Molecules 1.4.2 now on the App Store
Searches of the Protein Data Bank had been failing if only one molecule met the search criteria, because then the PDB web services would return a web page rather than the normal text results. This is now accounted for, so hopefully all PDB searches should work.
A few amino acid residues had incorrect bonds, and they should all be fixed now. Thanks go to Dr. Steven Muskal of Eidogen-Sertanty for pointing this out. While you're at it, check out their iProtein iPad application, which interacts with Molecules.
The rendering performance of rotating molecules should be improved, particularly on the more powerful devices.
Finally, the visualization mode you select persists until you change it, even across multiple molecules.