Sean,
 
Apologies for not understanding...
 
You definitely need orthoscopic, but there's more to it. 
 
set orthoscopic
 
fetch 1bna, async=0
 
orient 1bna
 
cmd.matrix_copy(None,"1bna")
 
reset
 
from chempy.cpv import average
 
cmd.origin(position=average(*cmd.get_extent()))

 
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.
 
Cheers,
Warren
 
 
 


From: Sean Law [mailto:magicmen@hotmail.com]
Sent: Wed 6/3/2009 12:28 PM
To: matthew.franklin@imclone.com
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Principal Axes of Rotation

Matt,

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.

Sean

> Subject: Re: [PyMOL] Principal Axes of Rotation
> To: magicmen@hotmail.com
> CC: pymol-users@lists.sourceforge.net
> From: Matthew.Franklin@imclone.com
> Date: Wed, 3 Jun 2009 15:13:25 -0400
>
>
>
> Sean Law <magicmen@hotmail.com> 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,
> a wholly owned subsidiary of Eli Lilly & Company
> 180 Varick Street, 6th floor
> New York, NY 10014
> phone:(917)606-4116 fax:(212)645-2054
>
>
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