Re: [phenixbb] symmetry related bond restraint

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p = sgtbx.rt_mx("x-1,y,z") s = sgtbx.rt_mx("Y,X+1,-Z+1") print s.multiply(p) y,x,-z+1

Or, breaking it down into three steps and doing it manually, start with: x,y,z apply pre-shift (-1,0,0) => [x-1,y,z]: x-1,y,z apply pure rotation component of symop [Y,X,-Z]: y,x-1,-z apply post-translation of symop (0 1 1) => [x+0,y+1,z+1] y+0,x-1+1,-z+1 y,x,-z+1 Ralf Grosse-Kunstleve wrote:

On Fri, Aug 26, 2011 at 8:49 AM, Bryan Lepore mailto:[email protected]> wrote:

[ 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

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