
15 Jun
2021
15 Jun
'21
4:23 a.m.
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