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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
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  name, resn, resi, chain, alt, elem, q, b, segi,
using the python evaluator with a separate name space for each
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type (ATOM,HETATM), partial_charge, formal_charge,
atom.  The symbols defined in the name space are:
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text_type, numeric_type, ID, vdw
   
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  name, resn, resi, chain, alt, elem, q, b, segi,
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All strings must be explicitly quoted.  This operation typically takes several seconds per thousand atoms altered.
  type (ATOM,HETATM), partial_charge, formal_charge,
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  text_type, numeric_type, ID
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'''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 "sort" command on an object
 
 
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
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===EXAMPLES===
 
===EXAMPLES===
  alter (chain A),chain='B'
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alter (chain A),chain='B'
  alter (all),resi=str(int(resi)+100)
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alter (all),resi=str(int(resi)+100)
  sort
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sort
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===SEE ALSO===
 
===SEE ALSO===
  [[Cmd alter_state]], [[Cmd iterate]], [[Cmd iterate_state]], [[Cmd sort ]]
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[[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

SEE ALSO

Cmd alter_state, Cmd iterate, Cmd iterate_state, Cmd sort