#12299: Upgrade Jmol to 12.3.27, Advance Jmol Interactive Features in Flask
Notebook
--------------------------------------------------------------+-------------
Reporter: gutow | Owner:
jason, mpatel, was
Type: enhancement | Status:
needs_review
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:
--------------------------------------------------------------+-------------
Changes (by gutow):
* status: needs_work => needs_review
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.
>
> '''If you just want to try:''' Go to [http://gutow.no-ip.org:8080
> TestServer] and create yourself an account. I will try to keep it up-to-
> date and running, but it may be down when I am coding.
>
> '''Explicit Installation Instructions:''' (tested against 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 queues 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-all-in-one.patch")
> sage: hg_sagenb.apply("http://trac.sagemath.org/sage_trac/raw-
> attachment/ticket/12299/trac_12299_adv_jmol_nb.patch")
> sage: hg_sagenb.apply("http://trac.sagemath.org/sage_trac/raw-
> attachment/ticket/12299/trac_12299_old_wksht.patch")
> sage: hg_sagenb.apply("http://trac.sagemath.org/sage_trac/raw-
> attachment/ticket/12299/trac_12299_server_sync_and_UI.2.patch")
> sage: exit
> ./sage -f
> "http://www.uwosh.edu/faculty_staff/gutow/jmol-12.3.27.p0.spkg";
> ./sage -b
> }}}
>
> This should be merged in sagenb 0.9.1, which is #13121.
>
> '''Notes:'''
>
> If you are doing this in a different way you need to know:
>
> The development version of Jmol is necessary. Install this .spkg:
> http://www.uwosh.edu/faculty_staff/gutow/jmol-12.3.27.p0.spkg
>
> Several patches are necessary:
>
> Sage library: [attachment:trac_12299-all-in-one.patch]
>
> Sagenb: [attachment:trac_12299_adv_jmol_nb.patch],
> [attachment:trac_12299_old_wksht.patch],
> [attachment:trac_12299_server_sync_and_UI.2.patch]
>
> These patches include all the changes in #9238 plus.
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:''' (tested against 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 queues 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-all-in-one.patch")
sage: hg_sage.apply("http://trac.sagemath.org/sage_trac/raw-
attachment/ticket/12299/trac_12299_headless_java.patch")
sage: hg_sagenb.apply("http://trac.sagemath.org/sage_trac/raw-
attachment/ticket/12299/trac_12299_adv_jmol_nb.patch")
sage: hg_sagenb.apply("http://trac.sagemath.org/sage_trac/raw-
attachment/ticket/12299/trac_12299_old_wksht.patch")
sage: hg_sagenb.apply("http://trac.sagemath.org/sage_trac/raw-
attachment/ticket/12299/trac_12299_server_sync_and_UI.2.patch")
sage: exit
./sage -f "http://www.uwosh.edu/faculty_staff/gutow/jmol-12.3.27.p0.spkg";
./sage -b
}}}
This should be merged in sagenb 0.9.1, which is #13121.
'''Notes:'''
If you are doing this in a different way you need to know:
The development version of Jmol is necessary. Install this .spkg:
http://www.uwosh.edu/faculty_staff/gutow/jmol-12.3.27.p0.spkg
Several patches are necessary:
Sage library: [attachment:trac_12299-all-in-one.patch]
[attachment:trac_12299_headless_java.patch]
Sagenb: [attachment:trac_12299_adv_jmol_nb.patch],
[attachment:trac_12299_old_wksht.patch],
[attachment:trac_12299_server_sync_and_UI.2.patch]
These patches include all the changes in #9238 plus.
--
Comment:
I think this patch will solve the remote login problem. It does allow the
sage server to run Jmol even if the server is running as a user without a
GUI.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/12299#comment:128>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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