Hi Sara, You have to change the atom type of the O3- atoms to O3, and then add the hydrogens. For example, commands: setattr a idatmType O3 O3- addh see details of the "setattr" command: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 15, 2021, at 4:23 AM, Sara Luz Gomez Maya via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
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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