model.atoms — all atoms in the model

This is a standard Python list of all the atoms in the model. This can be used to query individual atom properties (e.g. coordinates) or to specify atoms for use in restraints, etc.

Atoms can be individually accessed in two ways:

• A string of the form 'ATOM_NAME:RESIDUE_#[:CHAIN_ID]', where ATOM_NAME is the four character IUPAC atom name as found in a PDB file, RESIDUE_# is a five character residue number as it occurs in the PDB file of a model, and the optional CHAIN_ID is the single character chain id as it occurs in the PDB file. For example, if 'm' is a model object, the carbonyl oxygen (O) in residue '10A' in chain 'A' is given by 'm.atoms['O:10A:A']'; if the chain has no chain id, 'm.atoms['O:10A']' would be sufficient.

• By numeric index, starting from zero, in standard Python fashion. For example, if 'm' is a model object, 'm.atoms[0]' is the first atom, 'm.atoms[-1]' is the last atom, and 'm.atoms[0:10]' is a list of the first 10 atoms (0 through 9). (Note that the atom numbers in PDB files and MODELLER restraint files start from 1, so will always be 1 larger than any index you use here.)

See Section 6.23 for more information about Atom objects. See also Sequence.residues and Sequence.chains for equivalent lists of residues and chains. See also model.atom_range(), for getting a contiguous range of atoms.