Re: [Jmol-users] JmolApplet.jar

2016-05-19 Thread Eric Martz 

Dear Bob,

1. Is JmolApplet.jar the /unsigned/ applet? I don't mind dropping 
that from the distribution.


2. JSmol/HTML5 is truly a life-saver! Bless you Bob and the other team 
members for JSmol! For most entries in the PDB, it is perfectly 
satisfactory and it is the default in FirstGlance.Jmol.Org.


Nevertheless, I consider JmolAppletSigned.jar to be essential. It is 
essential for NMR ensembles and large models. It gives much smoother 
rotation and faster operation for just about everything. 
FirstGlance.Jmol.Org has a checkbox and a preference setting (cookie) 
and a query parameter option to use Java.


I am close to releasing a new version of FirstGlance that includes a 
button to save a rocking or rotating animation (using 'capture'). In the 
default HTML5 mode, with high quality on (antialiasdisplay), it can take 
several minutes (even more on older computers or mobile devices) to 
generate the multi-GIF file. Generation is more than ten-times faster 
using the signed Java applet.


I will be quite upset if/when Oracle actually stops providing a Java 
browser plugin, at which time no Java applet will work, see the pink box at


http://proteopedia.org/w/Installing_and_enabling_Java

Best regards, Eric


On 5/18/16 1:04 AM, Robert Hanson wrote:

Two questions:

1. What would you think of dropping JmolApplet.jar from the 
distribution?

2. How about JmolAppletSigned.jar?

Could these, perhaps be in a separate zip for download, perhaps 
JmolAppletJava.zip?


--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] JmolApplet.jar

2016-05-18 Thread Rolf Huehne 
Am 18.05.16 um 22:41 schrieb Robert Hanson:
> I like the idea of an examples subdirectory; of course all my web links
> to chemapps will break in that case. Or I would have to duplicate
> everything there. I guess I could do that. But it complicates things.
>
Bob, I guess if you could convince the server administrator to install 
some rewrite rules you could avoid having to duplicate everything to 
keep the links intact.

Regards,
Rolf

--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] JmolApplet.jar

2016-05-18 Thread Robert Hanson 
I like the idea of an examples subdirectory; of course all my web links to
chemapps will break in that case. Or I would have to duplicate everything
there. I guess I could do that. But it complicates things.

On Wed, May 18, 2016 at 10:06 AM, Philip Bays  wrote:

> Is it posible to do the following:
> Keep the java in the distribution
> Put all of the examples and scripts in separate directory.   This would of
> course require changing the script to find the required files, but they
> would be available for playing with for development purposes (I find them
> very helpful!), but could be removed when transferring the relevant files
> to the server.
>
> Phil
>
> > On May 18, 2016, at 5:38 AM, Angel Herráez  wrote:
> >
> > I certainly would prefer to have Java available in the distribution. For
> large
> > proteins and complexes there is still a significant difference in
> performance.
> >
> > Maybe the nonsigned variant can be dropped / separated into the other
> > download
> >
> > On the other hand, I would vote for not having the extra files in the
> > distribution like examples, scripts, copy of jQuery etc
> > Just leave what is needed for an operative JSmol, HTML5+Java
> >
> >
> >
> >
> >
> --
> > Mobile security can be enabling, not merely restricting. Employees who
> > bring their own devices (BYOD) to work are irked by the imposition of MDM
> > restrictions. Mobile Device Manager Plus allows you to control only the
> > apps on BYO-devices by containerizing them, leaving personal data
> untouched!
> > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> > ___
> > Jmol-users mailing list
> > Jmol-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> Philip Bays
> Emeritus Professor of Chemistry
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
>
>
>
>
> --
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data
> untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> ___
> 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
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
--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] JmolApplet.jar

2016-05-18 Thread Philip Bays 
Is it posible to do the following:
Keep the java in the distribution
Put all of the examples and scripts in separate directory.   This would of 
course require changing the script to find the required files, but they would 
be available for playing with for development purposes (I find them very 
helpful!), but could be removed when transferring the relevant files to the 
server.

