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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: | |
| − | + | name, resn, resi, chain, alt, elem, q, b, segi, | |
| − | using the python evaluator with a separate name space for each | + | type (ATOM,HETATM), partial_charge, formal_charge, |
| − | atom. The symbols defined in the name space are: | + | 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 | |
| − | |||
| − | All strings must be explicitly quoted. This operation typically | ||
| − | takes several seconds per thousand atoms altered. | ||
| − | |||
| − | WARNING: You should always issue a | ||
after modifying any property which might affect canonical atom | after modifying any property which might affect canonical atom | ||
ordering (names, chains, etc.). Failure to do so will confound | ordering (names, chains, etc.). Failure to do so will confound | ||
subsequent "create" and "byres" operations. | subsequent "create" and "byres" operations. | ||
| − | + | ||
===USAGE=== | ===USAGE=== | ||
alter (selection),expression | alter (selection),expression | ||
| − | + | ||
===EXAMPLES=== | ===EXAMPLES=== | ||
| − | + | alter (chain A),chain='B' | |
| − | + | alter (all),resi=str(int(resi)+100) | |
| − | + | sort | |
| − | + | ||
===SEE ALSO=== | ===SEE ALSO=== | ||
| − | + | [[Cmd alter_state]], [[Cmd iterate]], [[Cmd iterate_state]], [[Cmd sort ]] | |
[[Category:Commands|alter]] | [[Category:Commands|alter]] | ||
Revision as of 08:38, 16 January 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 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
alter (chain A),chain='B' alter (all),resi=str(int(resi)+100) sort