You should find a Java icon in your menu bar (at the top of the screen): a black coffee cup with steam rising. Display a web page containing the Jmol applet. Under the Advanced tab, check Java Console: Hide Console. Run Java Preferences (in Applications:Utilities).
So first you need to open the Java Console. The state script cannot be obtained from the Jmol Script Console, but it can be copied or dragged from the Java Console. Obtaining the State ScriptĬaution: this procedure often fails: see the red paragraph below. Summary Block (highlight) the state script in the Java Console, then drag and drop it into the Jmol Script Console. The following methods have been tested in Leopard OS 10.5.8 (Java 1.5.0_30) and Lion OS 10.7 (Java 1.6.0_26). The details depend on the computer being used. 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. 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. Java presents some technical obstacles to copying and pasting scripts.
#Firstglance jmol how to#
(It is not a state script.) Step by step instructions are here: How to insert a ConSurf result into a Proteopedia green link. This is a bit easier than the steps below because the requisite script can be copied from a web page. 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).Įxample 2: After you color a protein by evolutionary conservation using ConSurf, you may wish to install that color scheme in a Proteopedia page. Sometimes it is useful to obtain a script from one place, and run it in Jmol somewhere else.Įxample 1: Certain molecular scenes are generated much more easily in FirstGlance in Jmol than elsewhere (e.g. Jmol scripts are groups of Jmol commands that, when executed in Jmol, produce a desired molecular scene.
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