date:20131219

Re: [Jmol-users] an error in chrome?

2013-12-19 Thread Rolf Huehne

Am 20.12.2013 01:12, schrieb Pshemak Maslak:
> I am referring to: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?USE=HTML5
>
> Loading spartan (load data/square_planar.spartan) or xyx.gz files (load
> data/water.xyz.gz)in Chrome (but not in Firefox) gives an error popup:
>
> " JmolCore.js: synchronous binary file transfer is requested but not
> available
>
> The models load as expected when the message is dismissed (OK).
>
> 1. Is this related to:
> http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Reading_binary_files?
>
Yes.

> 2. Is that expected behavior? Can that popup be removed?
>
Yes, it is the expected behaviour for binary transfers in Chrome. You 
can deactivate the popup by setting a variable to 'false' before 
actually initializing JSmol:

   Jmol._alertNoBinary = false;

Regards,
Rolf

-- 

Rolf Huehne
Postdoc

Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@fli-leibniz.de
Website: http://www.fli-leibniz.de

   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Dennys Klein

VAT No: DE 153 925 464
Register of Associations: No. 296, Amtsgericht Jena
Tax Number: 162/141/08228


--
Rapidly troubleshoot problems before they affect your business. Most IT 
organizations don't have a clear picture of how application performance 
affects their revenue. With AppDynamics, you get 100% visibility into your 
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] an error in chrome?

2013-12-19 Thread Pshemak Maslak


I am referring to: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?USE=HTML5

Loading spartan (load data/square_planar.spartan) or xyx.gz files (load 
data/water.xyz.gz)in Chrome (but not in Firefox) gives an error popup:


   " JmolCore.js: synchronous binary file transfer is requested but not
   available

The models load as expected when the message is dismissed (OK).

1. Is this related to: 
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Reading_binary_files?


2. Is that expected behavior?  Can that popup be removed?

PM




--
Rapidly troubleshoot problems before they affect your business. Most IT 
organizations don't have a clear picture of how application performance 
affects their revenue. With AppDynamics, you get 100% visibility into your 
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] passing commands across frames

2013-12-19 Thread Robert Hanson

There's no problem with j2s location breaking anything that I know of.


On Thu, Dec 19, 2013 at 3:39 PM, adriano ceccarelli <
adriano.ceccare...@unito.it> wrote:

> Dear Bob,
> thanks very much for your help.
>
> Having seen that the misplacement of the J2S folder breaks the
> jmol-to-jsmol conversion, and having decided that one copy of J2S in each
> subfolder of my site is definitely too much…. :-))  I was just trying to
> re-write the whole thing with JSmol, so the former jmobutton’s are now
> jmol.jmolbutton’s, etc. Would that work across frames in the way you
> suggested? I tried to make it work but to no avail…. may be it’s me… :-((
>
> Ciao
>
> Adriano
>
>
> Il giorno 18/dic/2013, alle ore 19:32, Robert Hanson 
> ha scritto:
>
> OK, I see. What you need to do is to define one frame's variables in terms
> of the other. Presumably you have JSmol.min.js loading into each frame,
> right? Then to set the controls on frameB to run commands in FrameA if they
> are Jmol buttons, you must execute:
>
> frameB.Jmol = frameA.Jmol
>
> and, possibly, if your applet is named "jmolApplet0"
>
> frameB.jmolApplet0 = frameA.jmolApplet0
>
>
> Bob
>
>
>
> On Wed, Dec 18, 2013 at 12:09 PM, Robert Hanson wrote:
>
>> Yes, that could be a problem. The methods of one frame are probably not
>> usable by another frame because they see different variable spaces. I'm
>> afraid JSmol is not "frame-friendly" (I'm assuming these are really old
>> pages, right? I hope you are not using frames still for new designs.) I'll
>> take a quick look.
>>
>>
>> On Tue, Dec 17, 2013 at 10:01 AM, adriano ceccarelli <
>> adriano.ceccare...@unito.it> wrote:
>>
>>> Dear all,
>>> having to deal with JSmol and frames, the applet in one frame and the
>>> various buttons etc on the other frame, I notice that the latter will not
>>> pass on anything to the applet. However, using ordinary href or button tags
>>> and appropriately targeting the frame with the applet seems to work. I was
>>> just curious to understand why it is so (my mistake? JSmol limit? bug?),
>>> and if there is a way out or if I should convert all the pre-existing into
>>> ordinary tags.
>>> Namely, a jmolbutton will work as a , a jmolHtml will
>>> work as a  while I can’t see what could replace a JmolRadioGroup.
>>>
>>> All comments/suggestions very much appreciated
>>>
>>> Thanks
>>> Ciao
>>>
>>> Adriano
>>>
>>>*Prof. Adriano Ceccarelli*
>>> *Università degli Studi di Torino*
>>> *Neuroscience Institute Cavalieri Ottolenghi*
>>> *Dipartimento di Scienze Cliniche e Biologiche*
>>> *Regione Gonzole 10, 10043 Orbassano (Torino) - Italy*
>>> *office: +39(0)116705409 <%2B39%280%29116705409>*
>>> *fax: +39(0)112365409 <%2B39%280%29112365409>*
>>> *mail: adriano.ceccare...@unito.it *
>>>
>>>
>>>
>>> --
>>> Rapidly troubleshoot problems before they affect your business. Most IT
>>> organizations don't have a clear picture of how application performance
>>> affects their revenue. With AppDynamics, you get 100% visibility into
>>> your
>>> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of
>>> AppDynamics Pro!
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
> --
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics
> Pro!
>
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get

