it 
 just seems messy to me. A quick look suggested it's a very complicated bit of 
 code, made more so by all the static references. 
 
 Not a high priority.
 
 Bob 
 
 On Sat, Nov 13, 2010 at 1:08 PM, Jonathan Gutow gu...@uwosh.edu wrote:
 I cannot recall a reason for them being static.  I do recall we had some 
 issues that required us to make sure that some things were protected.  I may 
 have time to look at the code this afternoon.  Any module in particular?
 
 Jonathan
 On Nov 12, 2010, at 7:36 PM, Robert Hanson wrote:
 
 Jonathan, Angel? Do either of you know why there are so many static fields 
 in WebExport? I'd like to make them nonstatic.
 
 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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
 --
 Centralized Desktop Delivery: Dell and VMware Reference Architecture
 Simplifying enterprise desktop deployment and management using
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 Oshkosh, WI 54901
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 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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
 --
 Centralized Desktop Delivery: Dell and VMware Reference Architecture
 Simplifying enterprise desktop deployment and management using
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Re: [Jmol-developers] Worrying news for Mac users!

2010-10-22 Thread Jonathan Gutow

This is definitely not goodThus I think it is in our best interest  
to begin experimenting with OpenJDK on the Mac.  The biggest problem I  
foresee is that this will kill the usefulness of Jmol in web pages on  
MacOS.  We'll be back to the same problem we had with chime where it  
ran on fewer and fewer platforms.  Of course we can also encourage  
people to switch over to Linux.  Most versions are not quite as glitzy  
as MacOS, but like MacOS they're more stable and more functional than  
Windows.

To some extent I understand the objection to the overhead incurred by  
Java, but for most applications maintaining different code bases for  
different platforms is not necessary to get good performance on a  
modern computer.  I personally hope this ends up hurting Apple.  If  
they don't release the work they've done so far, they really deserve  
to get damaged by this move.

Jonathan
On Oct 22, 2010, at 5:48 AM, Egon Willighagen wrote:

 On Fri, Oct 22, 2010 at 12:33 PM, Rzepa, Henry  
 h.rz...@imperial.ac.uk wrote:
 http://lists.apple.com/archives/Java-dev/2010/Oct/msg00248.html

 That expresses future aspirations, rather than testable reality.   
 There is nothing for
 OS X  at http://openjdk.java.net/

 You can find instructions floating around on the web on how to build
 it... this is one hit:

 http://confluence.concord.org/display/CCTR/Build+OpenJDK+Java+1.7.0+on+Mac+OS+X+10.5

 The argument is that implementing  Java for  OS X would almost  
 certainly require Apple to release source code for the graphical  
 implementations. If that does not happen, then the actual  
 experience on the  Mac may become  a poor one.

 True. Just like we have seen with the Classpath libraries...

 Well, you only payed minimal money for OS/X, so what can you  
 expect? ;)

 Jobs appears to want to take  OS X towards  iOS, which is away from  
 using a mouse and towards using gestures. I think that adapting   
 Java for that sort of environment is going to require major work.

 Yeah, that is one good reason for Jobs to drop Java... of course, if
 he would have gone Open Source, he could have shared this burden...

 Egon

 -- 
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 University of Cambridge
 Homepage: http://egonw.github.com/
 LinkedIn: http://se.linkedin.com/in/egonw
 Blog: http://chem-bla-ics.blogspot.com/
 PubList: http://www.citeulike.org/user/egonw/tag/papers

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 contest
 Create new apps  games for the Nokia N8 for consumers in  U.S. and  
 Canada
 $10 million total in prizes - $4M cash, 500 devices, nearly $6M in  
 marketing
 Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi  
 Store
 http://p.sf.net/sfu/nokia-dev2dev
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800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






--
Nokia and ATT present the 2010 Calling All Innovators-North America contest
Create new apps  games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store 
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Re: [Jmol-developers] Promising followup to Worrying news for Mac users!

2010-10-22 Thread Jonathan Gutow

I've done a little digging over lunch.  Here's one page that suggests  
that OpenJDK can be installed on MacOS.  Don't know when I'll have  
time to pursue this.  If anyone else can experiment please let us know  
what you discover.

http://wikis.sun.com/display/OpenJDK/Darwin10Build

Jonathan
On Oct 22, 2010, at 8:09 AM, Jonathan Gutow wrote:

 This is definitely not goodThus I think it is in our best interest
 to begin experimenting with OpenJDK on the Mac.  The biggest problem I
 foresee is that this will kill the usefulness of Jmol in web pages on
 MacOS.  We'll be back to the same problem we had with chime where it
 ran on fewer and fewer platforms.  Of course we can also encourage
 people to switch over to Linux.  Most versions are not quite as glitzy
 as MacOS, but like MacOS they're more stable and more functional than
 Windows.

 To some extent I understand the objection to the overhead incurred by
 Java, but for most applications maintaining different code bases for
 different platforms is not necessary to get good performance on a
 modern computer.  I personally hope this ends up hurting Apple.  If
 they don't release the work they've done so far, they really deserve
 to get damaged by this move.

