Dear JD,
Yes, there is actually a "define plane" command that takes an atom specification and various options.  You can use the resulting plane (shown as a disc) for distance and angle measurements.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>

It can also be done with the Axes/Planes/Centroids tool.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>

Best,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 3, 2013, at 6:09 AM, Jean Didier Pie Marechal <JeanDidier.Marechal@uab.cat> wrote:

> Dear all,
>
> is there a way to define a plane from the command line. Something that would work providing a list of atoms or a selection.
> Cheers,
> JD