Re: [Jmol-users] minimize constraints in a script

2013-12-19 Thread Whitwell, George

Perfect, thanks.

We're having some fun, now.

George

From: Robert Hanson [hans...@stolaf.edu]
Sent: Wednesday, December 18, 2013 10:15 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] minimize constraints in a script

Generally the minimization runs in its own thread. If it is desired to wait 
until the process has completed prior to continuing, use set 
useMinimizationThread false.

So I'm guessing that without that the rotation command halts the ongoing 
minimization before you notice anything.

On Wed, Dec 18, 2013 at 7:19 PM, Whitwell, George 
mailto:gwhitw...@ncwc.edu>> wrote:

Greetings,

I'm trying to explore rotational steric hindrance with partial success.  From 
the console, this series of commands:

minimize constraint {C5} {C3} {C1} {H6} 60   // or whatever angle is 
indicated

minimize

minimize energy

work as advertised.  I can:

rotate branch {C3} {C1} 60 60

and repeat the minimization at a new torsion angle.  Of course, I want to use 
the power of Jmol script to automate the investigation.  When I run these lines:

zap; load SYNC "file:///C:/Compchem/s-pentane/spentane.xyz"

rotdeg = 120

var steps=360/rotdeg

measure delete

measure {C5}{C3}{C1}{H6}

for (var i=0;ihttp://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

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

--
Rapidly troubleshoot problems before they affect your business. Most IT 
organizations don't have a clear picture of how application performance 
affects their revenue. With AppDynamics, you get 100% visibility into your 
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] why do I get averaged values?

2013-12-19 Thread Whitwell, George

Mastery is a beautiful thing.  I was forgetting that I was using array methods. 
 Thanks for your patience.

The label approach had completely eluded me, as well.  Bonus!

Cheers, George


From: Robert Hanson [hans...@stolaf.edu]
Sent: Wednesday, December 18, 2013 12:51 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] why do I get avereaged values?

You're forgetting that

({1.53}[1][17]).elemno

is an average.