 Jonathan
 On Oct 22, 2010, at 5:48 AM, Egon Willighagen wrote:

 On Fri, Oct 22, 2010 at 12:33 PM, Rzepa, Henry
 h.rz...@imperial.ac.uk wrote:
 http://lists.apple.com/archives/Java-dev/2010/Oct/msg00248.html

 That expresses future aspirations, rather than testable reality.
 There is nothing for
 OS X  at http://openjdk.java.net/

 You can find instructions floating around on the web on how to build
 it... this is one hit:

 http://confluence.concord.org/display/CCTR/Build+OpenJDK+Java+1.7.0+on+Mac+OS+X+10.5

 The argument is that implementing  Java for  OS X would almost
 certainly require Apple to release source code for the graphical
 implementations. If that does not happen, then the actual
 experience on the  Mac may become  a poor one.

 True. Just like we have seen with the Classpath libraries...

 Well, you only payed minimal money for OS/X, so what can you
 expect? ;)

 Jobs appears to want to take  OS X towards  iOS, which is away from
 using a mouse and towards using gestures. I think that adapting
 Java for that sort of environment is going to require major work.

 Yeah, that is one good reason for Jobs to drop Java... of course, if
 he would have gone Open Source, he could have shared this burden...

 Egon

 -- 
 Dr E.L. Willighagen
 Postdoctoral Research Associate
 University of Cambridge
 Homepage: http://egonw.github.com/
 LinkedIn: http://se.linkedin.com/in/egonw
 Blog: http://chem-bla-ics.blogspot.com/
 PubList: http://www.citeulike.org/user/egonw/tag/papers

 --
 Nokia and ATT present the 2010 Calling All Innovators-North America
 contest
 Create new apps  games for the Nokia N8 for consumers in  U.S. and
 Canada
 $10 million total in prizes - $4M cash, 500 devices, nearly $6M in
 marketing
 Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi
 Store
 http://p.sf.net/sfu/nokia-dev2dev
 ___
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 https://lists.sourceforge.net/lists/listinfo/jmol-developers

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 Chemistry Department gu...@uwosh.edu
 UW-Oshkosh   Office: 
 920-424-1326
 800 Algoma Boulevard FAX:920-424-2042
 Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






 --
 Nokia and ATT present the 2010 Calling All Innovators-North America  
 contest
 Create new apps  games for the Nokia N8 for consumers in  U.S. and  
 Canada
 $10 million total in prizes - $4M cash, 500 devices, nearly $6M in  
 marketing
 Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi  
 Store
 http://p.sf.net/sfu/nokia-dev2dev
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






--
Nokia and ATT present the 2010 Calling All Innovators-North America contest
Create new apps  games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java

Re: [Jmol-developers] Call to jmolApplet with AppletID = 0 does not generate jmolApplet0, but some other jmolAppletXX...

2010-10-16 Thread Jonathan Gutow

Bob,

Thanks, that allowed me to track it down.  Thanks for the suggestion...I guess 
it should have been obvious to try getting things to work outside of Sage again 
and then figure out what was going on.  It relates to some bits of Jmol.js that 
I was using modified versions of to deal with the asynchronous updates from the 
server.  I think I have found a way to use  Jmol.js directly in all cases so 
that I don't have to copy updates to specialized functions.  I'll play with it 
some more.  But it looks like it was a bug that was well worth tracking down.  
Things will be much easier to maintain in the future, if I am right.

Jonathan
On Oct 14, 2010, at 8:56 AM, Robert Hanson wrote:

 Good. It must be something very odd about that particular page, I think. 
 
 On Wed, Oct 13, 2010 at 5:16 PM, Jonathan Gutow gu...@uwosh.edu wrote:
 
 On Oct 13, 2010, at 2:57 PM, Robert Hanson wrote:
 
  show me a simpler demo that does this, not the sage page.
 Good, idea.  I can write a simple page that does the wake and sleep on
 two applets, not inside Sage.  Don't think I'll have time the rest of
 the week to work on it.  But I will try to get to it this weekend.  In
 the meantime I have a workaround that solves the problem for Sage.
 Hopefully, we'll track this down.
 
 Jonathan
 
  Dr. Jonathan H. Gutow
 Chemistry Department gu...@uwosh.edu
 UW-Oshkosh   Office:920-424-1326
 800 Algoma Boulevard FAX:920-424-2042
 Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow
 
 
 
 
 
 
 --
 Beautiful is writing same markup. Internet Explorer 9 supports
 standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2  L3.
 Spend less time writing and  rewriting code and more time creating great
 experiences on the web. Be a part of the beta today.
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 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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
 --
 Beautiful is writing same markup. Internet Explorer 9 supports
 standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2  L3.
 Spend less time writing and  rewriting code and more time creating great
 experiences on the web. Be a part of the beta today.
 http://p.sf.net/sfu/beautyoftheweb
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UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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Re: [Jmol-developers] Call to jmolApplet with AppletID = 0 does not generate jmolApplet0, but some other jmolAppletXX...

2010-10-14 Thread Jonathan Gutow

Yeah, that's on my list. It relates to having set antialiasdisplay to
true, but I haven't pursued it beyond that.

Jonathan
On Oct 14, 2010, at 6:21 AM, Robert Hanson wrote:

Jonathan -- something I don't understand. When I go to that site and
ask for the static image, I get messed up numbers -- much larger
font. This is even when I use the latest Jar file:

https://141.233.197.45:4443/home/pub/0/?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar

Since that's the signed applet, I opened a console and saved the PNG
image directly. No problem. What could be going wrong there?

