Figure 3 (Using Layers). In this figure frames are used to display three html files on the same page: this one (green), which contains the figure legend; the one above (magenta), which contains the Jmol image; and the one to the left (yellow), which contains the buttons. A 4 row by 2 column table was used in the right-hand frame to layout the text and buttons.

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Button that displays protein as a cartoon that is colored by structure, and displays the FMN ligand as spacefilled and colored by cpk (atom type)

jmolButton("select *;cartoon on;wireframe off;spacefill off;color structure;select ligand;spacefill on;color cpk","X")

Button toggles spinning on and off script:

jmolCheckbox("set spin y 45;spin on","spin off","")

Button creates a molecular surface about the protein. The script for this button is stored in a separate file.

jmolButton("script './Figure3/button3.spt'","X")

The button3.spt text file contains:
select protein
cartoon off
wireframe off
spacefill off
isosurface select(protein) ignore(not protein) color red sasurface 0.0
select ligand
spacefill on
color cpk
moveto 1.0 -374 -902 215 129.6

Button zooms in and out on the ligand

jmolButton("moveto 1 0 1000 0 0","X")