[PyMOL] discrepancy between python and commandline script

[Pawel <pa...@gm...>]

Hello,

I'm trying to understand what seems like an inconsistency between PyMOL 
commandline and python scripts. I have the following commandline script:

    delete all
    load ../4lzt_quasi.pdb, full
    cmd.create("anew", "full", 1, 1)
    cmd.alter_state(1,"anew" , "x,y,z = x+nm[(ID-1)*3],
    y+nm[(ID-1)*3+1], z+nm[(ID-1)*3+2]")
    iterate_state 1, full & id 1, print x, y,z
    iterate_state 1, anew & id 1, print x, y,z

Which I then run:

    PyMOL>@pymoltest1.txt
    ...
    PyMOL>iterate_state 1, full & id 1, print x, y,z
    2.69099998474 4.58500003815 13.6999998093
      IterateState: iterated over 1 atom coordinate states.
    PyMOL>iterate_state 1, anew & id 1, print x, y,z
    2.41267466545 5.63420581818 12.6615524292
      IterateState: iterated over 1 atom coordinate states.

Now I have this python script:

    cmd.delete( all)
    cmd.load( "../4lzt_quasi.pdb", "full")
    cmd.create("anew", "full", 1, 1)
    cmd.alter_state(1,"anew" , "x,y,z = x+nm[(ID-1)*3],
    y+nm[(ID-1)*3+1], z+nm[(ID-1)*3+2]")
    xyz1=[]
    cmd.iterate_state(1, 'full & id 1', 'xyz1.append([x,y,z])')
    xyz2=[]
    cmd.iterate_state(1, 'anew & id 1', 'xyz2.append([x,y,z])')
    print xyz1
    print xyz2

Which I run:

    PyMOL>run pymoltest1.py
    [[2.690999984741211, 4.585000038146973, 13.699999809265137]]
    [[2.5646746158599854, 4.600205898284912, 13.65555191040039]]

Why am I getting different coordinates for the second atom? The second 
set of coordinates from the first script are actually the coordinates of 
the 5th atom in my structure (CA of a LYS). I'm guessing that the 
alter_state command is somehow doing something different in one and the 
other case but it's hard to understand why.

Thanks for the help,
Pawel