Bob

On Wed, Oct 13, 2010 at 8:45 AM, Jonathan Gutow gu...@uwosh.edu
wrote:
I've encountered the problem on webkit browsers and FF on Mac
Linux. Haven't tested FF Windows.

You can see this problem by going to the link below and performing the
following steps:
https://141.233.197.45:4443/home/pub/0/
***ignore the security warnings. I am using a self-signed certificate
so that my students can use normal campus passwords.
1) Put the first applet (applet0) to sleep by clicking on the Sleep
link.
2) Wake it up by clicking on the Wake link.
3) Try putting it back to sleep.
You will find that applet0 does not exist.

You will have no problem with this cycle with the second applet
(applet1) because that is properly recreated.

Jonathan
On Oct 13, 2010, at 8:03 AM, Angel Herráez wrote:

I had assumed the problem was this test. But your results suggest
not. Is there something earlier or later in the code that is also
checking the appletID? I hadn't noticed anything.

Can't see what or where. jmolApplet() directly calls _jmolApplet()
which tests the ID.

What browser are you testing on? I only did Firefox Win

--
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3.
Spend less time writing and rewriting code and more time creating
great
experiences on the web. Be a part of the beta today.
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Chemistry Department gu...@uwosh.edu
UW-Oshkosh Office:
920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107

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
--
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3.
Spend less time writing and rewriting code and more time creating
great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb
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UW-Oshkosh Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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https

Re: [Jmol-developers] Larger font in exported images...

2010-10-14 Thread Jonathan Gutow

Actually, I was just looking at some images I exported from the
application (12.0.17). I see the same thing when I have set the
antialiasdisplay on. So, I think it is a double application of the
effect to the fonts.

Jonathan
On Oct 14, 2010, at 7:34 AM, Jonathan Gutow wrote:

Yeah, that's on my list. It relates to having set antialiasdisplay to
true, but I haven't pursued it beyond that.

Jonathan
On Oct 14, 2010, at 6:21 AM, Robert Hanson wrote:

Jonathan -- something I don't understand. When I go to that site and
ask for the static image, I get messed up numbers -- much larger
font. This is even when I use the latest Jar file:

https://141.233.197.45:4443/home/pub/0/?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar

Since that's the signed applet, I opened a console and saved the PNG
image directly. No problem. What could be going wrong there?

Bob

On Wed, Oct 13, 2010 at 8:45 AM, Jonathan Gutow gu...@uwosh.edu
wrote:
I've encountered the problem on webkit browsers and FF on Mac
Linux. Haven't tested FF Windows.

You can see this problem by going to the link below and performing
the
following steps:
https://141.233.197.45:4443/home/pub/0/
***ignore the security warnings. I am using a self-signed
certificate
so that my students can use normal campus passwords.
1) Put the first applet (applet0) to sleep by clicking on the Sleep
link.
2) Wake it up by clicking on the Wake link.
3) Try putting it back to sleep.
You will find that applet0 does not exist.

You will have no problem with this cycle with the second applet
(applet1) because that is properly recreated.

Jonathan
On Oct 13, 2010, at 8:03 AM, Angel Herráez wrote:

I had assumed the problem was this test. But your results suggest
not. Is there something earlier or later in the code that is also
checking the appletID? I hadn't noticed anything.

Can't see what or where. jmolApplet() directly calls _jmolApplet()
which tests the ID.

What browser are you testing on? I only did Firefox Win

Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh Office:
920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107

If nature does not answer first what we want,
it is better to take what answer we get.

Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh Office:
920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

--
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3.
Spend less time writing

Re: [Jmol-developers] Call to jmolApplet with AppletID = 0 does not generate jmolApplet0, but some other jmolAppletXX...

2010-10-13 Thread Jonathan Gutow

Maybe the culprit is earlier or later.  I am setting n as a variable  
in a function that calls jmolApplet.  The following change solves the  
problem but it is a bad kludge:

var n = 0;
var nquote = +n;
jmolApplet([width,height],scriptStr, nquote);

This makes a new jmolApplet0 to replace the one that was destroyed.   
Using n directly creates a jmolAppletXX, where XX = _jmol.appletCount.

I had assumed the problem was this test.  But your results suggest  
not.  Is there something earlier or later in the code that is also  
checking the appletID?  I hadn't noticed anything.

Jonathan
On Oct 13, 2010, at 5:21 AM, Angel Herráez wrote:

 Jonathan, I'm running this test (out of Jmol.js):

 var appletCount = 1;
 function test(a,b,nameSuffix) {
 nameSuffix == undefined  (nameSuffix = appletCount);
 alert(nameSuffix);
 }
 var x = 0;
 test(0,0,x); // returns zero
 x = 0;
 test(0,0,x); // returns zero

 So how are you setting the n variable?


 --
 Beautiful is writing same markup. Internet Explorer 9 supports
 standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2  L3.
 Spend less time writing and  rewriting code and more time creating  
 great
 experiences on the web. Be a part of the beta today.
 http://p.sf.net/sfu/beautyoftheweb
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UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






--
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Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
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Re: [Jmol-developers] Call to jmolApplet with AppletID = 0 does not generate jmolApplet0, but some other jmolAppletXX...

