Get Coordinates I

There are several ways to extract or load atomic coordinates in PyMOL using the python API.

Extract coordinates using get_model

This is the fastest method to extract coordinates. It considers the object rotation matrix.

xyz = cmd.get_model('sele', 1).get_coord_list()

Extract coordinates using iterate_state

This is much slower than the first method. It does not consider the object rotation matrix.

xyz = []
cmd.iterate_state(1, 'sele', 'xyz.append([x,y,z])', space=locals(), atomic=0)

Load coordinates using alter_state

This is the most convenient way to load coordinates and works equivalent to iterate_state.

xyz = [...] # some Nx3 list with coordinates
xyz_iter = iter(xyz)
cmd.alter_state(1, 'sele', '(x,y,z) = xyz_iter.next()', space=locals())

Load coordinates using update

This example gets a copy of the coordinates in Python, rotates the object about the Z axis, and then updates the coordinates in the original object.

model = cmd.get_model('pept')
for a in model.atom:
    a.coord = [ -a.coord[1], a.coord[0], a.coord[2]]

cmd.load_model(model, "_tmp")
cmd.update("pept", "_tmp")
cmd.delete("_tmp")

Load coordinates using load_coords

This method is experimental and buggy, but it's the fastest method to load coordinates. There is a count mistake in the state argument (must use state+1). The xyz argument must be a list of lists (no tuples). It only works for complete objects, not atom selections.

import pymol.experimenting
pymol.experimenting.loadable = cmd.loadable
pymol.experimenting.load_coords(xyz, object, state+1)