Copying and pasting scripts

Jmol scripts are groups of Jmol commands that, when executed in Jmol, produce a desired molecular scene. Sometimes it is useful to obtain a script from one place, and run it in Jmol somewhere else. For example, certain molecular scenes are generated much more easily in FirstGlance in Jmol than elsewhere (e.g. showing contacts to a ligand). Such a scene can be reproduced in Proteopedia.Org by generating the state script in FirstGlance, and executing it in Proteopedia's molecular Scene Authoring Tools (see instructions).

Java presents some technical obstacles to copying and pasting scripts. Below are described known workarounds.

Applet

We'll assume you have obtained a molecular scene in a web page, in the Jmol applet, and that you wish to regenerate this scene in a Jmol applet elsewhere. The goal is to display the state script for the desired molecular scene, copy and paste the state script into the Jmol console, and run the state script. The details depend on the computer being used.

Apple Mac OS X

Copying the State Script

The state script cannot be copied (or dragged) from the Jmol Script Console, but it can be copied from the Java Console. So first you need to open the Java Console. While displaying a web page containing the Jmol applet, you should find a Java icon in your menu bar (at the top of the screen): a black coffee cup with steam rising. Click on it, and then on Open Java Console.

Application

(please provide details here)

Contributors

EricMartz, AngelHerraez