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 Eric Pettersen UCSF Computer Graphics Lab

On Oct 12, 2021, at 10:07 AM, Prathvi Singh via Chimera-users <chimera-users@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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users