On Fri, Aug 26, 2011 at 8:49 AM, Bryan Lepore
[ dev-837 ]
I am trying to understand a symmetry operation from coot as it bears on phenix bond in the geometry restraints. in essence:
in coot, origin-pre-shift is (-1 0 0) and the symmetry-related atom I want is
Y,X,-Z + (0 1 1)
however, the correct operation in phenix is
Y,X,-Z+1
... I suspect I simply do not understand the transformation. if i could at least confirm this math is correct, i'd appreciate it.
Yes, correct: from cctbx import sgtbx p = sgtbx.rt_mx("x-1,y,z") s = sgtbx.rt_mx("Y,X+1,-Z+1") print s.multiply(p) You have two rotation-translation matrices, which you have to multiply in the correct order: first you shift the structure p * x then you apply the symmetry operation s * p * x Ralf