[Chimera-users] domains as ellipsoids?

[Elaine Meng]

On Jul 24, 2009, at 7:20 AM, Stefano Ciurli wrote:

> Hello Elaine,
> I am writing to ask you the following: I need to define the  
> relative orientation of two domains of a protein, and I am not sure  
> about how to do it. I was thinking of approximating the domains as  
> ellipsoids and then calculate the angles between the axes of the  
> ellipsoids. I wonder if you have a better way to define the  
> orientation, or if Chimera can do things like calculate ellipsoids  
> axes and their orientation.
> Regards
> Stefano

Hi Stefano,
There is an Axes tool (under Tools... Structure Analysis).  It does  
not give ellipsoids, just the long axis, shown as a cylinder.  You  
can define axes for helices or for any set of atoms (e.g. a domain),  
and then choose any two axes for an angle calculation.  For details, see

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ 
structuremeas/structuremeas.html#axes>

or just click the Help button on the dialog to see your local copy of  
this information.  Eventually we want to also allow defining  
centroids and planes, but only the axes measurements are available  
currently.

Please send chimera questions to chimera-users at cgl.ucsf.edu rather  
than to me personally, unless private data are included.  This allows  
others to benefit, or to answer the question if I am unavailable.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                       http://www.cgl.ucsf.edu/home/meng/index.html