“alter” changes atomic properties using an expression evaluated within a temporary namespace for each atom.

alter selection, expression

alter chain A, chain='B' 
alter all, resi=str(int(resi)+100) 
sort 

Symbols defined (* = read only):

name, resn, resi, resv, chain, segi, elem, alt, q, b, vdw, type, partial_charge, formal_charge, elec_radius, text_type, label, numeric_type, model*, state*, index*, ID, rank, color, ss, cartoon, flags

All strings must be explicitly quoted. This operation typically takes several seconds per thousand atoms altered.

You may need to issue a “rebuild” in order to update associated representations.

WARNING: You should always issue a “sort” command on an object after modifying any property which might affect canonical atom ordering (names, chains, etc.). Failure to do so will confound subsequent “create” and “byres” operations.

alter_state | iterate | iterate_state | sort | cmd.alter | commands