[Chimera-users] addh command not working

[Prathvi Singh]

Hi,

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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