Hello everyone,
I've been trying to write a script to orient two particular molecules with
respect to one another. I do this by calculating a translation vector
between the two and then using cmd.translate to move the second object to
the desired location. However, this didn't seem to have the desired effect
and moved the second molecule somewhere else.
I investigated further and tried using a translation of [1, 0, 0], which I
supposed would just alter the x coordinate of my molecule. Instead it
translated the molecule by 1A (I checked the magnitude of the actual
translation to be sure) along an arbitrary axis. This axis also changed
after deleting and recreating the object with its original coordinates.
Am I doing something wrong, or did I not understand properly how translate
works? I've pasted some sample input/output just below.
Thanks,
Kyle
----------------------------------------
First time:
PyMOL>iterate_state 1, glycan* and id 1, print x, y, z
3.39400005341 1.43299996853 -0.0
IterateState: iterated over 1 atom coordinate states.
PyMOL>translate [1, 0, 0], glycan*
PyMOL>iterate_state 1, glycan* and id 1, print x, y, z
3.77618098259 2.14793467522 -0.585493266582
IterateState: iterated over 1 atom coordinate states.
----------------------------------------
Second time:
PyMOL>iterate_state 1, glycan* and id 1, print x, y, z
3.39400005341 1.43299996853 -0.0
IterateState: iterated over 1 atom coordinate states.
PyMOL>translate [1, 0, 0], glycan*
PyMOL>iterate_state 1, glycan* and id 1, print x, y, z
2.96896576881 2.08610153198 -0.626740753651
IterateState: iterated over 1 atom coordinate states.
----------------------------------------
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