date:20130924

Re: [Jmol-users] switching to JSmol

2013-09-24 Thread Amjad Farooq

Angel,

Thanks bro! I fully understand now.

Jmol2.js is to simply convert pre-existing Jmol pages into JSmol. Or one
can create a new page using JSmol scripts. I have done the latter and it is
working for me. I am happy.

Thank you again.
Amjad




On Tue, Sep 24, 2013 at 1:26 PM, Angel Herráez  wrote:

> PLEASE, read the replies and the wiki. You keep asking the same
> questions, sorry.
>
> > But, JSmol can run alone without Jmol2.js.
>
> The use of JSmol can be coded manually by you in the page or be coded
> by Jmol2.js in a page that was written for Jmol.js and JmolApplets
>
>
> > How does Jmol2.js improve the functionality of JSmol.
>
> It does not. There is no issue of functionality.
>
>
> > And why should one use it?! That is not clear to me.
>
> You don't need to use it. It is there to facilitate people converting
> their existing pages into JSmol.
>
>
>
>
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Re: [Jmol-users] switching to JSmol

2013-09-24 Thread Angel Herráez

PLEASE, read the replies and the wiki. You keep asking the same 
questions, sorry.

> But, JSmol can run alone without Jmol2.js.

The use of JSmol can be coded manually by you in the page or be coded 
by Jmol2.js in a page that was written for Jmol.js and JmolApplets


> How does Jmol2.js improve the functionality of JSmol.

It does not. There is no issue of functionality.

 
> And why should one use it?! That is not clear to me.

You don't need to use it. It is there to facilitate people converting 
their existing pages into JSmol.



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Re: [Jmol-users] switching to JSmol

2013-09-24 Thread Amjad Farooq

Ok.

But, JSmol can run alone without Jmol2.js.

How does Jmol2.js improve the functionality of JSmol.

And why should one use it?! That is not clear to me.






On Tue, Sep 24, 2013 at 12:38 PM, Angel Herráez wrote:

> Amjad Farooq wrote:
>
> > But, for Jmol features to work on the client machine, it must have
> > Java installed. Am I right?
>
> NO. If you set to use HTML5 JSmol you DO NOT need any Java.
>
>
> > Jmol2.js does not completely do away with Java.
>
> It does. No more Java. Jmol2.js makes you use JSmol.
>
>
> > But, JSmol is a completely stand-alone application,
>
> No. It is a javascript object inside a webpage. No application. Not
> stand-alone.
>
> > albeit with less
> > functionality.
>
> No. JSmol has the same functionality as Jmol.
>
>
> > How does Jmol2.js improve JSmol? Please explain.
>
> Jmol2.js introduces JSmol in your page.
>
>
> I thought we had this set clear!
>
>
>
> --
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Re: [Jmol-users] switching to JSmol

2013-09-24 Thread Angel Herráez

Amjad Farooq wrote:

> But, for Jmol features to work on the client machine, it must have 
> Java installed. Am I right? 

NO. If you set to use HTML5 JSmol you DO NOT need any Java.


> Jmol2.js does not completely do away with Java.

It does. No more Java. Jmol2.js makes you use JSmol.


> But, JSmol is a completely stand-alone application, 

No. It is a javascript object inside a webpage. No application. Not 
stand-alone.

> albeit with less 
> functionality.

No. JSmol has the same functionality as Jmol.


> How does Jmol2.js improve JSmol? Please explain.

Jmol2.js introduces JSmol in your page.


I thought we had this set clear!


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Re: [Jmol-users] switching to JSmol

2013-09-24 Thread Amjad Farooq

Bob,

Thanks for the clarification.

But, for Jmol features to work on the client machine, it must have Java
installed. Am I right? Jmol2.js does not completely do away with Java.

But, JSmol is a completely stand-alone application, albeit with less
functionality.

How does Jmol2.js improve JSmol? Please explain.

