[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)).
Tom
-------- 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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