[Chimera-users] addh command not working

Eric Pettersen pett at cgl.ucsf.edu
Tue Oct 12 10:45:47 PDT 2021

Hi Prathvi,
	Despite you deleting all those atoms, Chimera still knows that that is a backbone carbonyl of a peptide and that the carbon atom is connect to two other heavy atoms.  Therefore it adds no hydrogens to it.  To get Chimera to treat it as simply a standalone carbonyl entity you need to change the residue name to something other than a standard peptide residue name before you open the file.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Oct 12, 2021, at 10:07 AM, Prathvi Singh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 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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