[cctbxbb] Lattice options & changes of basis

Tue Sep 20 00:35:02 PDT 2011

Hi Ralf,

Well that hit the spot - here's what I ended up with:

from cctbx.sgtbx.lattice_symmetry import metric_subgroups
from cctbx import crystal
input_symmetry = crystal.symmetry(
    unit_cell=(20, 20, 20, 90, 90, 90),
    space_group_symbol = "P23")
groups = metric_subgroups(input_symmetry=input_symmetry, max_delta = 0.0)
for item in groups.result_groups:
    cell = item['ref_subsym'].unit_cell().parameters()
    spacegroup_name = item['ref_subsym'].space_group().type(
        ).universal_hermann_mauguin_symbol()
    reindex = item['cb_op_inp_best'].as_hkl()

    print '%20s' % spacegroup_name, '%6.2f %6.2f %6.2f %6.2f %6.2f %6.2f' % \
          cell, reindex

which works perfectly.

Many thanks,

Graeme

From: cctbxbb-bounces at phenix-online.org [mailto:cctbxbb-bounces at phenix-online.org] On Behalf Of Ralf Grosse-Kunstleve
Sent: 19 September 2011 17:23
To: cctbx mailing list
Subject: Re: [cctbxbb] Lattice options & changes of basis

Hi Graeme, try this:

from cctbx.sgtbx.lattice_symmetry import metric_subgroups
from cctbx import crystal
input_symmetry = crystal.symmetry(
  unit_cell=(20, 30, 40, 90, 90, 90),
  space_group_symbol="P222")
groups = metric_subgroups(input_symmetry=input_symmetry, max_delta=1.4)
groups.show()
for item in groups.result_groups:
  print item['cb_op_inp_best'].as_hkl()

See also the implemenation of the .show() method in cctbx/sgtbx/lattice_symmetry.py.

Ralf

On Mon, Sep 19, 2011 at 8:13 AM, <Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk>> wrote:
Hi Folks,

I have a very simple question which I *know* can be done with cctbx, using the Python API, but I cannot for the life of me figure out how to do it. I have even read the code, it's just not clear.

I have a Bravais lattice and cell, say oP and 20, 30, 40, 90, 90, 90 - what I would like back is a list of pointgroup, cell, reindexing operation for all compatible unique settings i.e. 1 x P1, 3 x P2, 1 x P222 - from a Python loop. At the moment I run iotbx.lattice symmetry and grep the results, which is not a great idea. It would also be useful to give the reindex operations to centred lattices.

I have also stared at phenix.explore_metric_symmetry and remain puzzled despite my attempt to essentially duplicate the code. I just can't get the reindex operation out.

Has anyone some simple code to do this?

I tried piggybacking on pointgroup tools but that did not lead to enlightenment. I suspect using elementary ish operations would be better...

Thanks,

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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