Great! I'll give that a try.
Sean
Subject: RE: [PyMOL] Principal Axes of Rotation
Date: Wed, 3 Jun 2009 12:55:51 -0700
From: war...@delsci.com
To: magic...@hotmail.com; matthew.frank...@imclone.com
CC: pymol-users@lists.sourceforge.net
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:magic...@hotmail.com]
Sent: Wed 6/3/2009 12:28
PM
To: matthew.frank...@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: magic...@hotmail.com
> CC:
pymol-users@lists.sourceforge.net
> From:
matthew.frank...@imclone.com
> Date: Wed, 3 Jun 2009 15:13:25
-0400
>
>
>
> Sean Law <magic...@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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