[chimerax-users] Re: Select all truncated amino acids in model (though ISOLDE?)

5 Jun 2025

      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`.