In the earlier version of Avogadro (version 1.2.0), there was an option of Importing the file from PDB. Though Avogadro used to crash on trying to import heavier molecules like 5my1, simpler molecules like 1crn could be directly imported and visualised. This functionality is missing in the latest binary (when I built it from source, i.e. from git://github.com/OpenChemistry/openchemistry.git).