Using Java for Rendering Structures

From Proteopedia

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Proteopedia now uses the version of Jmol that supports running with HMTL5/Javascript or the traditional Java. Proteopedia defaults to the HMTL5/Javascript of Jmol.

However, as Java remains the best for performance, when present we encourage you to use Java to render the 3D visualizations on Proteopedia.

Users with Java installed on their computer can select Proteopedia to run Jmol in Java mode on a page-by-page basis or registered users can set Java mode as your default option. How to do each of these two options is explained below.

NOTE: TABLETS AND PORTABLE DEVICES THAT DO NOT HAVE THE OPTION TO INSTALL JAVA ONLY HAVE THE CHOICE OF RUNNING JMOL WITH HMTL5/Javascript. See Java#Detecting your Java version to look into whether you have Java installed.

Rendering Structures with Jmol in Java-mode on a page-by-page basis

Append the code below to the URL of a Proteopedia page to render structures with Jmol using Java.

?_USE=SIGNED

For, example to view the page

http://proteopedia.org/wiki/index.php/G_protein-coupled_receptor

using Java-based Jmol, the URL of the Proteopedia page would be

http://proteopedia.org/wiki/index.php/G_protein-coupled_receptor?_USE=SIGNED

.

You may now be prompted to accept the certificate for the signed Java applet. Note, you will not see this if you have already selected the checkbox option to remember you trusted it already.

When the structure scene appears, you'll see Jmol_S in the bottom right corner of the Proteopedia structure scenes on that page, indicating you are viewing it with the signed Java-based Jmol applet.

Setting your default to render Proteopedia's structures with Jmol in Java-mode

See also

• Java
• Jmol