[Chimera-users] measure rotation command questions

Joseph Atherton j.atherton at mail.cryst.bbk.ac.uk
Mon Aug 15 02:47:46 PDT 2016

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,


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 at 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

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