How to fetch from RCSB and OPM#

Goal#

Programmatically download structures from the RCSB PDB and membrane-oriented coordinates from the Orientations of Proteins in Membranes (OPM) database.

Minimal example#

from moleculekit.molecule import Molecule

# Download directly from RCSB by 4-character PDB ID
mol = Molecule("3PTB")
print(mol.numAtoms)

Parameters that matter#

Function	Key parameters	What it does
`Molecule(pdbid)`	4-character string	Fetches and parses the PDB entry
`rcsbFindLigands(pdbid)`	`pdbid`	Returns a list of ligand component IDs for that entry
`get_opm_pdb(pdbid, keep=False, keepaltloc="A", validateElements=False)`	`pdbid`, `keep`	Downloads the OPM-oriented structure; `keep=True` also returns dummy membrane atoms
`align_to_opm(mol, molsel="all", maxalignments=3, opmid=None, macrotype="protein")`	`mol`, `opmid`	Aligns `mol` to its OPM counterpart by sequence search

Common variations#

# List the ligands bound in a structure, then fetch
from moleculekit.rcsb import rcsbFindLigands

ligands = rcsbFindLigands("3PTB")
print(ligands)

mol = Molecule("3PTB")

# Fetch a membrane protein in its OPM orientation
from moleculekit.opm import get_opm_pdb

mol, thickness = get_opm_pdb("1BL8")

# Align your own structure to its OPM equivalent
from moleculekit.opm import align_to_opm

mol = Molecule("my_structure.pdb")
mol_opm = align_to_opm(mol, maxalignments=3)

Gotchas#

RCSB downloads respect the server rate limits; avoid hammering the API in tight loops.
Set the LOCAL_PDB_REPO environment variable to a local PDB mirror directory to avoid repeated network downloads.
OPM membership requires a known PDB ID or a successful BLAST sequence alignment; structures absent from OPM will raise or return None.
get_opm_pdb() with keep=False (default) strips the dummy membrane atoms that OPM adds; pass keep=True if you need them for visualization.

See also#