[Chimera-users] Alignment of symmetry axes via Chimera

[Elaine Meng]

Hi Dana,
Hmm, I can't think of any way to align symmetry axes directly, as opposed to aligning atoms or fitting to density. 
 
You can calculate and display the principal axes of a set of atoms (command "measure inertia" gives ellipsoid, command "define axis" gives major axis), but of course that is not the same as an axis of symmetry.  

You can specify exact rotations and translations with the commands "turn" and "move" ... but figuring out the needed transformation may be difficult. 
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>

One possibility is to construct a multimer of one peptide with specified symmetry using the "sym" command, then superimpose the second peptide onto one copy of the first peptide.  The difficult part is correctly describing the axis of symmetry and the desired relationship between copies.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>

Another possibility (also somewhat approximate) is superimposing the peptides, then orienting them so that the axis of symmetry is aligned with some laboratory axis (e.g. in plane of screen left to right), which may be hard depending on the relationship between the peptide and that axis, then translating one copy along the axis  (e.g. "move x 50 mod 1").

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 1, 2012, at 11:05 PM, danashah at post.tau.ac.il wrote:

> Hi all,
> I've only joined this mailing list lately, so pardon me if this question was asked and answered before.
> 
> We have two different peptides, each contains a 4-fold symmetry axis.
> We would like to align those two symmetry axes, without superimpose one peptide on the other, since they should be continuous.
> 
> Is there a way to do that via Chimera (gui or no gui)?
> 
> I was able to find this conversation:
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003140.html
> but it doesn't solve our specific situation.
> 
> Best,
> Dana.