Alter: Difference between revisions
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===DESCRIPTION=== | ===DESCRIPTION=== | ||
'''alter''' changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in the name space are: | '''alter''' changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in the name space, which are are explained in [[Iterate]] are: | ||
name, resn, resi, chain, alt, elem, q, b, segi, | name, resn, resi, chain, alt, elem, q, b, segi, | ||
type (ATOM,HETATM), partial_charge, formal_charge, | type (ATOM,HETATM), partial_charge, formal_charge, | ||
Revision as of 16:19, 18 February 2007
DESCRIPTION
alter changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in the name space, which are are explained in Iterate are:
name, resn, resi, chain, alt, elem, q, b, segi, type (ATOM,HETATM), partial_charge, formal_charge, text_type, numeric_type, ID, vdw
All strings must be explicitly quoted. This operation typically takes several seconds per thousand atoms altered.
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.
USAGE
alter (selection),expression
EXAMPLES
- Change chain label and residue index
alter (chain A),chain='B'
alter (all),resi=str(int(resi)+100)
sort
- Change van der Waals radius of a given atom
alter (name P), vdw=1.90
Not that is if dots, spheres, mesh or surface representation is used. You have to refresh the view with
rebuild