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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