2010-10-13 Thread Jonathan Gutow

I've encountered the problem on webkit browsers and FF on Mac   
Linux.  Haven't tested FF Windows.

You can see this problem by going to the link below and performing the  
following steps:
https://141.233.197.45:4443/home/pub/0/
***ignore the security warnings.  I am using a self-signed certificate  
so that my students can use normal campus passwords.
1) Put the first applet (applet0) to sleep by clicking on the Sleep  
link.
2) Wake it up by clicking on the Wake link.
3) Try putting it back to sleep.
You will find that applet0 does not exist.

You will have no problem with this cycle with the second applet  
(applet1)  because that is properly recreated.

Jonathan
On Oct 13, 2010, at 8:03 AM, Angel Herráez wrote:

 I had assumed the problem was this test.  But your results suggest
 not.  Is there something earlier or later in the code that is also
 checking the appletID?  I hadn't noticed anything.

 Can't see what or where. jmolApplet() directly calls _jmolApplet()
 which tests the ID.

 What browser are you testing on? I only did Firefox Win



 --
 Beautiful is writing same markup. Internet Explorer 9 supports
 standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2  L3.
 Spend less time writing and  rewriting code and more time creating  
 great
 experiences on the web. Be a part of the beta today.
 http://p.sf.net/sfu/beautyoftheweb
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






--
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2  L3.
Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb
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Re: [Jmol-developers] Call to jmolApplet with AppletID = 0 does not generate jmolApplet0, but some other jmolAppletXX...

2010-10-13 Thread Jonathan Gutow

Bob,
It doesn't matter.  I've tried it with the old version that is on my  
publicly accessible test site and with the latest version.  The  
problem must be somewhere other than that comparison statement.  If  
you want to verify it for yourself, I am planning to update my  
publicly accessible site.  I can do it in two steps: first I'll update  
Jmol.js ; then later I'll update the Sage js libraries with my  fix.   
I'm mystified, since that is the only place in the code I could find  
anything that  might do what I am seeing.  Again simply passing a  
string representation of the number as the appletID solves the problem  
with both versions of Jmol.js.  For the time being that is what I have  
done for SageMath, but I would like to figure out what is going on.   
I'll keep looking, but if you have any ideas let me know.

thanks,
Jonathan
On Oct 13, 2010, at 12:59 PM, Robert Hanson wrote:

 wrong Jmol.js
 /* Jmol 11.7 script library Jmol.js  12:17 AM 4/20/2009 Bob Hanson

 should be 4/5/2010



 function _jmolApplet(size, inlineModel, script, nameSuffix) {

   /*  AngelH, mar2007
   Fixed percent / pixel business, to avoid browser errors:
   put px where needed, avoid where not. 
   */
   with (_jmol) {
 if (! nameSuffix)
   nameSuffix = appletCount;

 appletSuffixes.push(nameSuffix);
 ++appletCount;






 On Wed, Oct 13, 2010 at 8:45 AM, Jonathan Gutow gu...@uwosh.edu  
 wrote:
 I've encountered the problem on webkit browsers and FF on Mac 
 Linux.  Haven't tested FF Windows.

 You can see this problem by going to the link below and performing the
 following steps:
 https://141.233.197.45:4443/home/pub/0/
 ***ignore the security warnings.  I am using a self-signed certificate
 so that my students can use normal campus passwords.
 1) Put the first applet (applet0) to sleep by clicking on the Sleep
 link.
 2) Wake it up by clicking on the Wake link.
 3) Try putting it back to sleep.
 You will find that applet0 does not exist.

 You will have no problem with this cycle with the second applet
 (applet1)  because that is properly recreated.

 Jonathan
 On Oct 13, 2010, at 8:03 AM, Angel Herráez wrote:

  I had assumed the problem was this test.  But your results suggest
  not.  Is there something earlier or later in the code that is also
  checking the appletID?  I hadn't noticed anything.
 
  Can't see what or where. jmolApplet() directly calls _jmolApplet()
  which tests the ID.
 
  What browser are you testing on? I only did Firefox Win
 
 
 
   
 --
  Beautiful is writing same markup. Internet Explorer 9 supports
  standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2  L3.
  Spend less time writing and  rewriting code and more time creating
  great
  experiences on the web. Be a part of the beta today.
  http://p.sf.net/sfu/beautyoftheweb
  ___
  Jmol-developers mailing list
  Jmol-developers@lists.sourceforge.net
  https://lists.sourceforge.net/lists/listinfo/jmol-developers

  Dr. Jonathan H. Gutow
 Chemistry Department gu...@uwosh.edu
 UW-Oshkosh   Office: 
 920-424-1326
 800 Algoma Boulevard FAX:920-424-2042
 Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






 --
 Beautiful is writing same markup. Internet Explorer 9 supports
 standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2  L3.
 Spend less time writing and  rewriting code and more time creating  
 great
 experiences on the web. Be a part of the beta today.
 http://p.sf.net/sfu/beautyoftheweb
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers



 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107


 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-developers] Call to jmolApplet with AppletID = 0 does not generate jmolApplet0, but some other jmolAppletXX...

