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> 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 Documentation on MediaWiki is probably completely outdated.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> 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
>>
>> ------------------------------------------------------------------------------
>> Dive into the World of Parallel Programming. The Go Parallel Website,
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>> _______________________________________________
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>>
>>
>>
>> ------------------------------------------------------------------------------
>> Dive into the World of Parallel Programming. The Go Parallel Website,
>> sponsored by Intel and developed in partnership with Slashdot Media, is your
>> hub for all things parallel software development, from weekly thought
>> leadership blogs to news, videos, case studies, tutorials and more. Take a
>> look and join the conversation now. http://goparallel.sourceforge.net/
>>
>>
>> _______________________________________________
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>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming. The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and more. Take a
> look and join the conversation now.
> http://goparallel.sourceforge.net/_______________________________________________
> Jmol-users mailing list
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054
------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
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