[Chimera-users] measure rotation

Elaine Meng meng at cgl.ucsf.edu
Mon May 11 14:23:54 PDT 2020

Hi Jesse,
I'm not sure, but it *might* be a misunderstanding of what this command does. 


This command does not evaluate how to best fit or match the two models. It reports the current rotation and translation between the coordinate systems of the two models, which would be zero unless one model was moved relative to the other, either manually or with some other tool or command such as Fit in Map, match, or matchmaker. (Moving everything collectively, such as rotating or zooming to get a better view, does not change the positions of models relative to each other.)

Centering just moves the view and doesn't change the coordinates of the structure.

Imagine you have two copies of the protein, one before fitting and one after fitting.  Is the rotation between the two really around an axis that falls inside the protein?

I may have misapprehended the situation, but this command is commonly misunderstood.
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 8, 2020, at 3:38 PM, Jesse M. Hansen <jhansen6 at uw.edu> wrote:
> hi
> I repeatedly have this issue and no idea how to fix it.  I send the same files to colleague and they cannot reproduce it.  We cannot figure out whether it's some minor detail I am doing, or it's my version of chimera.
> When I try "measure rotation #1 #2" the axis ends up either pretty off center or WAY far away (like 20 protein widths away).  
> have tried:
> 	• centering volume and resaving, fitting models into map and resaving.  Opening and all looks correct. 
> 	• tried opening pdb first then maps, or maps first then pdb. Both seem to give different results but neither are precisely down the actual axis of my helical protein despite having centered it.
> 	• adding "coordinateSystem #" to the command has no effect.  The axis that appears is now as long as my box, but it's still not centered
> thanks
> Jesse
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