View source for MediaWiki/Simple Tags

== Simple tags in the Jmol Extension for MediaWiki ==
__TOC__

These tags will write a link 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.

The tags take a text string that specifies the model to be retrieved from a file previously uploaded to the wiki or from one of the databases accessible to Jmol.

The text for the link may be specified (otherwise, it will be the same model id)

The wikicode is displayed to the right of each example.

=== jmolFile tag ===
<table>
<tr>
<td style="vertical-align:top;">
Let's see the 3D structure of <jmolFile text='cyclohexane'>Chair.cml</jmolFile>
in the chair conformation.

The structure is retrieved from a file previously uploaded to this wiki.
</td>
<td style="vertical-align:top;">
 <nowiki><jmolFile text='cyclohexane'>Chair.cml</jmolFile></nowiki>
</td>
<tr>
</table>

=== jmolMol tag ===
<table>
<tr>
<td style="vertical-align:top;">
See the structure of something <jmolMol text='in your coffee'>caffeine</jmolMol>

The structure is retrieved from the NCI CACTUS server, or from another server defined by the wiki administrator. 
The contents of the tag must be some ID understood by the server.
</td>
<td style="vertical-align:top;">
 <nowiki><jmolMol text='in your coffee'>caffeine</jmolMol></nowiki>
</td>
</tr>
</table>

=== jmolSmiles tag ===
<table>
<tr>
<td style="vertical-align:top;">
The link <jmolSmiles text='nitrobenzene'>c1ccccc1[N+](=O)[O-]</jmolSmiles> will open a popup window displaying the structure of nitrobenzene.

The structure is retrieved from the NCI CACTUS server. The contents of the tag may be a SMILES string, a name or any other ID allowed by the server.
</td>
<td style="vertical-align:top;">
 <nowiki><jmolSmiles text='nitrobenzene'>c1ccccc1[N+](=O)[O-]</jmolSmiles></nowiki>
</tr>
</table>

=== jmolPdb tag ===
<table>
<tr>
<td style="vertical-align:top;">
The <jmolPdb text='adipocyte lipid binding protein'>1ab0</jmolPdb> is a small globular protein.

The structure is retrieved from the RCSB PDB server (or another PDB server, as configured by the wiki administrator). 
The contents of the tag must be the 4-character PDB ID.
</td>
<td style="vertical-align:top;">
 <nowiki><jmolPdb text='adipocyte lipid binding protein'>1ab0</jmolPdb></nowiki>
</td>
</tr>
</table>


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