[Chimera-users] plane normal axis

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 7 10:09:55 PDT 2015

Hi Oliver,
If you have a plane defined in Axes/Planes/Centroids, you can write out its information including the normal (Save button on that tool), then place atoms at either end allowing you to define the axis.  There are a few steps...

In my little test, the plane output information included:

plane name, ID, center, normal, radius
plane: p1 ( 19.023,  17.733,   7.080) (-0.380,  0.757,  0.531) 24.199

Then I used Tools… Build Structure, Start Structure, add atom at specific coordinates to add two atoms, one at the center of that plane and one to show the normal.  The  latter's coordinates are (center + normal) coordinates, and you can multiply the normal coordinates by some constant to make the axis longer.  For example, I multiplied the normal coordinates by 10 before adding them to the center coordinates to give the position of the second atom as:

x 15.223   y 25.303   z 12.390

Then I selected the two new atoms and used them to define an axis in Axes/Planes/Centroids, see attached image.
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 Apr 6, 2015, at 5:01 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Alternatively, would it be possible (or is there some way already) to define a separate axis that is the normal of a plane? In this case I’m working with an ion channel, so I’m looking for a consistent way to represent the change in orientation of particular extramembrane domains with respect to the channel axis. If I could define an axis for the membrane plane normal, I could at least measure the absolute orientation of the principal axes of particular domains or individual helices with respect to the channel axis. It seems like the plane normal is computed already (because there is an option in axes/planes/centroids) to align screen x/y/z to it, but I can’t see a way to generate it as a separate axis that I can use for measuring angles etc.
> Thanks for all your help as always!
> Oliver.

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