CaspR is a web-tool for molecular replacement.
In association with CaspR, you can use RMSDcalc to superimpose up to 6 structures on the same reference and compute the RMSD, a povray image and a graphical view of the structural alignment, and magicPDB, to modify a PDB file (renumber atoms and residues, change chainID, apply deletions, display fasta, split chains ...).

see online : homepage