Thanks a lot Tristan! In case anyone else needs this, here is a ChatGPT-polished version of that that can be saved locally and executed in the command line with runscript path/to/select_incomplete_residues.py atom-spec. Best wishes, Matthias #!/usr/bin/env python """ Incomplete-residue finder ======================== Select **all amino‑acid residues missing one or more heavy template atoms**. Optionally limit the search to a user‑specified atom selection. Selection priority (highest → lowest) ------------------------------------- 1. **Command‑line spec** following the script name (quoted if it has spaces). Example inside ChimeraX: ``` runscript /path/to/select_incomplete_residues.py #1/A ``` 2. **Current GUI selection** if no command‑line spec is given. 3. **Whole model** – ISOLDE‑selected model → first atomic model in the session. import sys from chimerax.atomic import ( Residue, concise_residue_spec, selected_atoms, # ← ChimeraX convenience to get currently selected atoms ) from chimerax.core.commands import run from chimerax.core.errors import UserError # ----------------------------------------------------------------------------- # Helper functions # ----------------------------------------------------------------------------- def _pick_model(sess): """Return an atomic model if none is implied by user selection.""" isolde = getattr(sess, "isolde", None) if isolde and isolde.selected_model is not None: return isolde.selected_model for m in sess.models.list(): if hasattr(m, "residues"): return m raise UserError("No atomic model with residues found in the session.") def _atoms_from_spec(sess, spec: str): """Return atoms matching *spec* (empty collection if spec is invalid/empty).""" if not spec: return None try: # Use ChimeraX commands to create the selection, then read it back. run(sess, "select clear") run(sess, f"select {spec}") return selected_atoms(sess) except Exception as err: sess.logger.warning(f"Failed to apply selection '{spec}': {err}") run(sess, "select clear") return None def _candidate_residues(sess, sel_spec): """Determine which residues to analyse based on the priority rules.""" # 1 – explicit selection string atoms = _atoms_from_spec(sess, sel_spec) if atoms and len(atoms): return atoms.unique_residues # 2 – current GUI selection atoms = selected_atoms(sess) if atoms and len(atoms): return atoms.unique_residues # 3 – fall back to whole model mdl = _pick_model(sess) return mdl.residues # ----------------------------------------------------------------------------- # Main logic # ----------------------------------------------------------------------------- def main(sess): # Merge all argv tokens into a single selection spec (may contain spaces) sel_spec = " ".join(sys.argv[1:]) if len(sys.argv) > 1 else None residues = _candidate_residues(sess, sel_spec) protein_res = residues[residues.polymer_types == Residue.PT_AMINO] incomplete = [r for r in protein_res if r.is_missing_heavy_template_atoms()] if not incomplete: sess.logger.info("✅ No incomplete residues found in the chosen target set.") run(sess, "select clear") return spec = concise_residue_spec(sess, incomplete) run(sess, f"select {spec}") sess.logger.info(f"⚠️ Selected {len(incomplete)} incomplete protein residues.") # ----------------------------------------------------------------------------- # Script entry point (ChimeraX injects 'session') # ----------------------------------------------------------------------------- try: session # noqa: F401 – provided by ChimeraX except NameError as exc: raise RuntimeError("This script must be run inside UCSF ChimeraX.") from exc else: main(session) From: Tristan Croll <tcroll@altoslabs.com> Date: Thursday, June 5, 2025 at 13:57 To: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at> Cc: Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Select all truncated amino acids in model (though ISOLDE?) 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`.