The at the bottom of the toolbar will let you write scripts to JSmol. Simply enter a script in JSmol's scripting language and hit enter to apply it. Let's start with some basic commands:
- select protein
- color blue
- select nucleic
- color green
- select hetero
- color orange
This same sequence of commands could be written in one line using semicolons (;) to separate each command, as such: select protein; color blue; select nucleic; color green; select hetero; color orange;.
With the cursor in the text box, use the arrow keys to cycle through previously applied commands. The up arrow will traverse backward in history; the down arrow will traverse forward (more recent). If you write a command incorrectly, the web page will display an error alert with more details.