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“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) 


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.

See Also

command/alter.txt · Last modified: 2013/08/19 21:01 (external edit)