The current version of JSmolExtension does support both HTML5/Javascript and
Java.
Proteopedia detects and supports mobile clients, switching between Java and
HTML5 based on the client available engine. Proteopedia also supports editing
of Jmol scenes from iPad.
Some examples of the current version of JSmolExtension available at
http://proteopedia.org/w/User:Jaime_Prilusky/JSmolExtension
Installing the JSmolExtension on MediaWiki is straightforward. Download the
extension either from
http://proteopedia.org/wiki/support/JSmolExtension/JSmolExtension.zip or from
http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-extensions/ and follow
the few steps from the readme.txt file.
Please let me know if you encounter any problem.
Jaim
--
Dr Jaime Prilusky
Head Bioinformatics
R&D Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot - Israel
eml: jaime.prilu...@weizmann.ac.il<mailto:jaime.prilu...@weizmann.ac.il>
fax: 972-8-9344113
tel: 972-8-9344959
OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)
On Feb 6, 2015, at 8:48 AM, Jim Hu
<jim.hu.bio...@gmail.com<mailto:jim.hu.bio...@gmail.com>> wrote:
I think you might want to consider the JSmol extension from Proteopedia for
MediaWiki, or some way to switch between Jmol and JSmol based on the client (I
don't recall whether Proteopedia does that). One reason I've switched EcoliWiki
to JSmol and developed the JSmol2wp Wordpress plugin is so that more users can
see the applets even if they are on mobile or don't know how to deal with the
Java security restrictions on other machines. If I was doing it for a user base
like a class, where I had more control over the machines being used, I might
prefer the Java based Jmol. But for a lot of web uses JSmol will reach a larger
base of users, IMO.
Jim
On Feb 5, 2015, at 7:53 PM, Brenton Horne
<brentonho...@ymail.com<mailto:brentonho...@ymail.com>> wrote:
Hi, Nico
Yep that was me that asked about the extension on the talk page @ MW. Yeah, I
saw that Angel & Bob were listed as editors/contributors in Sourceforge and
other places hence why I thought they may be able to help me.
Brenton
On 6/02/2015 11:27 AM, Nicolas Vervelle wrote:
Hi Brenton,
Documentation on MediaWiki is probably completely outdated.
I was the one who wrote it originally, but it was a long time ago, and since
modifications have been made to the extension and many versions of MW have been
released.
Are you also the one who asked about this on the extension talk page in MW ?
https://www.mediawiki.org/wiki/Extension_talk:Jmol
I'm currently travelling until mid February, I can't do much until then.
Other people here will probably help you, since the extension is running on
several wikis I believe.
Nico
On Thu, Feb 5, 2015 at 9:38 PM, Brenton Horne
<brentonho...@ymail.com<mailto:brentonho...@ymail.com>> wrote:
Hi,
I see many developers of Jmol also helped develop the MediaWiki Jmol
extension, hence why I felt this would be a decent enough place to ask
for help with it. I followed the installation instructions @ MediaWiki's
Extension:Jmol page, without any obvious problems.
Then when all the steps were finished (including checking
special:version to see if the extension was added, which it was) I
tested it out by adding <jmolPdb>3EIG</jmolPdb> (and other Jmol-related
wikitext like <jmolFile>(S)-nicotine.sdf</jmolFile> where
(S)-nicotine.sdf is the name of a file on my Wiki) to a random page and
clicking submit. This resulted in me being left at a blank submit page
(i.e., with PAGENAME?action=submit in the address bar). I have tried and
retried this just in case I encountered some random server problem, but
each time I got the same results.
I have since customized my Jmol.body.php file and the structure/naming
of the jsmol extension direct according to the file locations specified
in Jmol.body.php in an attempt to overcome this problem. I have had some
(sort of) success in that now I can save a page with these tags in it
without that submit error, but JSmol applet still isn't embedded into
the page. Rather where these tags are placed the PDB ID or file name
appears and is hyperlinked to a javascript command.
If it helps this is my current Jmol.body.php script:
https://drive.google.com/file/d/0B1_sXH68hMWBT1VrMTRNbzJSOHM/view?usp=sharing.
Thanks for your time,
Brenton
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=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054
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