2010-10-13 Thread Jonathan Gutow


On Oct 13, 2010, at 2:57 PM, Robert Hanson wrote:

 show me a simpler demo that does this, not the sage page.
Good, idea.  I can write a simple page that does the wake and sleep on  
two applets, not inside Sage.  Don't think I'll have time the rest of  
the week to work on it.  But I will try to get to it this weekend.  In  
the meantime I have a workaround that solves the problem for Sage.   
Hopefully, we'll track this down.

Jonathan

  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-developers] Call to jmolApplet with AppletID = 0 does not generate jmolApplet0, but some other jmolAppletXX...

2010-10-12 Thread Jonathan Gutow

Yes, that would work, but I'm trying to avoid using any of the  
internals of Jmol.js in the code for Sage, in case we decide to change  
the internals.  I think the culprit is the test in _jmolApplet to see  
whether a value was passed in the appletID.  I believe a value of zero  
in appletID returns a false in the if statement, while non-zero #s and  
strings work fine.  I don't think that behavior matches the documented  
behavior of the call.  However, I didn't want to check in a fix  
without making sure what the behavior is supposed to be and that it  
won't mess up some other expected behavior.

Jonathan
On Oct 11, 2010, at 10:55 PM, Robert Hanson wrote:

 Jonathan, if it's important to you to have the applets come in as  
 applet 0, then what you should do is use

 _jmol.appletCount = 0

 and then go from there.

 On Mon, Oct 11, 2010 at 8:39 PM, Jonathan Gutow gu...@uwosh.edu  
 wrote:
 I think this is an issue for Angel.

 When I make the following call on a page that has other applets on  
 it after having destroyed jmolApplet0 to save memory.  It creates an  
 applet that is not given the name jmolApplet0.  I think we are  
 running up against a misinterpretation of 0 in the tests near the  
 beginning of _jmolApplet.

 The call is

 jmolApplet([width,height], scriptStr,n);  //where n = 0, verified by  
 properly setting some other variables.

 This is the last of the fixes for the Jmol in Sage interface  
 update.  A workaround I would like to avoid is to send the zero in  
 quotes (ie. 0).

 Things work as expected for n =1 or greater.

 Jonathan
 Dr. Jonathan H. Gutow
 Chemistry Departmentgu...@uwosh.edu
 UW-Oshkosh  Office:  
 920-424-1326
 800 Algoma BoulevardFAX:920-424-2042
 Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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 Spend less time writing and  rewriting code and more time creating  
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 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107


 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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800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-developers] Call to jmolApplet with AppletID = 0 does not generate jmolApplet0, but some other jmolAppletXX...

2010-10-12 Thread Jonathan Gutow

I'll double check.  I thought so.  I'll probably get back to it this  
evening.

Jonathan
On Oct 12, 2010, at 8:00 AM, Robert Hanson wrote:

 Jonathan,

 That was fixed long ago. Are you using

 http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/appletweb/Jmol.js

 ?

 Bob


 On Tue, Oct 12, 2010 at 7:53 AM, Jonathan Gutow gu...@uwosh.edu  
 wrote:
 Yes, that would work, but I'm trying to avoid using any of the
 internals of Jmol.js in the code for Sage, in case we decide to change
 the internals.  I think the culprit is the test in _jmolApplet to see
 whether a value was passed in the appletID.  I believe a value of zero
 in appletID returns a false in the if statement, while non-zero #s and
 strings work fine.  I don't think that behavior matches the documented
 behavior of the call.  However, I didn't want to check in a fix
 without making sure what the behavior is supposed to be and that it
 won't mess up some other expected behavior.

 Jonathan
 On Oct 11, 2010, at 10:55 PM, Robert Hanson wrote:

  Jonathan, if it's important to you to have the applets come in as
  applet 0, then what you should do is use
 
  _jmol.appletCount = 0
 
  and then go from there.
 
  On Mon, Oct 11, 2010 at 8:39 PM, Jonathan Gutow gu...@uwosh.edu
  wrote:
  I think this is an issue for Angel.
 
  When I make the following call on a page that has other applets on
  it after having destroyed jmolApplet0 to save memory.  It creates an
  applet that is not given the name jmolApplet0.  I think we are
  running up against a misinterpretation of 0 in the tests near the
  beginning of _jmolApplet.
 
  The call is
 
  jmolApplet([width,height], scriptStr,n);  //where n = 0, verified by
  properly setting some other variables.
 
  This is the last of the fixes for the Jmol in Sage interface
  update.  A workaround I would like to avoid is to send the zero in
  quotes (ie. 0).
 
  Things work as expected for n =1 or greater.
 
  Jonathan
  Dr. Jonathan H. Gutow
  Chemistry Departmentgu...@uwosh.edu
  UW-Oshkosh  Office:
  920-424-1326
  800 Algoma BoulevardFAX:920-424-2042
  Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow
 
 
   
 --
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  standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2  L3.
  Spend less time writing and  rewriting code and more time creating
  great
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  --
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  Professor of Chemistry
  St. Olaf College
  1520 St. Olaf Ave.
  Northfield, MN 55057
  http://www.stolaf.edu/people/hansonr
  phone: 507-786-3107
 
 
  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
   
 --
  Beautiful is writing same markup. Internet Explorer 9 supports
  standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2  L3.
  Spend less time writing and  rewriting code and more time creating
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 Chemistry Department gu...@uwosh.edu
 UW-Oshkosh   Office: 
 920-424-1326
 800 Algoma Boulevard FAX:920-424-2042
 Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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 Spend less time writing and  rewriting code and more time creating  
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 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107


 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

Re: [Jmol-developers] Call to jmolApplet with AppletID = 0 does not generate jmolApplet0, but some other jmolAppletXX...

