Difference between revisions of "Sandbox"

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(→‎Get the model from a different server)
(→‎Get the model from a different server)
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<jmol><jmolApplet>
 
<jmol><jmolApplet>
 
<signed>true</signed>
 
<signed>true</signed>
−
<name>1CRN</name><color>[xFFFFAA]</color><size>300</size>
+
<name>1CRN</name><color>[xFFAAAA]</color><size>300</size>
 
<urlContents>http://biomodel.uah.es/model3j/glc_bd_p.pdb</urlContents>
 
<urlContents>http://biomodel.uah.es/model3j/glc_bd_p.pdb</urlContents>
 
</jmolApplet></jmol>
 
</jmolApplet></jmol>

Revision as of 20:01, 1 December 2008

This is a page for testing.

Jmol extension for MediaWiki

This uses uploadedFileContents tag with an XYZ file:

For some reason, checkboxes are not working with the extension.

Color atoms:


This one uses the inlineContents tag, with straight MOL data on the left applet and with added pipe characters (|) on the right applet:

None of them work. This seems due to a defective parsing of newlines by the extension.

Let's test the same with inline PDB data:

The right applet works. The difference with MOL format is likely because MOL requires the lines in a certain order, while PDB relies on the starting keyword. I think that the extension is inserting extra newlines and quotes, that spoil the MOL parser but not the PDB parser. The newlines are ignored by Jmol.js, or replaced by pipes. Manually added pipes restore a proper start of line for the PDB parser. --AngelHerraez 22:11, 30 November 2008 (CET)


Finally, if we insert the MOL data without any newlines and with pipes:

things work, so IT IS the newlines.

Get the model from a different server

(Uses urlContents).

I'm not sure if the use of the signed applet is allowed in the configuration of the Jmol MediaWiki Extension for the Jmol Wiki (I rather think it is not). But this example is working with the unsigned applet even if I set <signed>true</signed> or <signed>false</signed>.

Supposedly the unsigned applet should not load a model coming from a different web domain, as per Java security rules... What's going on?

Using <signed>true</signed>:
 Using <signed>false</signed>:

Using a pop-up window

An image used for illustration and a caption for requesting the Jmol model:

Ethane s.gif
Staggered ethane

Contributors

AngelHerraez

Retrieved from "https://wiki.jmol.org/index.php?title=Sandbox&oldid=5502"