Difference between revisions of "MediaWiki/Basic Example"

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This page demonstrates basic uses of the [[:mw:Extension:Jmol|Jmol MediaWiki extension]].
 
This page demonstrates basic uses of the [[:mw:Extension:Jmol|Jmol MediaWiki extension]].
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These are new tags introduced in the 3.3_dev version of the Jmol MediaWiki Extension. They all open a new (pop-up) window filled with a JmolApplet. The applet will fit the window, which is resizable.
  
 
== Examples with <tt>&lt;jmolFile&gt;</tt> ==
 
== Examples with <tt>&lt;jmolFile&gt;</tt> ==
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This feature is currently under development.
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This tag creates a link that opens a JmolApplet and loads the model from a file that has been previously uploaded to the wiki. The model is displayed in the default rendering (ball and stick, CPK color, black background).
  
 
The code
 
The code
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gives
 
gives
 
<jmolFile>Chair.cml</jmolFile>
 
<jmolFile>Chair.cml</jmolFile>
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to display molecular data from [[:File:Chair.cml|File:Chair.cml]].
  
 
The code
 
The code
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gives
 
gives
 
<jmolFile text="Show ethanol">Ethanol.xyz</jmolFile>
 
<jmolFile text="Show ethanol">Ethanol.xyz</jmolFile>
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to display molecular data from [[:File:Ethanol.xyz|File:Ethanol.xyz]].
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== Examples with <tt>&lt;jmolPdb&gt;</tt> ==
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This feature is currently under development.
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This tag creates a link that opens a JmolApplet and loads a model from the PDB database server. The model is displayed in the default rendering (ball and stick, CPK color, black background).
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The code
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<tt><nowiki><jmolPdb>1ALE</jmolPdb></nowiki></tt>
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gives
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<jmolPdb>1ALE</jmolPdb>
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to display 1ALE molecular data directly from [[:en:Protein Data Bank|Protein Data Bank]].
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The code
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<tt><nowiki><jmolPdb text="Show 1ALE">1ALE</jmolPdb></nowiki></tt>
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gives
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<jmolPdb text="Show 1ALE">1ALE</jmolPdb>
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to display 1ALE molecular data directly from [[:en:Protein Data Bank|Protein Data Bank]].
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== Examples with <tt>&lt;jmolSmiles&gt;</tt> ==
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This feature is currently under development.
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This tag creates a link that opens a JmolApplet and loads a model from the Cactus NIH server, constructed from a SMILES string, CAS number, InChI key or chemical name. The model is displayed in the default rendering (ball and stick, CPK color, black background).
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The code
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<tt><nowiki><jmolSmiles>CCCNC</jmolSmiles></nowiki></tt>
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gives
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<jmolSmiles>CCCNC</jmolSmiles>
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to display molecular data directly associated to [[:en:SMILES|SMILES string]] CCCNC.
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The code
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<tt><nowiki><jmolSmiles>aspirin</jmolSmiles></nowiki></tt>
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gives
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<jmolSmiles>aspirin</jmolSmiles>
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to display molecular data associated to that name.
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The code
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<tt><nowiki><jmolSmiles text="Show CCCNC">CCCNC</jmolSmiles></nowiki></tt>
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gives
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<jmolSmiles text="Show CCCNC">CCCNC</jmolSmiles>
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to display molecular data directly associated to [[:en:SMILES|SMILES string]] CCCNC.
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[[Category:Pages Using Jmol MW Extension]]

Latest revision as of 23:28, 24 November 2011

This page demonstrates basic uses of the Jmol MediaWiki extension.

These are new tags introduced in the 3.3_dev version of the Jmol MediaWiki Extension. They all open a new (pop-up) window filled with a JmolApplet. The applet will fit the window, which is resizable.

Examples with <jmolFile>

This feature is currently under development.

This tag creates a link that opens a JmolApplet and loads the model from a file that has been previously uploaded to the wiki. The model is displayed in the default rendering (ball and stick, CPK color, black background).

The code <jmolFile>Chair.cml</jmolFile> gives Chair.cml to display molecular data from File:Chair.cml.

The code <jmolFile text="Show ethanol">Ethanol.xyz</jmolFile> gives Show ethanol to display molecular data from File:Ethanol.xyz.

Examples with <jmolPdb>

This feature is currently under development.

This tag creates a link that opens a JmolApplet and loads a model from the PDB database server. The model is displayed in the default rendering (ball and stick, CPK color, black background).

The code <jmolPdb>1ALE</jmolPdb> gives 1ALE to display 1ALE molecular data directly from Protein Data Bank.

The code <jmolPdb text="Show 1ALE">1ALE</jmolPdb> gives Show 1ALE to display 1ALE molecular data directly from Protein Data Bank.

Examples with <jmolSmiles>

This feature is currently under development.

This tag creates a link that opens a JmolApplet and loads a model from the Cactus NIH server, constructed from a SMILES string, CAS number, InChI key or chemical name. The model is displayed in the default rendering (ball and stick, CPK color, black background).

The code <jmolSmiles>CCCNC</jmolSmiles> gives CCCNC to display molecular data directly associated to SMILES string CCCNC.

The code <jmolSmiles>aspirin</jmolSmiles> gives aspirin to display molecular data associated to that name.

The code <jmolSmiles text="Show CCCNC">CCCNC</jmolSmiles> gives Show CCCNC to display molecular data directly associated to SMILES string CCCNC.