Frequently, people deposit just CA atoms, and you may need a molecule containing all of the atoms. This is easy to do in O but many people do it wrong. Suppose the CA coordinates are in a file ca.pdb which has the correct sequence and consists of residues 1-365. Start O and do the following:
s_a_i ca.pdb ca copy all_residue_type ca_residue_type s_init all merge ca 1 365 all 1 ; leg_aut_mc all 1 365 leg_aut_sc all 2 364
This will create everything from residue 2 to 364 with the side chains taking up the most common rotamer. Use Baton_build to make the first and last residue.