Amjad







On Tue, Sep 24, 2013 at 12:11 PM, Grossman, Robert B <
robert.gross...@uky.edu> wrote:

>  Amjad,
>
>  I have switched from Jmol Java applet to JSmol.  It was very easy.
>
>  (1) After downloading JSmol into a folder called jsmol, I put a symlink
> to it in a folder in my application, called /nosession.
>
>  (2) I changed every instance of
> 
>
>  in my application to
>
>   type="text/javascript">
>  type="text/javascript">
>
> The order of these two resources was important.
>
>  (3) In Jmol2.js, I changed
>
>  Jmol.Info = {
>
>jarPath: "java",
>   jarFile: "",
>   j2sPath: "j2s",
>
>  to
>
>  Jmol.Info = {
>
>jarPath: "/nosession/jsmol/java",
>   jarFile: "",
>   j2sPath: "/nosession/jsmol/j2s",
>
>  That's all it took.  The only problem I encountered was that one of the
> Jmol methods I was using, jmolLoadInline(), we not yet implemented in
> Jmol2.js.  Bob Hanson kindly provided me with a fresh version of Jmol2.js
> that had the method.
>
>  -- Bob G.
>
>   From: Amjad Farooq 
> Reply-To: 
> Date: Tue, 24 Sep 2013 10:26:34 -0400
> To: 
> Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol
> -- part deux
>
>  Hi Robert,
>
> I am utterly confused now. What is this Jmol2.js? Are you saying that
> using this file one can run Jmol on the client machine even if it does not
> have a Java installed? In other words, Jmol2.js runs Java from the server
> side? Is that correct?
>
>  Can someone please elaborate on this point. I recently switched to JSmol
> simply because many of my collaborators complained about my Jmol interface
> not running on their machines due to Java issues. Now, if Jmol2.js can
> eliminate the need for client to have a fully functional Java, then why do
> I need to to switch to JSmol?
>
>  I am lost on this.
>
>  Amjad
>
> *AMJAD FAROOQ PhD DIC | Associate Professor
> Dept of Biochemistry & Molecular Biology | Miller School of Medicine |
> University of Miami | Miami | FL 33136
> Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami ,
> FL 33136
> am...@farooqlab.net | off 305-243-2429 | lab 305-243-9799 | fax
> 305-243-3955 | www.farooqlab.net*
>
>
>
>
>
> On Tue, Sep 24, 2013 at 9:49 AM, Grossman, Robert B <
> robert.gross...@uky.edu> wrote:
>
>>  I downloaded the new Jmol2.js file you gave me, and it works great!
>>  Thanks.
>>
>>  So with this new JSmol, all the Java is now running server-side, is
>> that correct?  I no longer have to worry about whether the user's Java is
>> enabled?
>>
>>   From: Robert Hanson 
>> Reply-To: 
>> Date: Mon, 23 Sep 2013 22:18:28 -0500
>> To: "jmol-users@lists.sourceforge.net" 
>> Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol
>> -- part deux
>>
>>   There may be a few differences like that. For now, just use
>>
>>  Jmol.script(yourAppid, 'load DATA "mydata"\n' + yourInlineData + '\nEND
>> "mydata" ')
>>
>>  or give this one a try:
>>
>> http://chemapps.stolaf.edu/jmol/jsmol/js/Jmol2.js
>>
>>
>>
>>
>> On Mon, Sep 23, 2013 at 3:15 PM, Grossman, Robert B <
>> robert.gross...@uky.edu> wrote:
>>
>>>  OK, I read a little further down in the Wiki and saw that I could
>>> accomplish the switch another way: leave the calls to jmolApplet(), etc.
>>> alone and instead use both JSmol.min.js and Jmol2.js as resources.  So I
>>> did so, and I also added a symlink to the jsmol/j2s folder in the same
>>> folder as the page that calls the "applet".  So now JSmol loads, but I get
>>> this alert:
>>>
>>>  jmolLoadInline not implemented
>>>
>>>  So, any chance of this method being implemented in the near future?
>>>  Or maybe it has already been implemented in a more recent version?  I'm
>>> using jsmol-13.3.4.  (BTW, I tried to download JSmol 13.3.5 from
>>> SourceForge, but decompression failed.  Instead I downloaded one of the
>>> 13.3.4 versions.)
>>>
>>>
>>> --
>>> October Webinars: Code for Performance
>>> Free Intel webinars can help you accelerate application performance.
>>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most
>>> from
>>> the latest Intel processors and coprocessors. See abstracts and register
>>> >
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=60133471&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

[Jmol-users] switching to JSmol

2013-09-24 Thread Grossman, Robert B

Amjad,

I have switched from Jmol Java applet to JSmol.  It was very easy.