You are using array methods, so add ".all" to those:



print 
({1.53}[1][17]).element.all.add("\t").add(({1.53}[1][17]).elemno.all).add("\t").add(({1.53}[1][17]).x.all).add("\t").add(({1.53}[1][17]).y.all).add("\t").add(({1.53}[1][17]).z.all)


but it might be simpler to use:

print {1.53}[1][17].label("%[element]\t%[elemno]\t%x\t%y\t%z")

in which case the formatting could be nicer:

print {1.53}[1][17].label("%[element]\t%[elemno]\t%5.3x\t%5.3y\t%5.3z")

or even

print {1.53}[1][17].label("%-3[element]%4.0[elemno]%10.3[xyz]")


Bob


On Wed, Dec 18, 2013 at 10:32 AM, Whitwell, George 
mailto:gwhitw...@ncwc.edu>> wrote:

when I use a command like:



print 
({1.53}[1][17]).element.add("\t").add(({1.53}[1][17]).elemno).add("\t").add(({1.53}[1][17]).x).add("\t").add(({1.53}[1][17]).y).add("\t").add(({1.53}[1][17]).z)



result:

C 2.4705882 -0.08696627 -0.8534151 1.8308194
C 2.4705882 -0.08696627 -0.8534151 1.8308194
C 2.4705882 -0.08696627 -0.8534151 1.8308194
C 2.4705882 -0.08696627 -0.8534151 1.8308194
C 2.4705882 -0.08696627 -0.8534151 1.8308194
H 2.4705882 -0.08696627 -0.8534151 1.8308194
H 2.4705882 -0.08696627 -0.8534151 1.8308194
H 2.4705882 -0.08696627 -0.8534151 1.8308194
H 2.4705882 -0.08696627 -0.8534151 1.8308194
H 2.4705882 -0.08696627 -0.8534151 1.8308194
H 2.4705882 -0.08696627 -0.8534151 1.8308194
H 2.4705882 -0.08696627 -0.8534151 1.8308194
H 2.4705882 -0.08696627 -0.8534151 1.8308194
H 2.4705882 -0.08696627 -0.8534151 1.8308194
H 2.4705882 -0.08696627 -0.8534151 1.8308194
H 2.4705882 -0.08696627 -0.8534151 1.8308194
H 2.4705882 -0.08696627 -0.8534151 1.8308194



the atoms really are different, evidenced by C and H in the output or as 
produced by:

 print 
({1.53}[1]).element.add("\t").add(({1.53}[1]).elemno).add("\t").add(({1.53}[1]).x).add("\t").add(({1.53}[1]).y).add("\t").add(({1.53}[1]).z)



result:
C 6 0.5630599 -1.1161811 1.47227



or:

print data({1.53},"xyz")



result:
17

C 0.56306   -1.116181.47227
C 0.57693   -2.346392.38065
C-0.82581   -0.787670.89831
C 1.221540.082812.15912
C-1.84993   -0.206571.87432
H 1.18245   -1.364360.61213
H 1.59096   -2.590172.67957
H 0.16333   -3.212661.87410
H 0.00023   -2.186283.28660
H 1.223700.954451.51206
H 2.25210   -0.142882.41288
H 0.710770.350293.07788
H-1.23407   -1.690830.45199
H-0.69344   -0.082740.08138
H-2.79985   -0.058831.37170
H-1.533910.755032.26115
H-2.02649   -0.865072.71782



I've tried other approaches to producing data with the "symbol, atno, x, y, z" 
format, such as:

modnum = 15

atnum = 17

for (var i=0;ihttp://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users




--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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

--
Rapidly troubleshoot problems before they affect your business. Most IT 
organizations don't have a clear picture of how application performance 
affects their revenue. With AppDynamics, you get 100% visibility into your 
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] help on conversion to Jmol 14/JSmol

2013-12-19 Thread Paul Pillot

It is but some platform report that java is enabled even when it is not…
Paul

Le 19 déc. 2013 à 11:24, Rolf Huehne  a écrit :

> Am 19.12.2013 17:17, schrieb Angel Herráez:
>> Note there is no automatic switch. Just not possible to detect Java
>> any more.
>> 
> I just asked a few days ago if the automatic detection of platforms not 
> providing Java is still there and Bob replied that it is.
> 
> Regards,
> Rolf
> -- 
> 
> Rolf Huehne
> Postdoc
> 
> Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
> Beutenbergstrasse 11
> 07745 Jena, Germany
> 
> Phone:   +49 3641 65 6205
> Fax: +49 3641 65 6210
> E-Mail:  rhue...@fli-leibniz.de
> Website: http://www.fli-leibniz.de
> 
>   Scientific Director: Prof. Dr. K. Lenhard Rudolph
>Head of Administration: Dr. Daniele Barthel
> Chairman of Board of Trustees: Dennys Klein
> 
> VAT No: DE 153 925 464
> Register of Associations: No. 296, Amtsgericht Jena
> Tax Number: 162/141/08228
> 
> 
> --
> Rapidly troubleshoot problems before they affect your business. Most IT 
> organizations don't have a clear picture of how application performance 
> affects their revenue. With AppDynamics, you get 100% visibility into your 
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users


