[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 


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


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.
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

More information about the Chimera-users mailing list