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Revision as of 06:23, 9 April 2007 by James (talk | contribs) (DESCRIPTION)
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iterate iterates over an expression with a separate name space for each atom. However, unlike the "alter" command, atomic properties can not be altered. Thus, iterate is more efficient than alter.

Iterate is a powerful tool that can be used to perform operations and aggregations using atomic selections, and store the results in any global object, such as the predefined stored object. For example, one could iterate over all of the alpha carbons and record their B Factors, or print out all of the secondary structure classifications of all the residues.

The iterate command only has access to certain properties. Those properties are:

  • name: the atom name
  • resn: the residue name
  • resi: the residue identifier (residue number)
  • chain: the chain name
  • alt:
  • elem: the chemical element
  • q
  • b: the B Factor
  • segi:
  • type (ATOM,HETATM): the atom type
  • formal_charge: the formal charge of the atom
  • partial_charge: the partial charger of the ato
  • numeric_type
  • text_type
  • ID
  • vdw

All strings in the expression must be explicitly quoted. This operation typically takes a second per thousand atoms.


The coordinates of the atom are not accessible via iterate. To use the coordinates of the atoms, see Cmd iterate_state.


iterate (selection),expression



  • The following example calculates the net charge on an object.
# create the global variable between Python and PyMOL
stored.net_charge = 0
# sum up the stored charges of all the atoms
iterate (all),stored.net_charge = stored.net_charge + partial_charge


  • The following example fills an array, stored.names with the names of all the residues.
# create the global variable between Python and PyMOL
stored.names = []
# get all of the names
iterate (all),stored.names.append(name)


  • The following prints the b-factors for all atoms around residue #1.
iterate resi 1, print round(b,2)


Cmd iterate_state, Cmd alter, Cmd alter_state