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
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
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
participants (2)
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Elaine Meng -
Joseph Atherton