Hi Matthias,

I don't believe there's a way to do this via the command interface at present, but it's pretty easy in Python:

from chimerax.atomic import Residue

m = session.isolde.selected_model #if using ISOLDE

protein = m.residues[m.residues.polymer_types==Residue.PT_AMINO]

incomplete = [r for r in protein if r.is_missing_heavy_template_atoms()]

... and then do with them what you will. One approach:

from chimerax.core.commands import run
from chimerax.atomic import concise_residue_spec
incomplete = iter(incomplete)
run(session, f'view {concise_residue_spec(session, [next(incomplete)])} pad 0.5')

... and then repeat that last line as needed until you hit `StopIteration`.

On Thu, Jun 5, 2025 at 10:54 AM Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi everyone,

Is it possible to create a selector or python script to identify/match all truncated amino acids in a model? If not possible directly in ChimeraX, could ISOLDE offer a solution through matching to residue template “TRUNC_CB”?

Thanks in advance,

Matthias

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