Hi, I made Molecular Dynamics studies on a wildtype enzyme and its mutants. To compare the structures (in pymol 40 states for each enzyme) I have to find out which state of the one enzyme has the best rms to the other enzyme. Are there possibilities to solve this problem in pymol or maybe in python? I have not much experience writing python scripts for pymol. The best solution is a list which shows the best rms and the states, or a list of all compared states with their rms values so I can simply see which one will be a good pair. My second question is: How to measure distances over all states and send them to an output - file?
Regards Daniel