(1) After downloading JSmol into a folder called jsmol, I put a symlink to it 
in a folder in my application, called /nosession.

(2) I changed every instance of


in my application to




The order of these two resources was important.

(3) In Jmol2.js, I changed

Jmol.Info = {

  jarPath: "java",
  jarFile: "",
  j2sPath: "j2s",

to

Jmol.Info = {

  jarPath: "/nosession/jsmol/java",
  jarFile: "",
  j2sPath: "/nosession/jsmol/j2s",

That's all it took.  The only problem I encountered was that one of the Jmol 
methods I was using, jmolLoadInline(), we not yet implemented in Jmol2.js.  Bob 
Hanson kindly provided me with a fresh version of Jmol2.js that had the method.

-- Bob G.

From: Amjad Farooq mailto:am...@farooqlab.net>>
Reply-To: 
mailto:jmol-users@lists.sourceforge.net>>
Date: Tue, 24 Sep 2013 10:26:34 -0400
To: mailto:jmol-users@lists.sourceforge.net>>
Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol -- 
part deux

Hi Robert,

I am utterly confused now. What is this Jmol2.js? Are you saying that using 
this file one can run Jmol on the client machine even if it does not have a 
Java installed? In other words, Jmol2.js runs Java from the server side? Is 
that correct?

Can someone please elaborate on this point. I recently switched to JSmol simply 
because many of my collaborators complained about my Jmol interface not running 
on their machines due to Java issues. Now, if Jmol2.js can eliminate the need 
for client to have a fully functional Java, then why do I need to to switch to 
JSmol?

I am lost on this.

Amjad

AMJAD FAROOQ PhD DIC | Associate Professor
Dept of Biochemistry & Molecular Biology | Miller School of Medicine | 
University of Miami | Miami | FL 33136
Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami , FL 
33136
am...@farooqlab.net | off 305-243-2429 | lab 
305-243-9799 | fax 305-243-3955 | www.farooqlab.net





On Tue, Sep 24, 2013 at 9:49 AM, Grossman, Robert B 
mailto:robert.gross...@uky.edu>> wrote:
I downloaded the new Jmol2.js file you gave me, and it works great!  Thanks.

So with this new JSmol, all the Java is now running server-side, is that 
correct?  I no longer have to worry about whether the user's Java is enabled?

From: Robert Hanson mailto:hans...@stolaf.edu>>
Reply-To: 
mailto:jmol-users@lists.sourceforge.net>>
Date: Mon, 23 Sep 2013 22:18:28 -0500
To: "jmol-users@lists.sourceforge.net" 
mailto:jmol-users@lists.sourceforge.net>>
Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol -- 
part deux

There may be a few differences like that. For now, just use

Jmol.script(yourAppid, 'load DATA "mydata"\n' + yourInlineData + '\nEND 
"mydata" ')

or give this one a try:

http://chemapps.stolaf.edu/jmol/jsmol/js/Jmol2.js




On Mon, Sep 23, 2013 at 3:15 PM, Grossman, Robert B 
mailto:robert.gross...@uky.edu>> wrote:
OK, I read a little further down in the Wiki and saw that I could accomplish 
the switch another way: leave the calls to jmolApplet(), etc. alone and instead 
use both JSmol.min.js and Jmol2.js as resources.  So I did so, and I also added 
a symlink to the jsmol/j2s folder in the same folder as the page that calls the 
"applet".  So now JSmol loads, but I get this alert:

jmolLoadInline not implemented

So, any chance of this method being implemented in the near future?  Or maybe 
it has already been implemented in a more recent version?  I'm using 
jsmol-13.3.4.  (BTW, I tried to download JSmol 13.3.5 from SourceForge, but 
decompression failed.  Instead I downloaded one of the 13.3.4 versions.)

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


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

2013-09-24 Thread Angel Herráez

Specific answers:


Grossman, Robert B wrote:
> So you need Java running on the client, but not enabled in the 
> browser. Is that right? 

