Hello,

1) Basically i hav three conformations (only 3 pdb) of the same molecule picked up from three different regions of a simulated trajectory.
I hv to calculte rmsd and superimpose structure. I tried the emsemble match but it seems that it can work on only two conformation.
Kindly suggest me how i can overcome this.

2) Is it possible to create a substructure (subset) of a molecule and do rmsd calcutn and superimposing only on the substructures for
the conformations i have.