[Chimera-users] addh command not working

Prathvi Singh prathvi at iitk.ac.in
Tue Oct 12 10:07:27 PDT 2021


I have a PDB file which I have trimmed such that it contains only two
residues, say residue-10 and residue-25 (I have given the numbers to denote
that the residues are far apart from each other in the primary structure of
the protein) and saved as a new PDB file. In order to prevent formation of
any pseudobonds between the two residues, I manually added a TER row in the
PDB file, just after the entry of the last atom of residue-10.

Now, when I delete all the atoms of residue-10 except the atoms of its
carbonyl group i.e., its backbone C-atom and covalently linked backbone
O-atom and run the "addh" command, chimera adds H-atoms to the relevant
atoms of residue-25 but doesn't adds H-atoms to the C-atom of residue-10
due to which its valency remains incomplete. Can you please tell me why it
is happening? Is there any way to overcome this problem?

Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016
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