[cctbxbb] Conversion from symmetry operation to matrix

[Graeme.Winter at Diamond.ac.uk]

Hi Ralf,

The t_den and r_den additions made the difference (also needed with the change_of_basis_op using rt_mx as starting point) - may be worth adding as an additional comment in the __init__ methods what these actually mean as it was not clear!

Many thanks,

Graeme

From: cctbxbb-bounces at phenix-online.org [mailto:cctbxbb-bounces at phenix-online.org] On Behalf Of Ralf Grosse-Kunstleve
Sent: 12 July 2011 20:18
To: cctbx mailing list
Subject: Re: [cctbxbb] Conversion from symmetry operation to matrix

Hi Graeme,

You can make it work like this:

def symop_to_mat(symop):
  return matrix.sqr(sgtbx.rt_mx(
    sgtbx.parse_string(symop), r_den=12, t_den=144).as_double_array()[:9]).transpose().elems

But I suggest using the change_of_basis_op type instead. See the complete script below.

Ralf


from cctbx import sgtbx
from cctbx.array_family import flex
from scitbx import matrix

def symop_to_mat(symop):
  return matrix.sqr(sgtbx.rt_mx(
    sgtbx.parse_string(symop), r_den=12, t_den=144).as_double_array()[:9]).transpose().elems

def run(args):
  assert len(args) == 0
  print symop_to_mat("1/2*z,-y+1/2*z,x")
  cb_op = sgtbx.change_of_basis_op("1/2*z,-y+1/2*z,x").inverse()
  print cb_op.as_hkl()
  miller_indices = flex.miller_index([(2,4,1)])
  print list(cb_op.apply(miller_indices))

if (__name__ == "__main__"):
  import sys
  run(args=sys.argv[1:])


On Tue, Jul 12, 2011 at 7:06 AM, <Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk>> wrote:
Dear All,

For a little while now I have been using some cctbx jiffy code to convert from symmetry operations to matrices to help with testing reindexing data. This works as

def symop_to_mat(symop):
    return matrix.sqr(sgtbx.rt_mx(
        sgtbx.parse_string(symop)).as_double_array()[:9]).transpose().elems

Which is plenty simple. However it just exploded when given "1/2*z,-y+1/2*z,x"  - reasonably really as this is not a rotation. It is however a valid reindexing operation to go from C2 to P1.

Does anyone have code which will handle this general transformation from a reindexing operation to a matrix, which will cope with the fact that the resulting matrix is not RT? I had a little jiffy I wrote using ccp4f lib (symop2mat - you can probably see it!) but I am trying to do away with things like that and do everything properly...

Many thanks in advance,

Graeme

Dr. Graeme Winter
Senior Software Scientist
Diamond Light Source

+44 1235 778091<tel:%2B44%201235%20778091> (work)
+44 7786 662784<tel:%2B44%207786%20662784> (work mobile)






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