--
Rapidly troubleshoot problems before they affect your business. Most IT 
organizations don't have a clear picture of how application performance 
affects their revenue. With AppDynamics, you get 100% visibility into your 
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] passing commands across frames

2013-12-19 Thread adriano ceccarelli

Dear Bob, 
thanks very much for your help.

Having seen that the misplacement of the J2S folder breaks the jmol-to-jsmol 
conversion, and having decided that one copy of J2S in each subfolder of my 
site is definitely too much…. :-))  I was just trying to re-write the whole 
thing with JSmol, so the former jmobutton’s are now jmol.jmolbutton’s, etc. 
Would that work across frames in the way you suggested? I tried to make it work 
but to no avail…. may be it’s me… :-((

Ciao

Adriano


Il giorno 18/dic/2013, alle ore 19:32, Robert Hanson  ha 
scritto:

> OK, I see. What you need to do is to define one frame's variables in terms of 
> the other. Presumably you have JSmol.min.js loading into each frame, right? 
> Then to set the controls on frameB to run commands in FrameA if they are Jmol 
> buttons, you must execute:
> 
> frameB.Jmol = frameA.Jmol
> 
> and, possibly, if your applet is named "jmolApplet0"
> 
> frameB.jmolApplet0 = frameA.jmolApplet0
> 
> 
> Bob
> 
> 
> 
> On Wed, Dec 18, 2013 at 12:09 PM, Robert Hanson  wrote:
> Yes, that could be a problem. The methods of one frame are probably not 
> usable by another frame because they see different variable spaces. I'm 
> afraid JSmol is not "frame-friendly" (I'm assuming these are really old 
> pages, right? I hope you are not using frames still for new designs.) I'll 
> take a quick look.  
> 
> 
> On Tue, Dec 17, 2013 at 10:01 AM, adriano ceccarelli 
>  wrote:
> Dear all,
> having to deal with JSmol and frames, the applet in one frame and the various 
> buttons etc on the other frame, I notice that the latter will not pass on 
> anything to the applet. However, using ordinary href or button tags and 
> appropriately targeting the frame with the applet seems to work. I was just 
> curious to understand why it is so (my mistake? JSmol limit? bug?), and if 
> there is a way out or if I should convert all the pre-existing into ordinary 
> tags.
> Namely, a jmolbutton will work as a , a jmolHtml will work 
> as a  while I can’t see what could replace a JmolRadioGroup.
> 
> All comments/suggestions very much appreciated
> 
> Thanks
> Ciao
> 
> Adriano
> 
> Prof. Adriano Ceccarelli
> Università degli Studi di Torino
> Neuroscience Institute Cavalieri Ottolenghi
> Dipartimento di Scienze Cliniche e Biologiche
> Regione Gonzole 10, 10043 Orbassano (Torino) - Italy
> office: +39(0)116705409
> fax: +39(0)112365409
> mail: adriano.ceccare...@unito.it
> 
> 
> --
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> 
> 
> 
> -- 
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
> 
> 
> If nature does not answer first what we want,
> it is better to take what answer we get. 
> 
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> 
> 
> 
> 
> -- 
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
> 
> 
> If nature does not answer first what we want,
> it is better to take what answer we get. 
> 
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> 
> --
> Rapidly troubleshoot problems before they affect your business. Most IT 
> organizations don't have a clear picture of how application performance 
> affects their revenue. With AppDynamics, you get 100% visibility into your 
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

--
Rapidly troubleshoot problems before they affect your business. Most IT 
organizations don't have a clear picture of how application performance 
affects their revenue. With AppDynamics, you get 100% visibility into your 
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] help on conversion to Jmol 14/JSmol

2013-12-19 Thread Angel Herráez

Note there is no automatic switch. Just not possible to detect Java 
any more.

