Iterate State

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Iterate state can be used to extract position data from an object or selection. The expression can use the variables x, y, and z which are the position of the current atom. One common usage is to extract the positions as a python list to alter then write back to the molecule using alter_state.


iterate_state state, (selection), expression


  • state = integer: state-index if positive number or any of these:
    • state = 0: all states
    • state = -1: current state
  • selection = string: atom selection
  • expression = string: expression in valid python syntax
  • space = dict: namespace dictionary (API only) {default: pymol namespace}
  • atomic = 0/1: provide atomic properties as variables if 1, or only x/y/z if 0 (atomic=0 gives some speed improvement) {default: 1}


From PyMOL command line

To get the sum of x coordinates:

stored.sum_x = 0.0
iterate_state 1,(all),stored.sum_x = stored.sum_x + x

To get a list of the positions in a selection

stored.pos = []
iterate_state 1, (all), stored.pos.append((x,y,z))

From Python

To get a list of positions

# either with global stored object
from pymol import stored
stored.pos = []
cmd.iterate_state(1, 'all', 'stored.pos.append((x,y,z))')

# or with local object, passed with space argument
pos = []
cmd.iterate_state(1, 'all', 'pos.append((x,y,z))', space={'pos': pos})


iterate, alter, Alter_State