#12299: Upgrade Jmol to 12.3.27, Advance Jmol Interactive Features in Flask
Notebook
--------------------------------------------------------------+-------------
Reporter: gutow | Owner:
jason, mpatel, was
Type: enhancement | Status:
needs_work
Priority: major | Milestone:
sage-pending
Component: notebook | Resolution:
Keywords: Jmol, 3D, notebook | Work issues:
Report Upstream: Fixed upstream, in a later stable release. | Reviewers:
Karl-Dieter Crisman, Steven Trogdon, Punarbasu Purkayastha, John Palmieri
Authors: Jonathan Gutow | Merged in:
Dependencies: #11080,#11078,#11503,#13121 | Stopgaps:
--------------------------------------------------------------+-------------
Description changed by gutow:
Old description:
> This ticket provides the following advanced interactive features to Jmol
> in the notebook:
>
> 1. Initial display is a static image created by Jmol (if a javaVM is
> available on the server) or Tachyon. This means all browsers and devices
> will at least be able to see a 3-D image.
> 1. The live applet can be loaded by clicking on a "Make Interactive..."
> button.
> 1. Colors can be changed without recalculating
> 1. spin on checkbox
> 1. high quality checkbox
> 1. Meshes can be displayed without recalculating (no sparkles either :))
> 1. Transparency can be adjusted without recalculating
> 1. Applet size can be adjusted
> 1. Applet can be displayed in its own window
> 1. Can download a file that the Jmol application can open to recreate
> the exact view shown on the web page. This allows for more sophisticated
> manipulation and the semi-automatic creation of web pages that include
> this live 3-D image.
> 1. Solves memory problems associated with opening too many Jmols at
> once, by automatically putting Jmols that are not being used to sleep.
>
> '''Explicit Installation Instructions for <=sage-5.1:'''
>
> 1. Install the flask notebook by following the instructions at #11080.
> 1. Then do the following to apply the patches and install an updated
> version of Jmol.
>
> {{{
> ./sage --hg -R devel/sage qimport -P http://trac.sagemath.org/sage_trac
> /raw-attachment/ticket/12299/trac_12299-all-in-one.patch
> ./sage --hg -R devel/sage qimport -P http://trac.sagemath.org/sage_trac
> /raw-attachment/ticket/12299/trac_12299_headless_java.patch
>
> ./sage --hg -R devel/sagenb qimport -P http://trac.sagemath.org/sage_trac
> /raw-attachment/ticket/12299/trac_12299_adv_jmol_nb.patch
> ./sage --hg -R devel/sagenb qimport -P http://trac.sagemath.org/sage_trac
> /raw-attachment/ticket/12299/trac_12299_old_wksht.patch
> ./sage --hg -R devel/sagenb qimport -P http://trac.sagemath.org/sage_trac
> /raw-attachment/ticket/12299/trac_12299_server_sync_and_UI.2.patch
>
> ./sage -f
> "http://www.uwosh.edu/faculty_staff/gutow/jmol-12.3.27.p2.spkg";
>
> ./sage -b
> }}}
>
> '''Explicit Installation Instructions for >sage-5.1:'''
>
> 1. Install sagenb 0.10.x by following the instructions at #13121 - those
> instructions include everything necessary to test this ticket.
>
> '''Notes:'''
>
> If you are doing this in a different way you need to:
>
> * Install this .spkg:
> [http://www.uwosh.edu/faculty_staff/gutow/jmol-12.3.27.p2.spkg]
> * Apply the following patches:
> 1. Sage library: [attachment:trac_12299-all-in-one.patch],
> [attachment:trac_12299_headless_java.patch]
> 1. Sagenb (merged in #13121):
> [attachment:trac_12299_adv_jmol_nb.patch],
> [attachment:trac_12299_old_wksht.patch],
> [attachment:trac_12299_server_sync_and_UI.2.patch]
New description:
This ticket provides the following advanced interactive features to Jmol
in the notebook:
1. Initial display is a static image created by Jmol (if a javaVM is
available on the server) or Tachyon. This means all browsers and devices
will at least be able to see a 3-D image.
1. The live applet can be loaded by clicking on a "Make Interactive..."
button.
1. Colors can be changed without recalculating
1. spin on checkbox
1. high quality checkbox
1. Meshes can be displayed without recalculating (no sparkles either :))
1. Transparency can be adjusted without recalculating
1. Applet size can be adjusted
1. Applet can be displayed in its own window
1. Can download a file that the Jmol application can open to recreate the
exact view shown on the web page. This allows for more sophisticated
manipulation and the semi-automatic creation of web pages that include
this live 3-D image.
1. Solves memory problems associated with opening too many Jmols at once,
by automatically putting Jmols that are not being used to sleep.
'''Explicit Installation Instructions for <=sage-5.1:'''
1. Install the flask notebook by following the instructions at #11080.
1. Then do the following to apply the patches and install an updated
version of Jmol.
{{{
./sage --hg -R devel/sage qimport -P http://trac.sagemath.org/sage_trac
/raw-attachment/ticket/12299/trac_12299-all-in-one.patch
./sage --hg -R devel/sage qimport -P http://trac.sagemath.org/sage_trac
/raw-attachment/ticket/12299/trac_12299_headless_java.patch
./sage --hg -R devel/sage qimport -P http://trac.sagemath.org/sage_trac
/raw-attachment/ticket/12299/trac-12299_java_doctest_opt.patch
./sage --hg -R devel/sagenb qimport -P http://trac.sagemath.org/sage_trac
/raw-attachment/ticket/12299/trac_12299_adv_jmol_nb.patch
./sage --hg -R devel/sagenb qimport -P http://trac.sagemath.org/sage_trac
/raw-attachment/ticket/12299/trac_12299_old_wksht.patch
./sage --hg -R devel/sagenb qimport -P http://trac.sagemath.org/sage_trac
/raw-attachment/ticket/12299/trac_12299_server_sync_and_UI.2.patch
./sage -f "http://www.uwosh.edu/faculty_staff/gutow/jmol-12.3.27.p2.spkg";
./sage -b
}}}
'''Explicit Installation Instructions for >sage-5.1:'''
1. Install sagenb 0.10.x by following the instructions at #13121 - those
instructions include everything necessary to test this ticket.
'''Notes:'''
If you are doing this in a different way you need to:
* Install this .spkg:
[http://www.uwosh.edu/faculty_staff/gutow/jmol-12.3.27.p2.spkg]
* Apply the following patches:
1. Sage library: [attachment:trac_12299-all-in-one.patch],
[attachment:trac_12299_headless_java.patch],[attachment:trac-
12299_java_doctest_opt.patch]
1. Sagenb (merged in #13121): [attachment:trac_12299_adv_jmol_nb.patch],
[attachment:trac_12299_old_wksht.patch],
[attachment:trac_12299_server_sync_and_UI.2.patch]
--
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/12299#comment:189>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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