On Thu, 27 Nov 2008, Bui Khanh Huy wrote:
Hi,
I notice that Chimera has slightly different in calculation of transform when I tried to rotate my EM density (200x200x200 mrc file) using Chimera. The origin of the density reported by Volume Viewer is 0,0,0
First, I print out the homologous transform matrix using:
om = chimera.openModels mlist = om.list() m = mlist[0] print m.openState.xform
The transformation is:
1 0 0 0 0 1 0 0 0 0 1 0
If I rotate the model using command:
roll z -30 1
Then print out the transform matrix again:
0.866025 0.5 0 -36.8852 -0.5 0.866025 0 61.2937 0 0 0 1
That would be weird because I didn't do any translation. So what is really happening in Chimera when I rotate the model?
Best,
Huy
The model is rotated about its center. So unless your model is centered at the origin there will be a translation component. If the rotation is R, and T is the translation to the center, then the actual rotation is: R' = T R (-T) Chimera has many different ways to choose the center. See <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#rotation> for details. Greg Couch UCSF Computer Graphics Lab