I have a system consisting of a molecule intercalated into DNA. For a very specific application, I need to remove all the Sodium atoms from a PDB file and, in turn, add hydrogens to all the DNA phosphate groups (whatever the oxygen). Since for chimera that atom type is identified as O3- (possibly resonance-equivalent terminal oxygen on tetrahedral center (phosphate, sulfate, N-oxide), I have tried:

labelopt info idatmType

label #0

addh spec O3-

but it did not work.

You can find attached herewith the pdb file. 

Any help is appreciated.

Regards,

Sara