Phil

> On May 18, 2016, at 5:38 AM, Angel Herráez  wrote:
> 
> I certainly would prefer to have Java available in the distribution. For 
> large 
> proteins and complexes there is still a significant difference in performance.
> 
> Maybe the nonsigned variant can be dropped / separated into the other 
> download
> 
> On the other hand, I would vote for not having the extra files in the 
> distribution like examples, scripts, copy of jQuery etc
> Just leave what is needed for an operative JSmol, HTML5+Java
> 
> 
> 
> 
> --
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu



--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] JmolApplet.jar

2016-05-18 Thread Angel Herráez 
Rolf,

> thought jQuery is needed for an operative JSmol.

JSmol uses a jQuery included into its files (that's why there are *.nojquery 
alternative files). 
That jquery folder is sort of a backup copy, but not used in the standard 
operation.

See http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Getting_the_Files
for a listing of which files are required.


> Maybe it would be sufficient to have a clearer separation between 
> necessary and optional/documentational stuff.

Good idea. That's what I tried to do in that Wiki page.




--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] JmolApplet.jar

2016-05-18 Thread Rolf Huehne 
On 05/18/2016 11:38 AM, Angel Herráez wrote:
> I certainly would prefer to have Java available in the distribution. For large
> proteins and complexes there is still a significant difference in performance.
>
I would agree with Angel. I still prefer the Java version because of the 
much better performance with larger structures. And the performance is 
also independent of the browser performance. I frequently get drops in 
performance even with smaller protein structures, depending on how busy 
the browser currently is (coping for example with all the background 
tasks from ads or other animations inside visited pages).
But being able to provide the HTML5 alternative is also important.

> Maybe the nonsigned variant can be dropped / separated into the other
> download
>
> On the other hand, I would vote for not having the extra files in the
> distribution like examples, scripts, copy of jQuery etc
> Just leave what is needed for an operative JSmol, HTML5+Java
>
I am not sure if this will really be more advantageous than 
disadvantageous, except for the quite large 'data' directory. And I 
thought jQuery is needed for an operative JSmol.
Maybe it would be sufficient to have a clearer separation between 
necessary and optional/documentational stuff.

Regards,
Rolf

-- 

Rolf Huehne
Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

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

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

VAT No: DE 153 925 464
Register of Associations: No. 230296, Amtsgericht Jena
Tax Number: 162/141/08228


--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] JmolApplet.jar

2016-05-18 Thread J. Bays 
That would be fine with me. First thing I do with a release is delete all
things Java.

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Norte Dame, IN

Sent from my iPad

On May 18, 2016, at 1:05 AM, Robert Hanson  wrote:

Two questions:

1. What would you think of dropping JmolApplet.jar from the
distribution?
2. How about JmolAppletSigned.jar?

Could these, perhaps be in a separate zip for download, perhaps
JmolAppletJava.zip?


-- 
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

--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j

___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] JmolApplet.jar

2016-05-18 Thread Jaime Prilusky 
Agreed. 
Signed Java can become handy in the distribution.
Files not needed for a functional JSmol, like examples, scripts, etc, can be on 
a separated download.

Jaim

> On 18 May 2016, at 12:38 PM, Angel Herráez  wrote:
> 
> I certainly would prefer to have Java available in the distribution. For 
> large 
> proteins and complexes there is still a significant difference in performance.
> 
> Maybe the nonsigned variant can be dropped / separated into the other 
> download
> 
> On the other hand, I would vote for not having the extra files in the 
> distribution like examples, scripts, copy of jQuery etc
> Just leave what is needed for an operative JSmol, HTML5+Java
> 
> 
> 
> 
> --
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] JmolApplet.jar

2016-05-18 Thread Angel Herráez 
I certainly would prefer to have Java available in the distribution. For large 
proteins and complexes there is still a significant difference in performance.

Maybe the nonsigned variant can be dropped / separated into the other 
download

On the other hand, I would vote for not having the extra files in the 
distribution like examples, scripts, copy of jQuery etc
Just leave what is needed for an operative JSmol, HTML5+Java




--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] JmolApplet.jar

2016-05-17 Thread Robert Hanson 
Two questions:

1. What would you think of dropping JmolApplet.jar from the
distribution?
2. How about JmolAppletSigned.jar?

Could these, perhaps be in a separate zip for download, perhaps
JmolAppletJava.zip?


-- 
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
--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users