I was searching online for some scripts/macros that I can use them to superimpose and compare the RMSD of two proteins (same sequence) based on my calculated results. I know PyMOL and MOLMOL provide such tools however I have tons of protein candidates to be compared.
Before I start to write the script by myself, I checked online and saw this software “MaxCluster” developed by the “Structural Bioinformatics group in Imperial College London” . This program can do all atom or backbone RMSD calculation (superposition/alignment too) as well as ensemble clustering. It works pretty FAST!! I used many times recently. To compare more than 3000 structures, it returns me the results in one minutes.
Good for try.