Subsections


structure.add_atom

Image structure Image list-add-relax-blue

Synopsis

Add an atom.

Defaults

structure.add_atom(mol_name=None, atom_name=None, res_name=None, res_num=None, pos=None, element=None, atom_num=None, chain_id=None, segment_id=None, pdb_record=None)

Keyword arguments

mol_name: The name of molecule container to create or add the atom to.

atom_name: The atom name.

res_name: The residue name.

res_num: The residue number.

pos: The atomic coordinates. For specifying different coordinates for each model of the ensemble, a list of lists can be supplied.

element: The element name.

atom_num: The optional atom number.

chain_id: The optional chain ID string.

segment_id: The optional segment ID string.

pdb_record: The optional PDB record name, e.g. `ATOM' or `HETATM'.

Description

This allows atoms to be added to the internal structural object. To use the same atomic coordinates for all models, the atomic position can be an array of 3 values. Alternatively different coordinates can be used for each model if the atomic position is a rank-2 array where the first dimension matches the number of models currently present.


The relax user manual (PDF), created 2016-10-28.