[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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