[Chimera-users] command line: how to add hydrogens to a phosphate group?

[Sara Luz Gomez Maya]

Hi,

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
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