[Chimera-users] access rotation and translation matrices

Thomas Goddard goddard at cgl.ucsf.edu
Thu Nov 5 09:35:29 PST 2009

Hi Lori,

   In Chimera 1.4 or 1.5 (not 1.3) you can use the "measure rotation" 
command, for example,

	measure rotation #0 #1

where #0 and #1 are the two maps rotated relative to one another to 
achieve alignment.  The output of this command appears in the Reply Log 
dialog (Favorites / Reply Log) and looks like:

Position of emd_1283.map (#1) relative to emd_1284.map (#0) coordinates:
   Matrix rotation and translation
      0.55487295  -0.27195706   0.78622857 -13.40355998
     -0.13475327   0.90320006   0.40751836 -21.18892297
     -0.82094918  -0.33206779   0.46451418 269.99782855
   Axis  -0.41678681   0.90570988   0.07731990
   Axis point 233.40170582   0.00000000 145.33465613
   Rotation angle (degrees)  62.52938781
   Shift along axis   7.27161565

The rotation is given in matrix form the first 3 columns of the matrix 
shown, and also as an axis and rotation angle.  The translation is given 
as the 4th column of the matrix.  We don't provide Euler angles.  Euler 
angles are a pain for several reasons, one of which is that there are 
varying conventions for how they are defined.  Perhaps you can use one 
of the above forms in other software.  If you have software that uses 
quaternions to specify rotation this is simply related to the axis and 
angle: q = (sin(angle/2)*axis, cos(angle/2)).


-------- Original Message --------
Subject: [Chimera-users] access rotation and translation matrices
From: Lori Nyland <lori.nyland at uvm.edu>
To: chimera-users at cgl.ucsf.edu
Date: 11/5/09 6:33 AM

> Hello,
> I have been trying to rotate a large volume relative to a reference 
> volume using the vop resample command. The problem is that both volumes 
> are nearly 2GB. However, If I were to bin the volumes (by n) and had 
> access to the rotation R(alpha, beta, gamma) and translation T(x,y,z) 
> matrices I could perform the rotation in an alternate program via R and nT.
> Thanks!
> Lori
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> Chimera-users at cgl.ucsf.edu
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