[Chimera-users] Angle between pseudobond and principal axis

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 1 10:09:33 PDT 2015

Hi Yasser,
You could use Axes/Planes/Centroids (or command “define”) to define axes and then measure angles between them.


For example, 
(1) select the two atoms on the end of the pseudobond and then use the Axes/Planes/Centroids tool (in menu under Tools… Structure Analysis) to define an axis from the selected atoms (remember to uncheck “Replace existing axes” if you want to keep any axes you already have).  Or, instead use the command:

define axis sel

Either way, the Axis/Planes/Centroids table of objects will then list the axis and it will be shown as a cylinder in the main window.

(2) define other axes that you want to measure angles with.  If you really mean just the X, Y, Z coordinate axes, I’ve attached a little PDB file “axes.pdb” of fake atoms for which you could define these axes with commands after you opened that file:

define axis name X @x1,x2
define axis name Y @x1,x3
define axis name Z @x1,x4

(3) then choose with the mouse (click, Ctrl-click) any pair of axes in the table of objects, and the crossing angle will be reported at the bottom of the dialog.  You could also use the “angle” command.

If you instead meant the principal axes of some other set of atoms, you could use Axes/Planes/Centroids or the “define” command to define a measurement-friendly first eigenvector (major axis) for that set of atoms.  However, this approach does not give second or third principal axes, only the first.

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

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> On Oct 1, 2015, at 1:21 AM, Yasser Almeida Hernández <yasser.almeida at gmail.com> wrote:
> Hi all,
> I want to measure the angle between a pseudobond and the X, Y, Z axis. How can I do so?
> Best
> Yasser
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> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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