No. There is no use of Java when you go for JSmol.


Amjad Farooq wrote:
> In other words, Jmol2.js runs Java 
> from the server side? Is that correct?

No. Jmol2.js (which is Javascript) adapts your (old) page to use 
JSmol (no Java) instead fo Jmol (Java applet).

> if Jmol2.js can eliminate the need for client to have a fully 
> functional Java, then why do I need to to switch to JSmol?

You ARE switching to JSmol, either by manually writing your pages or 
by using Jmol2.js to adapt your old pages without changing therm.



Grossman, Robert B wrote:
> So with this new JSmol, all the Java is now running server-side, is 
> that correct? 

No. Nothing running in the server.

> I no longer have to worry about whether the user's Java 
> is enabled?

Yes. No worries.




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Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

2013-09-24 Thread Amjad Farooq

Angel,

Thank you so much for the clarification. You were spot on.

I now fully understand the difference. I am happy with JSmol as I do not
want to rely on Java.

Amjad



On Tue, Sep 24, 2013 at 11:43 AM, Angel Herráez wrote:

> At the risk of being repetitive, let's set this clear:
>
> Old and new Jmol needs Java, both for the application (stand-alone
> program in your computer) and for the applet inside webpages (using
> the Java plugín which is installed/added to your browser when you
> install Java in the computer).
>
> Current policies of both Java and the browsers make more difficult to
> run Java applets, needing permissions, confirmation dialogs and so.
> Still, they runs nicekly once you are confident to give the
> permissions (except for pages with applets in local disk, which are
> nearly impossible to run now).
>
> Java runs in the client machine. The applet gets downloaded as part
> of the page.
>
>
> New JSmol (only used as objects inside webpages, no application here)
> does not use Java. It runs JavaScript + HTML5 code, in the browser.
> All modern browsers can run it (that means Internet Explorer mst be
> version 10, maybe 9 too --can't remember now; no problems with
> Safari, Chrome, Firefox, Opera?).
> There is NO Java requirement at all. This caters for those who don't
> want or are not allowed to install Java in their computer, and for
> devices that do not support Java --like iOS and Android
> tablets/phones.
>
> Javascript runs in the client machine too.
>
> So in any case the server only delivers the pages. There are a couple
> of exceptions (loading binary files, loading files from external
> databases) but we can omit that for this general description.
>
>
> What Jmol2.js does is convert your existing page with JmolApplets
> based on Jmol.js to the new Jmol-JSO format (that's Jmol JavaScript
> Object) --withuout you ever changing a bit in the page code**.
> Jmol-JSO may be set to use Java Jmol applets or use HTML4 JSmol. You
> need to configure that in your copy of Jmol2.js.
>
> (( ** Well, you do need to change 2 lines in your page headers. See
> the Wiki. ))
>
> Please re-read the documentation we have. I know it is not extensive,
> but I think it does explain most of these things.
>
> http://wiki.jmol.org/index.php/JSmol
>
> http://wiki.jmol.org/index.php/JSmol#Conversion_using_the_Jmol2.js_.27
> adapter.27_library
>
> And you are always welcome to contribute in the Wiki contents.
>
> Good luck with your J(S)mol prjects!
>
>
>
> --
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> from
> the latest Intel processors and coprocessors. See abstracts and register >
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Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

2013-09-24 Thread Angel Herráez

At the risk of being repetitive, let's set this clear:

Old and new Jmol needs Java, both for the application (stand-alone 
program in your computer) and for the applet inside webpages (using 
the Java plugín which is installed/added to your browser when you 
install Java in the computer).

Current policies of both Java and the browsers make more difficult to 
run Java applets, needing permissions, confirmation dialogs and so. 
Still, they runs nicekly once you are confident to give the 
permissions (except for pages with applets in local disk, which are 
nearly impossible to run now).

Java runs in the client machine. The applet gets downloaded as part 
of the page.


