Table of Contents

alter

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

Usage

alter selection, expression

Examples

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

Notes

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
 
Copyright © Schrödinger, LLC. All Rights Reserved.