2010-10-12 Thread Jonathan Gutow

Let me check that I didn't accidentally pick up an outdated Jmol.js, I  
should get a chance this evening (its on my home computer).  That line  
doesn't look like what I remember.  Thanks for looking into it.  If  
we've got a fixed version already, then I'm in good shape.

Jonathan
On Oct 12, 2010, at 1:41 PM, Angel Herráez wrote:

 Jonathan, I know what you mean. The idea is that zero may be taken  
 as false (no id
 provided). However, my test now seems to behave (12.1.14)

 The line in Jmol.js that does the trick says
   nameSuffix == undefined  (nameSuffix = appletCount);

 but I really don't understand how this code works.

 What exact code are you using to destroy and recreate the applet?
 I have tried
 function destroy() {
  document.getElementById(cont).innerHTML=;
 }
 function create() {
  jmolSetDocument(0)
  document.getElementById(cont).innerHTML =  
 jmolApplet([width,height], scriptStr, n)
 }

 where cont is a div containing the applet




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Re: [Jmol-developers] Call to jmolApplet with AppletID = 0 does not generate jmolApplet0, but some other jmolAppletXX...

2010-10-12 Thread Jonathan Gutow

Bob,

This still doesn't work as it interprets a numeric zero as undefined.  Turning 
the zero into a string representation of zero causes the proper naming to be 
used.  You may be running up against the fact that different browsers return 
different things.  I've found I have to check for undefined, 'undefined', null 
and 'null' to cover all the browser variants.  How about:

if (!nameSuffix  nameSuffix!=0) nameSuffix = appletCount;

Jonathan


On Oct 12, 2010, at 5:19 PM, Robert Hanson wrote:

 
 
 2010/10/12 Angel Herráez angel.herr...@uah.es
 Jonathan, I know what you mean. The idea is that zero may be taken as false 
 (no id
 provided). However, my test now seems to behave (12.1.14)
 
 The line in Jmol.js that does the trick says
   nameSuffix == undefined  (nameSuffix = appletCount);
 
 but I really don't understand how this code works.
 
 
 It says: If nameSuffix is undefined, then assign the value of appletCount to 
 nameSuffix.
 
  
 What exact code are you using to destroy and recreate the applet?
 I have tried
 function destroy() {
  document.getElementById(cont).innerHTML=;
 }
 function create() {
  jmolSetDocument(0)
  document.getElementById(cont).innerHTML = jmolApplet([width,height], 
 scriptStr, n)
 }
 
 where cont is a div containing the applet
 
 
 
 
 --
 Beautiful is writing same markup. Internet Explorer 9 supports
 standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2  L3.
 Spend less time writing and  rewriting code and more time creating great
 experiences on the web. Be a part of the beta today.
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 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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
 --
 Beautiful is writing same markup. Internet Explorer 9 supports
 standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2  L3.
 Spend less time writing and  rewriting code and more time creating great
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800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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[Jmol-developers] Call to jmolApplet with AppletID = 0 does not generate jmolApplet0, but some other jmolAppletXX...

2010-10-11 Thread Jonathan Gutow

I think this is an issue for Angel.

When I make the following call on a page that has other applets on it after 
having destroyed jmolApplet0 to save memory.  It creates an applet that is not 
given the name jmolApplet0.  I think we are running up against a 
misinterpretation of 0 in the tests near the beginning of _jmolApplet.

The call is

jmolApplet([width,height], scriptStr,n);  //where n = 0, verified by properly 
setting some other variables.

This is the last of the fixes for the Jmol in Sage interface update.  A 
workaround I would like to avoid is to send the zero in quotes (ie. 0).

Things work as expected for n =1 or greater.

Jonathan
 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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Re: [Jmol-developers] current work/double bond view...

2010-09-17 Thread Jonathan Gutow

I've played with Bob's example and here is my opinion.  Before I used  
Jmol I thought the default should be double bonds all in one plane,  
but now feel that Jmol's present default where you see the double  
bonds no matter what the viewing angle is better.  I do think the  
scale of the double bond should be set smaller than the current  
default and like the idea of an option to make the double bond plane  
fixed relative to the molecule axes.  The double bonds in a fixed  
plane should be an option not the default.

Should we do a poll and maybe on the user's list?

Joanthan
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
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Re: [Jmol-developers] current work

2010-09-15 Thread Jonathan Gutow


On Sep 15, 2010, at 10:41 AM, Robert Hanson wrote:

 -- proposing a NEW DEFAULT for Jmol for 12.1 and 12.0:
   double bonds in the plane of the atoms, not twisty with  
 orientation.
This is the default I always expected, but the current default makes  
sure that you can tell which are double bonds. I'm  not sure if I  
really want it changed to what I expected
   double bond cylinders somewhat smaller than single bond  
 cylinders
 this is very good.
 -- smooth on-the-fly language switching
+
  Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow






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Re: [Jmol-developers] Error reading UHF GAMESS output...

