# [Chimera-users] fit in map output : coordinate representation of axis, axis point

Tom Goddard goddard at cgl.ucsf.edu
Tue Jan 27 15:27:25 PST 2009

```Hi Youngha,

Here's the description of the Fit in Map output from the Chimera
manual, displayed in a web browser by pressing the Help button on the
Fit in Map dialog.

"Transformation matrices. The transformation matrix of the fit model
relative to the reference map is reported in the Reply Log. The first
three columns of the matrix describe a rotation and the fourth describes
a translation (performed after the rotation). The transformation is also
described as an axis of rotation (a unit vector), point on the axis,
degrees of rotation, and shift parallel to the axis."

If you have specified the map voxel size in Angstroms in the Coordinates
panel of volume dialog then those are the units of the translation and
shift.  If you are fitting map #1 into map #0 then all positioning
parameters are relative to the coordinate frame of map #0.  The first 3
columns of the 3 by 4 transformation matrix are a rotation matrix, the
last column is a translation vector (rotation applied first then
translation).  The axis, axis point, rotation angle, and shift are just
another way of expressing the same transformation.  Euler angles are not
provided.

Tom

Example output fitting groel to rotated copy of itself:

Fit map groel.mrc in map groel.mrc using 1254 points
correlation = 0.7305, overlap = 1.131e+04
steps = 40, shift = 0.0106, angle = 2.64 degrees
Position of groel.mrc (#1) relative to groel.mrc (#0) coordinates:
Matrix rotation and translation
0.62732525  -0.77875617  -0.00136447   1.34502847
0.77875534   0.62732665  -0.00117890  -0.47283012
0.00177404  -0.00032304   0.99999837  -0.00375893
Axis   0.00054950  -0.00201508   0.99999782
Axis point   1.16654379   1.16890014   0.00000000
Rotation angle (degrees)  51.14694922
Shift along axis  -0.00206703

Tom

Hwang, Youngha,Ph.D. wrote:
> Hi, could anyone explain to me what axis points mean in chimera? What unit is
> used for them?  Is it related to the volume dimension? Is the rotation matrix
> based on Euler-angle representation?
>
> Thanks, Youngha.
>
>
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