MediaWiki/Tags for In-page Models

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Tags in the Jmol Extension for MediaWiki that will include models while the page loads

These tags will embed in the page a JSmol panel displaying a structure, at the same time the page is displayed.

Note that the page will take longer to load and to be responsive, particularly if more than one JSmol is embedded. For a quick loading page where models are only loaded later, on user action, see MediaWiki/Tags for Pop-up Models, [[MediaWiki/Tags for Pop-in Models|Tags for Pop-in Models}} and Simple Tags.

The tags are sub-tags of the <jmol> tag and in turn include several sub-tags, described below.

The wikicode is displayed to the right of each example.


jmolApplet tag

uploadedFileContents subtag

A model stored in a file in this wiki

Chair conformation of cyclohexane 

<jmol>
  <jmolApplet>
    <name>A</name> 
    <title>A model stored in a file in this wiki</title> 
    <caption>Chair conformation of cyclohexane</caption> 
    <color>greenTint</color> 
    <size>260</size> 
    <uploadedFileContents> Chair.cml </uploadedFileContents>
    <controls>spin popup</controls> 
    <frame> true </frame>
  </jmolApplet>
</jmol>

urlContents subtag

A file retrieved from the web

Murine adipocyte lipid binding protein at pH 4.5 (1AB0.pdb) 

<jmol>
  <jmolApplet>
    <name>B</name> 
    <title>A file retrieved from the web</title> 
    <caption>Murine adipocyte lipid binding protein at pH 4.5 (1AB0.pdb)</caption> 
    <color>blueTint</color> 
    <size>300</size> 
    <urlContents> https://files.rcsb.org/download/1ab0.pdb.gz </urlContents>
    <pspeed>2</pspeed> 
    <controls>spin popup</controls> 
    <frame> true </frame>
  </jmolApplet>
</jmol>

wikiPageContents subtag

This is 2-propanol

Data read from the page Models/2-propanol 

<jmol>
  <jmolApplet>
    <name>D</name> 
    <title>This is 2-propanol </title> 
    <color>yellowtint</color> 
    <size>260</size> 
    <caption>Data read from the page [[Models/2-propanol]]</caption> 
    <wikiPageContents> Models/2-propanol </wikiPageContents>
    <frame> true </frame>
  </jmolApplet>
</jmol>

script subtag

This box has a message, but might hold a 3D model
 
<jmol>
  <jmolApplet>
    <name>E</name> 
    <title>This box has a message, but might hold a 3D model</title> 
    <color>blueTint</color> 
    <size>150</size> 
    <script> echo Hi there! </script>
    <frame> true </frame>
  </jmolApplet>
</jmol>

inlineContents subtag

And also demonstrating controls.

This is 1-propanol 

<jmol>
  <jmolApplet>
    <name>C</name> 
    <color>lightGray</color> 
    <size>240</size> 
    <caption>This is 1-propanol</caption> 
    <frame> true </frame>
    <inlineContents> 
C3H8O 1-propanol
APtclcactv02181912073D 0   0.00000     0.00000
 
 12 11  0  0  0  0  0  0  0  0999 V2000
    0.5267   -0.4947   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5950    0.5458   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9499   -0.1649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7922    0.1691    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4436   -1.1185    0.8900 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4436   -1.1185   -0.8900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5119    1.1696    0.8900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5119    1.1696   -0.8900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0330   -0.7887   -0.8900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0330   -0.7887    0.8900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7490    0.5764    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5508   -0.4305   -0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  0  0  0  0
  1  6  1  0  0  0  0
  2  7  1  0  0  0  0
  2  8  1  0  0  0  0
  3  9  1  0  0  0  0
  3 10  1  0  0  0  0
  3 11  1  0  0  0  0
  4 12  1  0  0  0  0
M  END
    </inlineContents>
  </jmolApplet>

  <jmolButton>
    <script> spacefill on </script>
    <text> spacefill </text>
    <target> C </target>
  </jmolButton>

  <jmolLink>
    <script> spacefill 23% </script>
    <text> ball and stick </text>
    <target> C </target>
  </jmolLink>

  <jmolCheckbox>
    <scriptWhenChecked> spin on </scriptWhenChecked>
    <scriptWhenUnchecked> spin off </scriptWhenUnchecked>
    <checked> false </checked> 
    <text> spin </text>
    <target> C </target>
  </jmolCheckbox>

  <jmolMenu>
    <target> C </target>
    <item>
      <text> color CPK </text>
      <checked> true </checked>
      <script> color cpk </script>
    </item>
    <item>
      <text> blue </text>
      <script> color dodgerBlue </script>
    </item>
    <item>
      <text> green </text>
      <script> color green </script>
    </item>
  </jmolMenu>

  <jmolRadioGroup>
    <target> C </target>
    <vertical>false</vertical>
    <item>
      <text> color CPK </text>
      <checked> true </checked>
      <script> color cpk </script>
    </item>
    <item>
      <text> blue </text>
      <script> color dodgerBlue </script>
    </item>
    <item>
      <text> green </text>
      <script> color green </script>
    </item>
  </jmolRadioGroup>

</jmol>


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Contributors

AngelHerraez

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