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
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