[Chimera-users] Aligning planes with principal planes

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 5 10:24:43 PST 2010

Hi Thomas,
These are not exactly what you asked, but may be helpful:

Given two sets of atoms, the "align" command rotates the molecule to  
put one set in front and the other in back (center of screen along Z  
axis).  Each set could be one or more atoms.  Then you could rotate 90  
degrees with the "turn" command to re-align with a different axis.


The command "define" can define planes from sets of atoms.  The planes  
are displayed as thin disks.  I can't think of an automatic way to  
then rotate the molecule so that the plane is oriented exactly along  
some major plane of any coordinate system, but perhaps that could be  
done manually after the plane has been displayed.


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

On Feb 5, 2010, at 8:11 AM, Dipl.-Ing. Thomas Mitterfellner wrote:

> Hello!
> Is there a command in Chimera that turns a molecule in a way that a  
> plane (explicitly created or just the selected atoms defining the  
> plane) is parallel to the xy or the other principal planes?
> Thank you,
> Thomas

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