[Chimera-users] command line equivalent of Volume Viewer Centre - and radius-of-gyration.py

Elaine Meng meng at cgl.ucsf.edu
Thu May 17 08:55:58 PDT 2012

Hi Dieter,
I'm not sure if there is a command that does exactly the same thing as the Center button in Volume Viewer, but for a similar result you might try the "window" command:

The radius_of_gyration.py script is for atomic coordinates, not volume data, at least if you are talking about the script that was posted on the list a couple of months ago:


It reports center of mass and radius of gyration values in the Reply Log (under Favorites in the Chimera menu).  It doesn't move anything.

To calculate the center of mass of a density map (also not moving anything), you could use the command "measure center":

That gives the center in grid indices of your map rather than in x,y,z coordinates.
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 May 17, 2012, at 1:34 AM, Dieter Blaas wrote:

> Hi I am looking for a command line version of the CENTER command in VOLUME VIEWER. Can anybody please give me a hint!
> I'd like to use this command in a script to re-center a volume. I have also tried to the use the script radius_of_gyration.py but there is something I do not understand: I load the script with 'open file' but then nothing happens. Where is the output directed to? How could I use the output to re-center my volume?
> Thanks, Dieter

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