Reading Frames

Hello Everyone:

Could some one help with this..I am using DS Visualizer 1.5. Sometimes when I am doing an RMSD by opening one structure, and inserting the second (as described in the help section), the structures load from different reading frames, thus I can not do the RMSD. Could someone tell me how to load structures in from the same read reading frame. Everything works fine if both structures are in the same format (e.g. pdb or mol2), but when each structure loaded is of a different format, I get the reading frame problems.

Thanks.
Mark