ChimeraX Recipes

Inspecting molecule data structures

Here is how to inspect the Python molecular data structures, atoms, residues, and chains. Start ChimeraX and open a PDB atomic model

open 8aie

and show the Python Shell, menu Tools / General / Shell and type the following Python into the shell

    [<chimerax.atomic.structure.AtomicStructure at 0x7fa771aeceb0>]

    m = session.models[0]
    print(, m.num_atoms, 'atoms', m.num_residues, 'residues', m.num_chains, 'chains')
    8aie 4609 atoms 792 residues 2 chains

    a = m.atoms[50]
    print('Atom', a, 'at', a.coord, 'with bfactor', a.bfactor)
    Atom /A ILE 6 O at [5.626 -27.109 17.19] with bfactor 32.77000045776367

    r = a.residue
    print('Residue', r, 'has atoms', ', '.join( for atom in r.atoms))
    Residue /A ILE 6 has atoms N, CA, C, O, CB, CG1, CG2, CD1

    c = r.chain
    print('Chain', c.chain_id, 'is', c.description, 'with', c.num_residues, 'residues')
    Chain A is Aminotransferase class IV with 277 residues

There is information about the attributes of atoms, residues, chains, bonds, structures in the programming manual here, for instance, Atom properties.

Tom Goddard, November 23, 2022