[Chimera-users] How to define a center of rotation when applying a symmetry

Thomas Goddard goddard at cgl.ucsf.edu
Mon Jun 2 13:51:04 PDT 2008

Hi Giovanni,

   To convert icosahedron rotation matrices that act about origin 0,0,0 
to instead use a different center of rotation (cx,cy,cz) you would first 
shift by -cx,-cy,-cz then apply the rotation then shift by cx,cy,cz. 
I've attached an example script.  Note that "a.premultiply(b)" means to 
multiply b to the left of "a" which means that b acts after a.

   Note that the Chimera Multiscale dialog (Tools / Higher-Order 
Structure / Multiscale) will apply icosahedral symmetry and load the 
coordinates (use select all, then style show wire).  It doesn't allow 
you to change the icosahedron origin to something different from 0,0,0 
but you could modify your PDB coordinates to make that the origin.

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