New JSmol (only used as objects inside webpages, no application here) 
does not use Java. It runs JavaScript + HTML5 code, in the browser. 
All modern browsers can run it (that means Internet Explorer mst be 
version 10, maybe 9 too --can't remember now; no problems with 
Safari, Chrome, Firefox, Opera?).
There is NO Java requirement at all. This caters for those who don't 
want or are not allowed to install Java in their computer, and for 
devices that do not support Java --like iOS and Android 
tablets/phones.

Javascript runs in the client machine too. 

So in any case the server only delivers the pages. There are a couple 
of exceptions (loading binary files, loading files from external 
databases) but we can omit that for this general description.


What Jmol2.js does is convert your existing page with JmolApplets 
based on Jmol.js to the new Jmol-JSO format (that's Jmol JavaScript 
Object) --withuout you ever changing a bit in the page code**. 
Jmol-JSO may be set to use Java Jmol applets or use HTML4 JSmol. You 
need to configure that in your copy of Jmol2.js.

(( ** Well, you do need to change 2 lines in your page headers. See 
the Wiki. ))

Please re-read the documentation we have. I know it is not extensive, 
but I think it does explain most of these things.

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

http://wiki.jmol.org/index.php/JSmol#Conversion_using_the_Jmol2.js_.27
adapter.27_library

And you are always welcome to contribute in the Wiki contents.

Good luck with your J(S)mol prjects!


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Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

2013-09-24 Thread Maciek Wójcikowski

Dear Bob and Amjad,

No, for JSmol you don't need Java any more. JavaScript is not Java
(Oracle), but still is run on client side. Although JavaScript doesn't
require any plugins.

Just to cite header of Jmol2.js file, which Bob (Hanson) provided:

Script replacement for legacy Jmol.js that uses JSmol instead.
Can be used to turn most legacy Jmol.js-based sites to JSmol.
Presumes prior loading of JSmol.min.js

1) rename your current Jmol.js file Jmol_old.js in case you want to undo this

2) replace that file with this one

3) If you use JmolInitialize, put the Jar files from the java/ directory here
   in that designated directory and make a new subdirectory there called j2s.
   Then put all j2s/* files in that j2s subdirectory.

If you don't use JmolIinitialize, all the jar files should go into
a subdirectory named "java"
in the same directory as your web page, and all the JavaScript
should go into a subdirectory "j2s"
also in the same directory as your web page, just like it is here.

3) copy all j2s/* files into a directory on your site if you want to
use HTML5 (defaults to ./j2s)

4) copy all java/* files into a directory on your site if you want to
use Java (defaults to ./java)

5) try your page and see how it goes. You may still have some
problems, because not all of the
   methods in the original Jmol.js are included here. Let me know if
that's the case.





Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/9/24 Grossman, Robert B 

>  Maciek,
>
>  So you need Java running on the client, but not enabled in the browser.
>  Is that right?
>
>  -- Bob G.
>
>   From: Maciek Wójcikowski 
> Reply-To: 
> Date: Tue, 24 Sep 2013 15:56:34 +0200
> To: 
>
> Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol
> -- part deux
>
>  Both Java and JavaScript are computed on client side. The huge
> difference is that, as you mentioned, there's no need for Oracle Java
> plugin any more - every bit of JavaScript runs in the browser.
>
> 
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
>
> 2013/9/24 Grossman, Robert B 
>
>>  I downloaded the new Jmol2.js file you gave me, and it works great!
>>  Thanks.
>>
>>  So with this new JSmol, all the Java is now running server-side, is
>> that correct?  I no longer have to worry about whether the user's Java is
>> enabled?
>>
>>   From: Robert Hanson 
>> Reply-To: 
>> Date: Mon, 23 Sep 2013 22:18:28 -0500
>> To: "jmol-users@lists.sourceforge.net" 
>> Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol
>> -- part deux
>>
>>   There may be a few differences like that. For now, just use
>>
>>  Jmol.script(yourAppid, 'load DATA "mydata"\n' + yourInlineData + '\nEND
>> "mydata" ')
>>
>>  or give this one a try:
>>
>> http://chemapps.stolaf.edu/jmol/jsmol/js/Jmol2.js
>>
>>
>>
>>
>> On Mon, Sep 23, 2013 at 3:15 PM, Grossman, Robert B <
>> robert.gross...@uky.edu> wrote:
>>
>>>  OK, I read a little further down in the Wiki and saw that I could
>>> accomplish the switch another way: leave the calls to jmolApplet(), etc.
>>> alone and instead use both JSmol.min.js and Jmol2.js as resources.  So I
>>> did so, and I also added a symlink to the jsmol/j2s folder in the same
>>> folder as the page that calls the "applet".  So now JSmol loads, but I get
>>> this alert:
>>>
>>>  jmolLoadInline not implemented
>>>
>>>  So, any chance of this method being implemented in the near future?
>>>  Or maybe it has already been implemented in a more recent version?  I'm
>>> using jsmol-13.3.4.  (BTW, I tried to download JSmol 13.3.5 from
>>> SourceForge, but decompression failed.  Instead I downloaded one of the
>>> 13.3.4 versions.)
>>>
>>>
>>> --
>>> October Webinars: Code for Performance
>>> Free Intel webinars can help you accelerate application performance.
>>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most
>>> from
>>> the latest Intel processors and coprocessors. See abstracts and register
>>> >
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=60133471&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
>>
>>   
>> --
>> October Webinars: Code for Performance Free Intel webinars can help you
>> accelerate application performance. Explore tips for MPI, OpenMP, advanced
>> profiling, and more. Get the most from the latest Intel processor

Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

2013-09-24 Thread Grossman, Robert B

Maciek,

So you need Java running on the client, but not enabled in the browser.  Is 
that right?

-- Bob G.

From: Maciek Wójcikowski mailto:mac...@wojcikowski.pl>>
Reply-To: 
mailto:jmol-users@lists.sourceforge.net>>
Date: Tue, 24 Sep 2013 15:56:34 +0200
To: mailto:jmol-users@lists.sourceforge.net>>
Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol -- 
part deux

Both Java and JavaScript are computed on client side. The huge difference is 
that, as you mentioned, there's no need for Oracle Java plugin any more - every 
bit of JavaScript runs in the browser.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/9/24 Grossman, Robert B 
mailto:robert.gross...@uky.edu>>
I downloaded the new Jmol2.js file you gave me, and it works great!  Thanks.

So with this new JSmol, all the Java is now running server-side, is that 
correct?  I no longer have to worry about whether the user's Java is enabled?

From: Robert Hanson mailto:hans...@stolaf.edu>>
Reply-To: 
mailto:jmol-users@lists.sourceforge.net>>
Date: Mon, 23 Sep 2013 22:18:28 -0500
To: "jmol-users@lists.sourceforge.net" 
mailto:jmol-users@lists.sourceforge.net>>
Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol -- 
part deux

There may be a few differences like that. For now, just use

Jmol.script(yourAppid, 'load DATA "mydata"\n' + yourInlineData + '\nEND 
"mydata" ')

or give this one a try:

http://chemapps.stolaf.edu/jmol/jsmol/js/Jmol2.js




On Mon, Sep 23, 2013 at 3:15 PM, Grossman, Robert B 
mailto:robert.gross...@uky.edu>> wrote:
OK, I read a little further down in the Wiki and saw that I could accomplish 
the switch another way: leave the calls to jmolApplet(), etc. alone and instead 
use both JSmol.min.js and Jmol2.js as resources.  So I did so, and I also added 
a symlink to the jsmol/j2s folder in the same folder as the page that calls the 
"applet".  So now JSmol loads, but I get this alert:

jmolLoadInline not implemented

So, any chance of this method being implemented in the near future?  Or maybe 
it has already been implemented in a more recent version?  I'm using 
jsmol-13.3.4.  (BTW, I tried to download JSmol 13.3.5 from SourceForge, but 
decompression failed.  Instead I downloaded one of the 13.3.4 versions.)