2010-08-19 Thread Jonathan Gutow

It appears we have more problems than just the slight change in file 
format...At some point we changed things so that in UHF files (even the old 
format) the beta set of orbitals is not read.  I guess I haven't checked this 
in about 6-8 months.  Bob, I may need you to help me on this.

Jonathan
 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
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Re: [Jmol-developers] BCCE Workshop - Advanced Jmol / bug report

2010-08-19 Thread Jonathan Gutow

Bob,
Thanks.  You understand those readers better than I do.  I'll take a  
peek and see if my solution was anything like yours.

Jonathan
On Aug 19, 2010, at 8:33 AM, Robert Hanson wrote:

 done. I think this got included in 12.0.7 and 12.1.5

 On Wed, Aug 18, 2010 at 4:48 PM, Jonathan Gutow gu...@uwosh.edu  
 wrote:
 We'll figure it out.  I need to get my copy up and running again an  
 verify that that is now the consistent output format.
 On Aug 18, 2010, at 3:17 PM, Whitwell, George wrote:

  I can't imagine that it is.  The input file is about as simple as  
 it could be.
  The same line and row of hyphens appears in the acceptable file,  
 although preceded by different info:
 
  UHF=== OUTPUT
   -
   DENSITY CONVERGED
   -
 
  FINAL UHF ENERGY IS -107.5006542361 AFTER   6 ITERATIONS
 
   
   SPIN SZ   =0.000
   S-SQUARED =0.000
   
 
  LZ VALUE ANALYSIS FOR THE MOS
  
 
  RHF===OUTPUT
   -
   DENSITY CONVERGED
   -
  TIME TO FORM FOCK OPERATORS=   0.0 SECONDS (   0.0 SEC/ 
 ITER)
  TIME TO SOLVE SCF EQUATIONS=   0.0 SECONDS (   0.0 SEC/ 
 ITER)
 
  FINAL RHF ENERGY IS -107.5006542361 AFTER   6 ITERATIONS
 
  LZ VALUE ANALYSIS FOR THE MOS
  
 
  Could the intervening stuff be offending your reader?
 
 
  -Original Message-
  From: Jonathan Gutow [mailto:gu...@uwosh.edu]
  Sent: Wednesday, August 18, 2010 4:05 PM
  To: jmol-developers@lists.sourceforge.net
  Cc: Whitwell, George
  Subject: Re: [Jmol-developers] BCCE Workshop - Advanced Jmol / bug  
 report
 
  It seems to be coughing on the following line...
 
  LZ VALUE ANALYSIS FOR THE MOS
  
  I'm not sure what this is.  It relates to something called the LZ  
 degeneracy tolerance.  I don't see it in UHF calculation I've done  
 using GAMESS-US.
 
  George is this a special setting?
 
  Jonathan
  On Aug 18, 2010, at 2:40 PM, Jonathan Gutow wrote:
 
  It definitely doesn't work...This will take a little  
 tracing...I've certainly loaded unrestricted calculations before.   
 Thanks for spotting this.
  Jonathan
  On Aug 18, 2010, at 1:52 PM, Whitwell, George wrote:
 
  Bob et al,
  I greatly enjoyed the workshop and am on my way to including  
 Jmol in my teaching materials.  I'll let you know if anything  
 special pops out.
 
  I mentioned to Jonathan a problem I found reading GAMESS output  
 files.  If I use SCFTYP=UHF, Jmol chokes on the output.  I've  
 attached example files.
 
  Thanks,
  George
 
  Dr. George E. Whitwell
  Assistant Professor - Chemistry
  North Carolina Wesleyan College
  Rocky Mount, NC
  (252) 985-5159
  gwhitw...@ncwc.edu
 
  WGoutput.zip
 
  Dr. Jonathan H. Gutow
  Chemistry Departmentgu...@uwosh.edu
  UW-Oshkosh  Office:  
 920-424-1326
  800 Algoma BoulevardFAX: 
 920-424-2042
  Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow
 
   
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 920-424-1326
  800 Algoma BoulevardFAX:920-424-2042
  Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow
 
 

 Dr. Jonathan H. Gutow
 Chemistry Departmentgu...@uwosh.edu
 UW-Oshkosh  Office:  
 920-424-1326
 800 Algoma BoulevardFAX:920-424-2042
 Oshkosh, WI 54901
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 St. Olaf College
 1520 St. Olaf Ave.
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Re: [Jmol-developers] BCCE Workshop - Advanced Jmol / bug report

2010-08-18 Thread Jonathan Gutow

It definitely doesn't work...This will take a little tracing...I've certainly 
loaded unrestricted calculations before.  Thanks for spotting this.  
Jonathan
On Aug 18, 2010, at 1:52 PM, Whitwell, George wrote:

 Bob et al,
 I greatly enjoyed the workshop and am on my way to including Jmol in my 
 teaching materials.  I’ll let you know if anything special pops out.
  
 I mentioned to Jonathan a problem I found reading GAMESS output files.  If I 
 use SCFTYP=UHF, Jmol chokes on the output.  I’ve attached example files.
  
 Thanks,
 George
  
 Dr. George E. Whitwell
 Assistant Professor – Chemistry
 North Carolina Wesleyan College
 Rocky Mount, NC
 (252) 985-5159
 gwhitw...@ncwc.edu
  
 WGoutput.zip

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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Re: [Jmol-developers] BCCE Workshop - Advanced Jmol / bug report

2010-08-18 Thread Jonathan Gutow

It seems to be coughing on the following line...

