The FAQ says that the colors represent how strong a binding there is at a particular point on the ligand. So the colors must not represent the atoms of various elements within the ligand. But I have noticed that all the spheres of the same size have the same color. Is the size also a direct function of the binding energies, thus essentially reinforcing the message conveyed by the color? Also, it seems now that the actual ligand molecule is not even shown on the visual display - only the good binding points are shown and the ligand itself is invisible. Is that correct? If so, why is the ligand itself not being shown?

Remembered a post from last year mentioning spheres which goes here: http://www.hhmi.org/news/perryman_mccammon20060310.html

If you hold the left button with of the mouse when hovering over the graph, you can freeze the rotating image and turn it in all directions in such a way to put the position so that you can better monitor the coming and going.

Here's an image

http://www.hhmi.org/news/popups/perryman_pop.html

Hi,

I have often wondered myself on occasion if there is any rhyme or reason behind the graphics and if it's nothing short of inaccurate "Eye Candy" while the real work goes on invisible?

Either way, the average person probably just can see some graphics dancing and assumes something productive is being done.

It would be nice to have a more descriptive process and logic when you hover over it with the mouse or something. It might give more end users a more "fullfilling purpose."

This post got me thinking and wondering if there could be more than just colors at work, but 'gradients' of the colors also. Lighter red could symbolize lower binding energy while darker red could symbolize higher binding energies?

Transparency really weak and flashing. Such concepts could symbolize other functions or features? Video games already use such concepts and ideas to convey information automatically in a common sense form.

Is there anyone working on graphics/interface alone or specializing in it?