[chimerax-users] Re: Selecting the N or C-terminus of every chain in a PDB file

5 Jun 2024

      Hi André,
	As far as I know there is no way to do this with ChimeraX's command-line syntax, so I am going to assume you are asking how to do this in Python.  The following Python code will put the starting and ending backbone atom of each chain into a list named 'terminal_atoms':

from chimerax.atomic import all_atomic_structures, Residue
terminal_atoms = []
for s in all_atomic_structures(session):
        for chain in s.chains:
                ordered_bb_names = Residue.aa_min_ordered_backbone_names if chain.polymer_type == Residue.PT_AMINO \
                        else Residue.na_min_ordered_backbone_names
                existing_residues = chain.existing_residues
                terminals = []
                for terminal_residue, bb_names in [(existing_residues[0], ordered_bb_names),
                                (existing_residues[-1], reversed(ordered_bb_names))]:
                        for bb_name in bb_names:
                                a = terminal_residue.find_atom(bb_name)
                                if a:
                                        terminals.append(a)
                                        break
                        else:
                                print("No backbone atoms found in %s; skipping chain" % terminal_residue)
                                break
                else:
                        terminal_atoms.extend(terminals)

For your convenience, I've attached a file containing the above code.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab
...
On Jun 4, 2024, at 12:02 PM, André Graça via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi everyone!
I could not figure this one out just yet, but it might be easy (?): I am interested to make a quick selection that targets the first or last atom of all the chains present in a given PDB file.
/André Graça
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