Sometimes it can be handy to work with multiple structures in PyMOL using Python.

Here’s a snippet of code you might find useful: we iterate over all the α-carbon atoms in a protein and append to a list tuples such as (‘GLY’, 1). The dictionary, ‘reslist’, returns a list of residue names and indices for each molecule, where the key is a string containing the name of the molecule.

from pymol import cmd

# Create a list of all the objects, called 'mpls':
mols = cmd.get_object_list('*')

# Create an empty dictionary that will return a list of residues
# given the name of the molecule object
reslist = {}

# Set the dictionaries to be empty lists
for m in mols:  reslist[m] = []

# Use PyMOL's iterate command to go over every α-Carbon and append 
# a tuple consisting of the each residue's residue name ('resn') and
# residue index ('resi '):
for m in mols:  cmd.iterate('%s and n. ca'%m, 'reslist["%s"].append((resn,int(resi)))'%m)

This script assumes you only have protein molecules loaded, and ignores things like chain ID and insertion codes.

Once you have your list of residues, you can use it with the cmd.align command, e.g., to align a particular residue to a reference structure.