#12299: Advance Jmol Interactive Features in Flask Notebook
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Reporter: gutow | Owner: jason, mpatel, was
Type: enhancement | Status: needs_review
Priority: major | Milestone: sage-5.1
Component: notebook | Resolution:
Keywords: Jmol, 3D, notebook | Work issues:
Report Upstream: N/A | Reviewers:
Authors: gutow | Merged in:
Dependencies: #11080,#11078,#11503 | Stopgaps:
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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
> 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.
>
> The development version of Jmol is necessary. Install this .spkg:
> http://www.uwosh.edu/faculty_staff/gutow/jmol-12.3.27.p0.spkg
>
> Two patches are necessary:
>
> A patch to plot3d in Sage: attachment:trac_12299_plot_3D_static_img.patch
>
> A patch to a number of files in sagenb:
> attachment:trac_12299_adv_jmol_nb.patch
>
> These patches include all the changes in #9238 plus.
>
> NOTE TO REVIEWERS: Please check that things work for the notebook running
> in secure mode.
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
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:''' (tested agains 5.0)
1) Install the flask notebook by following the instructions in #11080. I
recommend installing the optional OpenSSL package. I have not been
getting consistent behavior using the system install on all my different
machines (probably a path issue).
2) Then do the following to apply the patches and install an updated
version of Jmol. The first two commands close any Hg cues left open by
the flask install (doesn't hurt to do that even if all the queues are
closed).
{{{
./sage
sage: hg_sage("qfinish -a")
sage: hg_sagenb("qfinish -a")
sage: hg_sage.apply("http://trac.sagemath.org/sage_trac/raw-
attachment/ticket/12299/trac_12299_plot_3D_static_img.patch")
sage: hg_sagenb.apply("http://trac.sagemath.org/sage_trac/raw-
attachment/ticket/12299/trac_12299_adv_jmol_nb.patch")
sage: exit
./sage -f "http://www.uwosh.edu/faculty_staff/gutow/jmol-12.3.27.p0.spkg";
./sage -b
}}}
The development version of Jmol is necessary. Install this .spkg:
http://www.uwosh.edu/faculty_staff/gutow/jmol-12.3.27.p0.spkg
Two patches are necessary:
A patch to plot3d in Sage: attachment:trac_12299_plot_3D_static_img.patch
A patch to a number of files in sagenb:
attachment:trac_12299_adv_jmol_nb.patch
These patches include all the changes in #9238 plus.
NOTE TO REVIEWERS: Please check that things work for the notebook running
in secure mode as well as the default insecure launched by the generic
"notebook()" command.
--
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/12299#comment:18>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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