RMSD calculation for whole PDBs

#### Describe the workflow you want to enable
From what I can understand PandasPDB.rmsd can calculate the rmsd only if both dataframes have the same length. However, if I want to compare 2 PDBs (one chain each) where the target protein (Uniprot ID) is the same (for example 2vua vs 2vu9) I can't because although the protein is the same one has a different purification tag and thus I cannot use the rsmd function
#### Describe your proposed solution
it should be pretty easy to calculate de identity between 2 structures and select only those residues. This can ofc be done manually by each user, but I think it would be a great improvement.

Start by reading the PandasPDB.rmsd entry point and its current assumptions about equal-length dataframes. Determine how residue identity should be established for structures such as 2vua and 2vu9, then define tests showing that differing purification tags are excluded and RMSD can be calculated for the remaining residues.

Written by the indexing model from the issue text.