[Chimera-users] domains as ellipsoids?

Stefano Ciurli stefano.ciurli at unibo.it
Fri Jul 24 10:04:12 PDT 2009

Thank you Elaine, I will try to follow the advice and instructions

On 24 lug 2009, at 18:57, Elaine Meng wrote:

> 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

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