Plot a Monomer Structure

This example demonstrates how to parse a monomer PDB file and plot the backbone trace using atomworks.io.

Custom thumbnail image for this example.

Key steps: - Load a PDB file - Visualize the backbone trace

## Import libraries

import io

from biotite.database import rcsb

from atomworks.io.utils.io_utils import load_any
from atomworks.io.utils.testing import get_pdb_path
from atomworks.io.utils.visualize import view


def get_example_path_or_buffer(pdb_id: str) -> io.StringIO | str:
    try:
        return get_pdb_path(pdb_id)
    except FileNotFoundError:
        return rcsb.fetch(pdb_id, format="cif")

## Load and plot the structure

example = get_example_path_or_buffer("6lyz")  # e.g. '/path/to/6lyz.cif' or io.StringIO(rcsb.fetch("6lyz", "cif"))
atom_array = load_any(example, model=1, extra_fields=["charge", "occupancy"])

# ... inspect the first 15 atoms
print(f"Structure has {atom_array.array_length()} atoms. First 15 atoms:")
atom_array[:15]

Structure has 1102 atoms. First 15 atoms:

AtomArray([
    Atom(np.array([ 3.287, 10.092, 10.329], dtype=float32), chain_id="A", res_id=1, ins_code="", res_name="LYS", hetero=False, atom_name="N", element="N", occupancy=1.0, charge=0, is_polymer=True),
    Atom(np.array([ 2.445, 10.457,  9.182], dtype=float32), chain_id="A", res_id=1, ins_code="", res_name="LYS", hetero=False, atom_name="CA", element="C", occupancy=1.0, charge=0, is_polymer=True),
    Atom(np.array([ 2.5  , 11.978,  9.038], dtype=float32), chain_id="A", res_id=1, ins_code="", res_name="LYS", hetero=False, atom_name="C", element="C", occupancy=1.0, charge=0, is_polymer=True),
    Atom(np.array([ 2.588, 12.719, 10.041], dtype=float32), chain_id="A", res_id=1, ins_code="", res_name="LYS", hetero=False, atom_name="O", element="O", occupancy=1.0, charge=0, is_polymer=True),
    Atom(np.array([1.006, 9.995, 9.385], dtype=float32), chain_id="A", res_id=1, ins_code="", res_name="LYS", hetero=False, atom_name="CB", element="C", occupancy=1.0, charge=0, is_polymer=True),
    Atom(np.array([ 0.016, 10.546,  8.377], dtype=float32), chain_id="A", res_id=1, ins_code="", res_name="LYS", hetero=False, atom_name="CG", element="C", occupancy=1.0, charge=0, is_polymer=True),
    Atom(np.array([-1.404, 10.093,  8.699], dtype=float32), chain_id="A", res_id=1, ins_code="", res_name="LYS", hetero=False, atom_name="CD", element="C", occupancy=1.0, charge=0, is_polymer=True),
    Atom(np.array([-2.269, 10.03 ,  7.451], dtype=float32), chain_id="A", res_id=1, ins_code="", res_name="LYS", hetero=False, atom_name="CE", element="C", occupancy=1.0, charge=0, is_polymer=True),
    Atom(np.array([-3.559,  9.362,  7.735], dtype=float32), chain_id="A", res_id=1, ins_code="", res_name="LYS", hetero=False, atom_name="NZ", element="N", occupancy=1.0, charge=0, is_polymer=True),
    Atom(np.array([ 2.441, 12.404,  7.789], dtype=float32), chain_id="A", res_id=2, ins_code="", res_name="VAL", hetero=False, atom_name="N", element="N", occupancy=1.0, charge=0, is_polymer=True),
    Atom(np.array([ 2.396, 13.826,  7.425], dtype=float32), chain_id="A", res_id=2, ins_code="", res_name="VAL", hetero=False, atom_name="CA", element="C", occupancy=1.0, charge=0, is_polymer=True),
    Atom(np.array([ 1.003, 14.071,  6.846], dtype=float32), chain_id="A", res_id=2, ins_code="", res_name="VAL", hetero=False, atom_name="C", element="C", occupancy=1.0, charge=0, is_polymer=True),
    Atom(np.array([ 0.719, 13.722,  5.679], dtype=float32), chain_id="A", res_id=2, ins_code="", res_name="VAL", hetero=False, atom_name="O", element="O", occupancy=1.0, charge=0, is_polymer=True),
    Atom(np.array([ 3.509, 14.142,  6.435], dtype=float32), chain_id="A", res_id=2, ins_code="", res_name="VAL", hetero=False, atom_name="CB", element="C", occupancy=1.0, charge=0, is_polymer=True),
    Atom(np.array([ 3.49 , 15.586,  5.874], dtype=float32), chain_id="A", res_id=2, ins_code="", res_name="VAL", hetero=False, atom_name="CG1", element="C", occupancy=1.0, charge=0, is_polymer=True)
])

# ... show the structure in a jupyter notebook
view(atom_array[atom_array.chain_id == "A"])

<py3Dmol.view object at 0x7fbeb8156900>