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: [email protected] [mailto:[email protected]] 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, mailto:[email protected]> 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 778091tel:%2B44%201235%20778091 (work)
+44 7786 662784tel:%2B44%207786%20662784 (work mobile)
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