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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.

Note about Atom Coordinates

The coordinates of the atom are not accessible via iterate. To inspect the coordinates of the atoms, see 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)


  • The following example shows a common task in PyMOL, changing the B-factor column to display some other property. Let's assume you have a file with a list of numbers, one per lines, for each alpha carbon in the protein. Furthermore, assume you want to map these values to the alpha carbons in the protein.
# set ALL b-factors to 0.
alter protName, b=0

# read the new bfactors from disk
f = open('fileName','r').readlines()

# set the alpha carbon bfactors.
alter protName and n. CA, b=f.pop(0)

# Spectrum color bfactors by alpha carbons.


Iterate_State, Alter, Alter_State, Color, Coloring with different color sprectrums.