I have hundreds of pdb structures produced by rosetta membrane abinitio from one sequence.
And I cluster them to get three clusters.
Now I want to align the structures within each clusters, so that I can get RMSD for each cluster.
I used to use MultiProt to align 3D structures, but seems it has a problem dealing with hundreds of structures.
Dose anyone know a better tool (or feature within rosetta, which I'm not aware) to dealing with alignment for many structures?
Thanks for your help!