[Chimera-users] R: help
giuseppe.falini at unibo.it
Thu Feb 11 21:48:05 PST 2010
I applied your suggestion and all works as you described.
The main problem is that I need of the second axis of the ellipsoid, since the comparing subunits mainly rotate along the main axis.
I hope that in the future you will develop this option
Da: Elaine Meng [mailto:meng at cgl.ucsf.edu]
Inviato: giovedì 11 febbraio 2010 20.21
A: Giuseppe Falini
Cc: chimera-users at cgl.ucsf.edu
Oggetto: Re: [Chimera-users] help
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,"
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.
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