Thanks Elaine- I think I will try defining the centre of mass as a marker and then measuring the distance between these markers as Tom suggested- this should give the translation to go with any measured rotation, Cheers, Joe On 12/08/2016 18:59, Elaine Meng wrote:
Hi Joe, This command only describes how one model has been moved relative to another, not how they would best superimpose. I don’t think you can “see” the amount of translation unless you had other knowledge, such as that the two models were originally exactly superimposed.
I can’t really add to the description of the information here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation>
The “showSlabs” option will show both the rotation and the shift, but as I understand it that is a different way of describing the relative transformation than the matrix.
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 Aug 11, 2016, at 4:47 AM, Joseph Atherton <j.atherton@mail.cryst.bbk.ac.uk> wrote:
Hi, When I use the command 'measure rotation' I get a matrix in the reply log.
1) The fourth column is 'translation'. At most the translation I see is 5 Angstrom, so how do I get these numbers (see below)? I also have a shift along axis reported, which seems a more reasonable number, but what if the shift is in a a different vector to the axis?
2) I can get depiction of the rotation axis, but can I also get a depiction of the translation vector?
Cheers, Joe
Position of model2 (#20) relative to model1.pdb (#1) coordinates: Matrix rotation and translation 0.98820614 -0.14982292 -0.03165001 43.44553134 0.14930460 0.98862441 -0.01816347 -23.90940685 0.03401127 0.01322376 0.99933396 -9.65968865 Axis 0.10195507 -0.21328736 0.97165512 Axis point 180.93496764 275.63881775 0.00000000 Rotation angle (degrees) 8.85455905 Shift along axis 0.14318049