[Chimera-users] Measure translation of two domains?

[Elaine Meng]

Hi Oliver,
As I understand it, the “measure rotation” output describes the relative transformation in two ways.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation>

The first way is the matrix, in which the translation is the 4th column.  I get the same numbers as you, so the overall translation is approx -8,-18, and 2 angstroms along the 3 orthogonal axes:

Position of 1bl8_1_0.pdb (#0) relative to 1bl8_1_1.pdb (#1) coordinates:
  Matrix rotation and translation
     1.00000000   0.00000000   0.00000000  -8.09800000
    -0.00000000   1.00000000  -0.00000000 -18.20100000
    -0.00000000   0.00000000   1.00000000   1.76900000

The second way describes the rotation, and then how much of the translation is along the axis of rotation only.  In this case  the direction of the axis isn’t meaningful because the rotation is zero anyway, so it just points it along one of the orthogonal axes, giving the same value as the last one in the matrix above.

  Axis   0.00000000   0.00000000   1.00000000
  Axis point   0.00000000   0.00000000   0.00000000
  Rotation angle (degrees)   0.00000000
  Shift along axis   1.76900000

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



On Jul 7, 2015, at 4:04 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi all, 
> 
> I’m puzzling how to measure the translation of two domains in Chimera, in a situation where there is small but non-zero translation.
> 
> I expected I could do this by first using match to superimpose the two selections, then using measure rotation to obtain the rotation (if any) and translation. This has worked fine for me in measuring rotation of domains. However, on a purely translational test case, this gives confusing results. I have attached two structures of 1bl8, one of which has been displaced from the other manually by 20 Å. If I match one to the other, it successfully superimposes the two structures. If I then use measure rotation to try to recover the translation, I get a message telling me that the rotation angle is near zero (which is not surprising), but when I check the reply log, the listed translation along the axis is only 1.7Å (see screenshot attached), rather than the 20Å I expect. 
> 
> What am I doing wrong here? Is there another command I ought to be using? Or am I misinterpreting the output?
> 
> Cheers,
> Oliver.
> 
> <1bl8_1_0.pdb><1bl8_1_1.pdb>
> <Screenshot 2015-07-07 19.01.34.png>