[phenixbb] symmetry related bond restraint

Ralf Grosse-Kunstleve rwgrosse-kunstleve at lbl.gov
Sat Aug 27 23:46:07 PDT 2011


On Fri, Aug 26, 2011 at 8:49 AM, Bryan Lepore <bryanlepore at gmail.com> 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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