Hi Sabrina, ChimeraX only has a list of names for the heavy atoms of the backbone. Hydrogens bonded to those backbone atoms are considered backbone hydrogens regardless of their name. Any other atoms in the residue are considered side chain atoms. The list of heavy backbone atom names is C, CA, N, O, OXT, and for non-standard PDB files, OT1 and OT2. --Eric Eric Pettersen UCSF Computer Graphics Lab

On Mar 5, 2024, at 1:39 AM, Sabrina Moffit via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX team,

So far I've found that these are the atom names classified as mainchain atoms by ChimeraX: ['H3', 'HA2', 'H2', 'CA', 'H', 'H1', 'HA', 'C', 'O', 'HA3', 'OXT', 'N'], by using such command: sel #1 & mainchain; info atoms sel.

I'm not sure if there are more atom names classified as mainchain atoms by ChimeraX. Could you please provide me with a comprehensive list of all the atom names of the mainchain atoms (and sideonly atoms as well, if possible) of all types of amino acids?

Thank you.

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