Keywords: manual

Next: model.residues all Up: The model class: handling Previous: model.group_restraints all Contents Index

## 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 6.19 for more information about `atom` objects. See also model.atom_range(), for getting a contiguous range of atoms.

Next: model.residues all Up: The model class: handling Previous: model.group_restraints all Contents Index