I am a student doing a project on the superposition algorithm.
I have to rotate 1 protein on top of the other protein after translation to match it as closey as possible.
In order to do that, I need to write the codes in java and also, to open a visualizer(jmol) at the same time to check the rotation(using matrices) of my protein structure to be sure.
How do I get about doing that?
Your help is greatly appreciated! :D
First you should try a basic hill-climbing algorithm and see how well that converges to reasonable solutions.