[Chimera-users] measure rotation command questions
j.atherton at mail.cryst.bbk.ac.uk
Mon Aug 15 02:47:46 PDT 2016
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,
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:
> 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 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 at mail.cryst.bbk.ac.uk> wrote:
>> 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?
>> 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
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