Apologies for not understanding...
You definitely need orthoscopic, but there's more to it. 
set orthoscopic
fetch 1bna, async=0
orient 1bna
from chempy.cpv import average

center origin
# now, the maximum extent in the X Y planes should be invariant to 180 degree rotations about the Y or X axes respectively.

From: Sean Law []
Sent: Wed 6/3/2009 12:28 PM
Subject: Re: [PyMOL] Principal Axes of Rotation


Unfortunately, as a somewhat experienced PyMOL user, I already have "orthoscopic view" turned off (along with depth cue turned off).  Thanks for your suggestion though.


> Subject: Re: [PyMOL] Principal Axes of Rotation
> To:
> CC:
> From:
> Date: Wed, 3 Jun 2009 15:13:25 -0400
> Sean Law <> wrote on 06/03/2009 12:52:45 PM:
> > Warren,
> >
> > After a deja vu moment, I realized that I had posed a similar
> > question to you before about this (although, we didn't really have a
> > resolution then). I had already tried your suggestion before I had
> > posted to the mailing list but perhaps an example would be more
> > appropriate in terms of what I'm seeing.
> >
> (snip - 180 degree rotation around x axis)
> > 7) You will now see that after 2 turns that the O3' atom is situated
> > well past the vertical (imaginary) line drawn by the position of
> > your cursor on your screen
> >
> This is almost certainly due to the "perspective" view which is on by
> default. As atoms move closer to your viewpoint, they appear bigger, and
> the inter-atomic distances also appear bigger, just as in real life. So,
> an atom which is far away and at a particular (apparent) x position, will
> be farther away from the center of the screen once you've done your 180
> degree rotation.
> This drawing mode was created to make structures look more realistic. If
> you don't like it, you can turn it off: under "Display", choose
> "Orthoscopic view". That should eliminate your "wobble effect".
> Hope that helps,
> Matt
> --
> Matthew Franklin , Ph.D.
> Senior Scientist, ImClone Systems,
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