Kryptonite, when applied, robs side chains of their forces. In the simplest form of implementation, a Kryptonite checkbox would be added to the View: Show Bonds (Sidechain) line item. When checked, all forces related to side chains are turned off.

Side chains would be robbed of their forces until the Kryptonite was removed. In this way, folding priority is given to backbone forces and geometry. Ideally, I would like to have the ability to turn on/off sidechain forces by amino acid type or even individual segments. However, this might be a difficult feature to implement. Therefore, being able to turn all sidechains on/off would be a step in the right direction.

In a more robust implementation, something that works more like Freeze/Unfreeze could be used. Applying Kryptonite to one segment at a time robs that segment's side chain from having any forces associated with it until the Kryptonite is removed. The graphic user interface could turn the selected segment's side chain to a pale green color until the Kryptonite is removed.

It seems to me that forces related to sidechains, while important to protein geometry probably occur at different rates and strengths during the formation process. Kryptonite would allow us to experiment with various influences of sidechain forces and bonding.

By the way, I originally wanted to call this feature "Cloak of Invisibility" but we already have a 'ci' feature.

phi16