--
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&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

-- 
October Webinars: Code for Performance Free Intel webinars can help you 
accelerate application performance. Explore tips for MPI, OpenMP, advanced 
profiling, and more. Get the most from the latest Intel processors and 
coprocessors. See abstracts and register > 
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk___
 Jmol-users mailing list 
Jmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users

--
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users


-- 
October Webinars: Code for Performance Free Intel webinars can help you 
accelerate application performance. Explore tips for MPI, OpenMP, advanced 
profiling, and more. Get the most from the latest Intel processors and 
coprocessors. See abstracts and register > 
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk___
 Jmol-users mai

Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

2013-09-24 Thread Maciek Wójcikowski

Both Java and JavaScript are computed on client side. The huge difference
is that, as you mentioned, there's no need for Oracle Java plugin any more
- every bit of JavaScript runs in the browser.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/9/24 Grossman, Robert B 

>  I downloaded the new Jmol2.js file you gave me, and it works great!
>  Thanks.
>
>  So with this new JSmol, all the Java is now running server-side, is that
> correct?  I no longer have to worry about whether the user's Java is
> enabled?
>
>   From: Robert Hanson 
> Reply-To: 
> Date: Mon, 23 Sep 2013 22:18:28 -0500
> To: "jmol-users@lists.sourceforge.net" 
> Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol
> -- part deux
>
>   There may be a few differences like that. For now, just use
>
>  Jmol.script(yourAppid, 'load DATA "mydata"\n' + yourInlineData + '\nEND
> "mydata" ')
>
>  or give this one a try:
>
> http://chemapps.stolaf.edu/jmol/jsmol/js/Jmol2.js
>
>
>
>
> On Mon, Sep 23, 2013 at 3:15 PM, Grossman, Robert B <
> robert.gross...@uky.edu> wrote:
>
>>  OK, I read a little further down in the Wiki and saw that I could
>> accomplish the switch another way: leave the calls to jmolApplet(), etc.
>> alone and instead use both JSmol.min.js and Jmol2.js as resources.  So I
>> did so, and I also added a symlink to the jsmol/j2s folder in the same
>> folder as the page that calls the "applet".  So now JSmol loads, but I get
>> this alert:
>>
>>  jmolLoadInline not implemented
>>
>>  So, any chance of this method being implemented in the near future?  Or
>> maybe it has already been implemented in a more recent version?  I'm using
>> jsmol-13.3.4.  (BTW, I tried to download JSmol 13.3.5 from SourceForge, but
>> decompression failed.  Instead I downloaded one of the 13.3.4 versions.)
>>
>>
>> --
>> October Webinars: Code for Performance
>> Free Intel webinars can help you accelerate application performance.
>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most
>> from
>> the latest Intel processors and coprocessors. See abstracts and register >
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=60133471&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
>
>  
> --
> October Webinars: Code for Performance Free Intel webinars can help you
> accelerate application performance. Explore tips for MPI, OpenMP, advanced
> profiling, and more. Get the most from the latest Intel processors and
> coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk___Jmol-users
>  mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> --
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most
> from
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from 
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

2013-09-24 Thread Amjad Farooq

Hi Robert,

I am utterly confused now. What is this Jmol2.js? Are you saying that using
this file one can run Jmol on the client machine even if it does not have a
Java installed? In other words, Jmol2.js runs Java from the server side? Is
that correct?

Can someone please elaborate on this point. I recently switched to JSmol
simply because many of my collaborators complained about my Jmol interface
not running on their machines due to Java issues. Now, if Jmol2.js can
eliminate the need for client to have a fully functional Java, then why do
I need to to switch to JSmol?

I am lost on this.

Amjad

*AMJAD FAROOQ PhD DIC | Associate Professor
Dept of Biochemistry & Molecular Biology | Miller School of Medicine |
University of Miami | Miami | FL 33136
Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami ,
FL 33136
am...@farooqlab.net | off 305-243-2429 | lab 305-243-9799 | fax
305-243-3955 | www.farooqlab.net*





On Tue, Sep 24, 2013 at 9:49 AM, Grossman, Robert B  wrote:

>  I downloaded the new Jmol2.js file you gave me, and it works great!
>  Thanks.
>
>  So with this new JSmol, all the Java is now running server-side, is that
> correct?  I no longer have to worry about whether the user's Java is
> enabled?
>
>   From: Robert Hanson 
> Reply-To: 
> Date: Mon, 23 Sep 2013 22:18:28 -0500
> To: "jmol-users@lists.sourceforge.net" 
> Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol
> -- part deux
>
>   There may be a few differences like that. For now, just use
>
>  Jmol.script(yourAppid, 'load DATA "mydata"\n' + yourInlineData + '\nEND
> "mydata" ')
>
>  or give this one a try:
>
> http://chemapps.stolaf.edu/jmol/jsmol/js/Jmol2.js
>
>
>
>
> On Mon, Sep 23, 2013 at 3:15 PM, Grossman, Robert B <
> robert.gross...@uky.edu> wrote:
>
>>  OK, I read a little further down in the Wiki and saw that I could
>> accomplish the switch another way: leave the calls to jmolApplet(), etc.
>> alone and instead use both JSmol.min.js and Jmol2.js as resources.  So I
>> did so, and I also added a symlink to the jsmol/j2s folder in the same
>> folder as the page that calls the "applet".  So now JSmol loads, but I get
>> this alert:
>>
>>  jmolLoadInline not implemented
>>
>>  So, any chance of this method being implemented in the near future?  Or
>> maybe it has already been implemented in a more recent version?  I'm using
>> jsmol-13.3.4.  (BTW, I tried to download JSmol 13.3.5 from SourceForge, but
>> decompression failed.  Instead I downloaded one of the 13.3.4 versions.)
>>
>>
>> --
>> October Webinars: Code for Performance
>> Free Intel webinars can help you accelerate application performance.
>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most
>> from
>> the latest Intel processors and coprocessors. See abstracts and register >
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=60133471&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
>
>  
> --
> October Webinars: Code for Performance Free Intel webinars can help you
> accelerate application performance. Explore tips for MPI, OpenMP, advanced
> profiling, and more. Get the most from the latest Intel processors and
> coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk___Jmol-users
>  mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> --
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most
> from
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from 
the latest Intel processors and coprocessors. See abs

Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

2013-09-24 Thread Grossman, Robert B

I downloaded the new Jmol2.js file you gave me, and it works great!  Thanks.

So with this new JSmol, all the Java is now running server-side, is that 
correct?  I no longer have to worry about whether the user's Java is enabled?

From: Robert Hanson mailto:hans...@stolaf.edu>>
Reply-To: 
mailto:jmol-users@lists.sourceforge.net>>
Date: Mon, 23 Sep 2013 22:18:28 -0500
To: "jmol-users@lists.sourceforge.net" 
mailto:jmol-users@lists.sourceforge.net>>
Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol -- 
part deux

There may be a few differences like that. For now, just use

Jmol.script(yourAppid, 'load DATA "mydata"\n' + yourInlineData + '\nEND 
"mydata" ')

or give this one a try:

http://chemapps.stolaf.edu/jmol/jsmol/js/Jmol2.js

On Mon, Sep 23, 2013 at 3:15 PM, Grossman, Robert B 
mailto:robert.gross...@uky.edu>> wrote:
OK, I read a little further down in the Wiki and saw that I could accomplish 
the switch another way: leave the calls to jmolApplet(), etc. alone and instead 
use both JSmol.min.js and Jmol2.js as resources.  So I did so, and I also added 
a symlink to the jsmol/j2s folder in the same folder as the page that calls the 
"applet".  So now JSmol loads, but I get this alert:

jmolLoadInline not implemented

So, any chance of this method being implemented in the near future?  Or maybe 
it has already been implemented in a more recent version?  I'm using 
jsmol-13.3.4.  (BTW, I tried to download JSmol 13.3.5 from SourceForge, but 
decompression failed.  Instead I downloaded one of the 13.3.4 versions.)

--
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&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

-- 
October Webinars: Code for Performance Free Intel webinars can help you 
accelerate application performance. Explore tips for MPI, OpenMP, advanced 
profiling, and more. Get the most from the latest Intel processors and 
coprocessors. See abstracts and register > 
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk___
 Jmol-users mailing list 
Jmol-users@lists.sourceforge.net 
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
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Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from 
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk___
Jmol-users mailing list
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Re: [Jmol-users] switching to JSmol

Re: [Jmol-users] switching to JSmol

Re: [Jmol-users] switching to JSmol

Re: [Jmol-users] switching to JSmol

Re: [Jmol-users] switching to JSmol

[Jmol-users] switching to JSmol

Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

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