1. The page source may by default activate either Java or HTML5 
formats.
2. If the URL has the special switch, it will override what the page 
source has. (I haven't experimented with this switch yet, implemented 
in Jmol 14)
3. You may add in your page source some javascript that detects e.g. 
the userAgent string and acts accordingly in setting the default 
variant. This I have done in a couple of pages. It is not fully 
foolproof since it relies of the userAgent. You may try to target 
Android and iOS devices.
4. In addition, you can add 2 links or buttons in your page that will 
reload with either option, Java or HTML5, per user choice. In that 
way no one will be cornered into a version that does not work in 
their system. It is also possible without page reload, reinjecting 
the Jmol object code into its container.

Sorry I cannot be more explanative now. Too many things to do before 
the holidays!
Henry, I will be happy to work along with you if you need help on 
this, at some later dates.





--
Rapidly troubleshoot problems before they affect your business. Most IT 
organizations don't have a clear picture of how application performance 
affects their revenue. With AppDynamics, you get 100% visibility into your 
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] help on conversion to Jmol 14/JSmol

2013-12-19 Thread Rolf Huehne

Am 19.12.2013 17:17, schrieb Angel Herráez:
> Note there is no automatic switch. Just not possible to detect Java
> any more.
>
I just asked a few days ago if the automatic detection of platforms not 
providing Java is still there and Bob replied that it is.

Regards,
Rolf
-- 

Rolf Huehne
Postdoc

Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@fli-leibniz.de
Website: http://www.fli-leibniz.de

   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Dennys Klein

VAT No: DE 153 925 464
Register of Associations: No. 296, Amtsgericht Jena
Tax Number: 162/141/08228


--
Rapidly troubleshoot problems before they affect your business. Most IT 
organizations don't have a clear picture of how application performance 
affects their revenue. With AppDynamics, you get 100% visibility into your 
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] help on conversion to Jmol 14/JSmol

2013-12-19 Thread Rolf Huehne

Am 19.12.2013 13:39, schrieb Jakubowski, Henry:
> Hi,
>
> I have what I believe is a trivial problem (for everyone but me) on
> converting Jmol 12 files to Jmol 14/JSmol, but as I am more of a
> cut-and-paste creator of Jmol files, I thought I would seek outside help.
>
> I’ve created about 100 Jmol files
> (http://employees.csbsju.edu/hjakubowski/classes/ch331/bcintro/list_of_Chime.htm)
> to accompany my web biochemistry book
> (http://employees.csbsju.edu/hjakubowski/classes/ch331/bcintro/default.html
> ).
>
> They are all based on Jmol 12. I just converted one after downloading
> the latest version of Jmol (14.1.3) yesterday. I modified a template
> model from David Marcey and Molvisions and pasted in button commands
> from my previous Jmol 12 verison. It works well on my PCs using all
> browsers.
>
> Here is the new
> file:http://employees.csbsju.edu/hjakubowski/Jmol14/Nucleosome/Nucleosome.htm
> .
>
> Somehow I magically thought it would work on my Nexus Android tablet as
> well. It didn’t as the file loads as a Jmol and not a JSmol file.
>
> I would greatly appreciate it if someone could look at the code and
> suggest changes I could make to allow my files to work on any platform
> (if this is possible). I think the fix is trivial (but again not for me).
>
> Once I get this file working well, I want to use it as a template to
> convert the rest over time.
>
JSmol is working with your example, at least on my Laptop. I could 
activate it sucessfully by adding the corresponding parameter to your 
example URL:
http://employees.csbsju.edu/hjakubowski/Jmol14/Nucleosome/Nucleosome.htm?_USE=HTML5

If this also works on your Android tablet it seems "just" to be a 
problem of the automatic switch. Maybe the "magic" behind this switch 
doesn't work well enough yet.
One way to overcome this would be by adding a manual switch between Jmol 
and JSmol.
Another way would be to use JSmol as default. But this will depend for 
example on the number of atoms in the other structures loaded in your 
pages. On my configuration JSmol handles the 13,000 Atoms from the 
nucleosome page fast enough. But I know that in other configurations 
JSmol might be ten times slower, which might be too slow as a default.
Or one could try to improve the automatic switch, for example by adding 
an Android-specific switch. Although there is Java supposed to be 
generally available on Android it is said to need specifically compiled 
Java programs. So the standard Jmol applet should never work on Android 
platforms.

