Version 6 is described here, compatible with MediaWiki 1.43
The Jmol Extension enables the use of several tags in the wikicode to insert JSmol objects (panels displaying interactive 3D modes of molecules or other structures) in different ways, and to interact with them via UI controls like buttons, links....
These render a link in the page that, when clicked by the user, will open a small window (pop-up) with a JSmol panel that displays a structure. No custom rendering or scripting on the structure is possible.
<jmolFile> | <jmolMol> | <jmolSmiles> | <jmolPdb> |
---|---|---|---|
A structure in a file previously uploaded to the wiki. (If enabled by the wiki administrators) |
A structure retrieved from the NCI CACTUS server (by name). | A structure retrieved from the NCI CACTUS server (by SMILES notation). | A structure is retrieved from a PDB server (by PDB_ID). |
This allows for more flexibility, using sub-tags nested inside it.
<jmol> |
---|
with sub-tags: |
jmolApplet | jmolAppletInlineButton | jmolAppletInlineLink | jmolAppletButton | jmolAppletLink |
---|---|---|---|---|
inserts a JSmol panel | inserts a button that, when clicked by the user, will be replaced by a JSmol panel | inserts a link that, when clicked by the user, will be replaced by a JSmol panel | inserts a button that, when clicked by the user, will open a small window (pop-up) with a JSmol panel | inserts a link that, when clicked by the user, will open a small window (pop-up) with a JSmol panel |
jmolButton | jmolLink | jmolCheckbox | jmolMenu | jmolRadioGroup |
---|---|---|---|---|
inserts a button that, when clicked by the user, will send commands to a JSmol panel | inserts a link that, when clicked by the user, will send commands to a JSmol panel | inserts a checkbox that, when clicked by the user, will send alternative commands to a JSmol panel | inserts a drop-down menu with options that will send commands to a JSmol panel | inserts a group of radio buttons that will send commands to a JSmol panel |
Note: this must be done by the administrator of the wiki.
Jmol
folder inside the extensions
folder of your wiki.extensions/Jmol
folder.jsmol.zip
file from the Jmol release.jsmol
subfolder): JSmol.min.js
and JSmol.GLmol.min.js
j2s
and php
extensions/Jmol/JSmol
folder.LocalSettings.php
adding a line wfLoadExtension('Jmol');
The utility copyJSmolForJmolExtension.php
is included as a convenient way to facilitate direct extraction of the needed files from Jmol-16.xx.xx-binary.zip
(steps 3 and 4 above). It is used like this:
copyJSmolForJmolExtension.php Jmol-xx.xx.xx-binary.zip /mediawiki/extensions/Jmol
The wiki may be configured to allow or deny several options of the Extension. These settings are usually added at the end of LocalSettings.php
, and in any case after the wfLoadExtension('Jmol');
line. The first value indicated is the default:
$wgJmolAuthorizeJmolFileTag = true / false : Authorize the use of the <jmolFile/> tag.
$wgJmolAuthorizeJmolMolTag = true / false : Authorize the use of the <jmolMol/> tag.
$wgJmolAuthorizeJmolPdbTag = true / false : Authorize the use of the <jmolPdb/> tag.
$wgJmolAuthorizeJmolSmilesTag = true / false : Authorize the use of the <jmolSmiles/> tag.
$wgJmolAuthorizeJmolTag = true / false : Authorize the use of the <jmol/> tag.
$wgJmolAuthorizeUploadedFile = false / true : Authorize the use of <uploadedFileContents>.
$wgJmolAuthorizeUrl = false / true : Authorize the use of <urlContents>.
$wgJmolDefaultScript = ... : Default script.
$wgJmolDefaultAppletSize = 400 : Size in pixels of the JSmol panel.
$wgJmolForceNameSpace = ... : Force the NameSpace where JSmol will go looking for wiki pages containing molecular data (using <wikiPageContents>).
$wgJmolShowWarnings = true / false : Display warnings when users try to use disabled features.
$wgJmolDefaultAppletColor
$wgJmolMaxAppletSize
$wgJmolDefaultRenderingEngine = HTML5 / WebGL
$wgJmolMolServer
$wgJmolPdbServer
$wgJmolPlatformSpeed
$wgJmolDefaultCaptionCSS (used in Proteopedia)
$wgJmolDefaultTitleCSS
Ok so expired certificate. Next step,
On Fri, Jan 17, 2025, 1:56 PM Angel Herraez aherraez@users.sourceforge.net
wrote:
Good morning, Bob
After all the email exchanges between Miguel and Jaime, I did not fully understand what the problem was and why it could not be solved, but...
*
Miguel is the owner of the jmol.org domain (and would pay for the SSL certificate)
*
The content is in fact in an Amazon Web Server managed by Jaime (so I assume that Weizmann pays for the hosting, or it is within a larger hoting plan). The subdomain wiki.jmol.org is redirected there.
*
They say that when the certificate is about to expire, emails are sent from AWS to Miguel. He says he did not receive them. So the SSL was inactivated for lack of response.
*
The http url is automatically directed to https (or so I think). And https is blocked by the browser as not trusted.
BTW, my changes to the wiki home page at SF that you had started (in 2017?) were again disregarded yesterday, without any warning. Finally I found how to check permissions and "added" Admins for editing (!!!), and the changes stay now. So I am going ahead with basic documentation of the extension there, and when I manage to revive the extension at MW official page, I will direct here for reference rather than to JmolWiki.
Cheers,
A.