LZ VALUE ANALYSIS FOR THE MOS
 
I'm not sure what this is.  It relates to something called the LZ degeneracy 
tolerance.  I don't see it in UHF calculation I've done using GAMESS-US. 

George is this a special setting?

Jonathan
On Aug 18, 2010, at 2:40 PM, Jonathan Gutow wrote:

 It definitely doesn't work...This will take a little tracing...I've certainly 
 loaded unrestricted calculations before.  Thanks for spotting this.  
 Jonathan
 On Aug 18, 2010, at 1:52 PM, Whitwell, George wrote:
 
 Bob et al,
 I greatly enjoyed the workshop and am on my way to including Jmol in my 
 teaching materials.  I’ll let you know if anything special pops out.
  
 I mentioned to Jonathan a problem I found reading GAMESS output files.  If I 
 use SCFTYP=UHF, Jmol chokes on the output.  I’ve attached example files.
  
 Thanks,
 George
  
 Dr. George E. Whitwell
 Assistant Professor – Chemistry
 North Carolina Wesleyan College
 Rocky Mount, NC
 (252) 985-5159
 gwhitw...@ncwc.edu
  
 WGoutput.zip
 
  Dr. Jonathan H. Gutow
 Chemistry Departmentgu...@uwosh.edu
 UW-Oshkosh  Office: 920-424-1326
 800 Algoma BoulevardFAX:920-424-2042
 Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow
 
 --
 This SF.net email is sponsored by 
 
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 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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Re: [Jmol-developers] BCCE Workshop - Advanced Jmol / bug report

2010-08-18 Thread Jonathan Gutow

We'll figure it out.  I need to get my copy up and running again an verify that 
that is now the consistent output format.  
On Aug 18, 2010, at 3:17 PM, Whitwell, George wrote:

 I can't imagine that it is.  The input file is about as simple as it could 
 be.  
 The same line and row of hyphens appears in the acceptable file, although 
 preceded by different info:
 
 UHF=== OUTPUT
  -
  DENSITY CONVERGED
  -
 
 FINAL UHF ENERGY IS -107.5006542361 AFTER   6 ITERATIONS
 
  
  SPIN SZ   =0.000
  S-SQUARED =0.000
  
 
 LZ VALUE ANALYSIS FOR THE MOS
 
 
 RHF===OUTPUT
  -
  DENSITY CONVERGED
  -
 TIME TO FORM FOCK OPERATORS=   0.0 SECONDS (   0.0 SEC/ITER)
 TIME TO SOLVE SCF EQUATIONS=   0.0 SECONDS (   0.0 SEC/ITER)
 
 FINAL RHF ENERGY IS -107.5006542361 AFTER   6 ITERATIONS
 
 LZ VALUE ANALYSIS FOR THE MOS
 
 
 Could the intervening stuff be offending your reader?
 
 
 -Original Message-
 From: Jonathan Gutow [mailto:gu...@uwosh.edu] 
 Sent: Wednesday, August 18, 2010 4:05 PM
 To: jmol-developers@lists.sourceforge.net
 Cc: Whitwell, George
 Subject: Re: [Jmol-developers] BCCE Workshop - Advanced Jmol / bug report
 
 It seems to be coughing on the following line...
 
 LZ VALUE ANALYSIS FOR THE MOS
 
 I'm not sure what this is.  It relates to something called the LZ degeneracy 
 tolerance.  I don't see it in UHF calculation I've done using GAMESS-US. 
 
 George is this a special setting?
 
 Jonathan
 On Aug 18, 2010, at 2:40 PM, Jonathan Gutow wrote:
 
 It definitely doesn't work...This will take a little tracing...I've 
 certainly loaded unrestricted calculations before.  Thanks for spotting 
 this.  
 Jonathan
 On Aug 18, 2010, at 1:52 PM, Whitwell, George wrote:
 
 Bob et al,
 I greatly enjoyed the workshop and am on my way to including Jmol in my 
 teaching materials.  I'll let you know if anything special pops out.
 
 I mentioned to Jonathan a problem I found reading GAMESS output files.  If 
 I use SCFTYP=UHF, Jmol chokes on the output.  I've attached example files.
 
 Thanks,
 George
 
 Dr. George E. Whitwell
 Assistant Professor - Chemistry
 North Carolina Wesleyan College
 Rocky Mount, NC
 (252) 985-5159
 gwhitw...@ncwc.edu
 
 WGoutput.zip
 
 Dr. Jonathan H. Gutow
 Chemistry Departmentgu...@uwosh.edu
 UW-Oshkosh  Office: 920-424-1326
 800 Algoma BoulevardFAX:920-424-2042
 Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow
 
 --
 This SF.net email is sponsored by 
 
 Make an app they can't live without
 Enter the BlackBerry Developer Challenge
 http://p.sf.net/sfu/RIM-dev2dev 
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers
 
 Dr. Jonathan H. Gutow
 Chemistry Departmentgu...@uwosh.edu
 UW-Oshkosh  Office: 920-424-1326
 800 Algoma BoulevardFAX:920-424-2042
 Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow
 
 

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow


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