Regards,
Rolf

-- 

Rolf Huehne
Postdoc

Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@fli-leibniz.de
Website: http://www.fli-leibniz.de

   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Dennys Klein

VAT No: DE 153 925 464
Register of Associations: No. 296, Amtsgericht Jena
Tax Number: 162/141/08228


--
Rapidly troubleshoot problems before they affect your business. Most IT 
organizations don't have a clear picture of how application performance 
affects their revenue. With AppDynamics, you get 100% visibility into your 
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] help on conversion to Jmol 14/JSmol

2013-12-19 Thread Jakubowski, Henry

Hi,

I have what I believe is a trivial problem (for everyone but me) on converting 
Jmol 12 files to Jmol 14/JSmol, but as I am more of a cut-and-paste creator of 
Jmol files, I thought I would seek outside help.

I've created about 100 Jmol files 
(http://employees.csbsju.edu/hjakubowski/classes/ch331/bcintro/list_of_Chime.htm)
 to accompany my web biochemistry book 
(http://employees.csbsju.edu/hjakubowski/classes/ch331/bcintro/default.html ).

They are all based on Jmol 12.  I just converted one after downloading the 
latest version of Jmol (14.1.3) yesterday.  I modified a template model from 
David Marcey and Molvisions and pasted in button commands from my previous Jmol 
12 verison.  It works well on my PCs using all browsers.

Here is the new file:   
http://employees.csbsju.edu/hjakubowski/Jmol14/Nucleosome/Nucleosome.htm .

Somehow I magically thought it would work on my Nexus Android tablet as well.  
It didn't as the file loads as a Jmol and not a JSmol file.

I would greatly appreciate it if someone could look at the code and suggest 
changes I could make to allow my files to work on any platform (if this is 
possible).  I think the fix is trivial (but again not for me).

Once I get this file working well, I want to use it as a template to convert 
the rest over time.
Thanks for any help.

Henry Jakubowski, Ph.D.
Professor and Chair, Chemistry Department
College St. Benedict/St John's University
241 Ardolf Science Center
37 S. College Ave.
St. Joseph, MN 56374

O:  320.363.5354
F:  320.363.5582
E:  hjakubow...@csbsju.edu
W: http://faculty.csbsju.edu/hjakubowski








[Description: HVJsignature]

Henry Jakubowski, Ph.D.
Professor and Chair, Chemistry Department; Head Biochemistry Program College 
St. Benedict/St John's University
241 Ardolf Science Center
37 S. College Ave.
St. Joseph, MN 56374

O:  320.363.5354
F:  320.363.5582
E:  hjakubow...@csbsju.edu
W: http://faculty.csbsju.edu/hjakubowski

[CentEmail2]

<><>--
Rapidly troubleshoot problems before they affect your business. Most IT 
organizations don't have a clear picture of how application performance 
affects their revenue. With AppDynamics, you get 100% visibility into your 
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] an error in chrome?

[Jmol-users] an error in chrome?

Re: [Jmol-users] passing commands across frames

Re: [Jmol-users] minimize constraints in a script

Re: [Jmol-users] why do I get averaged values?

Re: [Jmol-users] help on conversion to Jmol 14/JSmol

Re: [Jmol-users] passing commands across frames

Re: [Jmol-users] help on conversion to Jmol 14/JSmol

Re: [Jmol-users] help on conversion to Jmol 14/JSmol

Re: [Jmol-users] help on conversion to Jmol 14/JSmol

[Jmol-users] help on conversion to Jmol 14/JSmol

11 matches

Site Navigation

Mail list logo

Footer information