[Chimera-users] Specifier for the z-axis

[Elaine Meng]

Dear Yang,
Sorry, there is no option to specify a model's X, Y, or Z axis in the "angle" command. Other than doing the  math yourself with the axis information (e.g. use Save on the Axes/Planes/Centroids dialog to write info to a file), the only idea I have is to:

(1) use Build Structure, the Start Structure option to add 2 atoms that are along the Z axis, e.g. with x y z coordinates:
0 0 0
0 0 100
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>

Make sure that these two atoms are not moved separately from the map, so that they will be in the same coordinate system of the map.

(2) define axis for those two atoms

<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html>

(3) then measure angle between the axis created as described above and the plane

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 28, 2023, at 5:20 AM, Yang Shi via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Chimera-Team,
> 
> I am wondering if there is a specifier for the z-axis of a map. I would like to measure the angles between defined plains and Z-axis.
> 
> Best wishes,
> Yang