Slim down PSE file with superposed chains in multiple objects

slimmer

import numpy as np
import pymol2
token_resi = 25 # this present in all chains
filename = '👾👾👾.pse'

coords = {}
with pymol2.PyMOL() as pymol:
    pymol.cmd.load('crysalin_lattice.pse')
    for name in pymol.cmd.get_object_list():
        for chain in pymol.cmd.get_chains(name):
            coords[(name, chain)] = pymol.cmd.get_coords(f'{name} and chain {chain} and resi {token_resi} and name CA')

c = np.squeeze(np.array(list(coords.values())))
distances = np.sqrt( np.sum((c[:, np.newaxis, :] - c[np.newaxis, :, :]) ** 2, axis=-1) )
# get the ones that overlap in the upper triangle
close = np.tril(distances < 0.1)  # triangle bool default is False
np.fill_diagonal(close, False)
names = list(coords.keys())
morituri = [names[a] for a in np.where(close)[0]]

with pymol2.PyMOL() as pymol:
    pymol.cmd.load(filename)
    for name, chain in morituri:
        pymol.cmd.remove(f'{name} and chain {chain}')
    pymol.cmd.save(filename.replace('.pse', '.slim.pse'))