[Chimera-users] help

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 11 11:21:00 PST 2010

Dear Giuseppe,
You can use "Axes/Planes" (under Tools... Structure Analysis) to  
define an axis object for a selected set of atoms.  If "Mass  
weighting" is on and "Use helical correction" is off, the axis is  
equivalent to the longest axis of the ellipsoid from "measure  
inertia."   You could also choose not to use mass weighting, whereas  
the ellipsoid approach always uses mass weighting.  Currently, however  
the axis approach only gives the first principle axis; there is no  
option to also generate the second and third, as used to define an  

Axis and plane objects can also be created with the command "define,"  
for example:

define axis helical false mass true color red radius 2 sel

to show the mass-weighted principal axis of the currently selected  
atoms.  Axis and plane objects can be used in various distance and  
angle measurements using the Axes/Planes interface or commands.  In  
version 1.5 of Chimera (daily builds), there are also centroid objects  
and the tools is named "Axes/Planes/Centroids."

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 11, 2010, at 6:23 AM, Giuseppe Falini wrote:

> Dear Chimera team,
> I am using Chimera to create ellipsoids from specific sets of atoms.  
> The ellipsoids are shown in the graphic window as a surface model  
> and information about each ellipsoid are given in the reply log. In  
> it the ellipsoid vectors are reported among others info. I wonder if  
> you have a command to show vectors defining the ellipsoid instead of  
> the surface model in the graphic window.
> Thanks
> Regards
> giuseppe

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