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

Sara Luz Gomez Maya sara.gomezmaya at sns.it
Tue Jun 15 04:23:15 PDT 2021


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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210615/d0791b16/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: M3_frame370.pdb
Type: chemical/x-pdb
Size: 770799 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210615/d0791b16/attachment-0001.bin>

More information about the Chimera-users mailing list