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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Ralf,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Well that hit the spot – here’s what I ended up with:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">from cctbx.sgtbx.lattice_symmetry import metric_subgroups<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">from cctbx import crystal<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">input_symmetry = crystal.symmetry(<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> unit_cell=(20, 20, 20, 90, 90, 90),<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> space_group_symbol = "P23")<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">groups = metric_subgroups(input_symmetry=input_symmetry, max_delta = 0.0)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">for item in groups.result_groups:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> cell = item['ref_subsym'].unit_cell().parameters()<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> spacegroup_name = item['ref_subsym'].space_group().type(<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> ).universal_hermann_mauguin_symbol()<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> reindex = item['cb_op_inp_best'].as_hkl()<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> print '%20s' % spacegroup_name, '%6.2f %6.2f %6.2f %6.2f %6.2f %6.2f' % \<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> cell, reindex<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">which works perfectly.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Many thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Graeme<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> cctbxbb-bounces@phenix-online.org [mailto:cctbxbb-bounces@phenix-online.org]
<b>On Behalf Of </b>Ralf Grosse-Kunstleve<br>
<b>Sent:</b> 19 September 2011 17:23<br>
<b>To:</b> cctbx mailing list<br>
<b>Subject:</b> Re: [cctbxbb] Lattice options & changes of basis<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Graeme, try this:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">from cctbx.sgtbx.lattice_symmetry import metric_subgroups</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">from cctbx import crystal</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">input_symmetry = crystal.symmetry(</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New""> unit_cell=(20, 30, 40, 90, 90, 90),</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New""> space_group_symbol="P222")</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">groups = metric_subgroups(input_symmetry=input_symmetry, max_delta=1.4)</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">groups.show()</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">for item in groups.result_groups:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New""> print item['cb_op_inp_best'].as_hkl()</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal">See also the implemenation of the .show() method in cctbx/sgtbx/lattice_symmetry.py.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Ralf<o:p></o:p></p>
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<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Mon, Sep 19, 2011 at 8:13 AM, <<a href="mailto:Graeme.Winter@diamond.ac.uk">Graeme.Winter@diamond.ac.uk</a>> wrote:<o:p></o:p></p>
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<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi Folks,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I have a very simple question which I *<b>know</b>* 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.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Has anyone some simple code to do this?<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I tried piggybacking on pointgroup tools but that did not lead to enlightenment. I suspect using elementary ish operations would be better…<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thanks,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Graeme<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt">Dr. Graeme Winter</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt">Senior Software Scientist</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt">Diamond Light Source</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt"><a href="tel:%2B44%201235%20778091" target="_blank">+44 1235 778091</a> (work)</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt"><a href="tel:%2B44%207786%20662784" target="_blank">+44 7786 662784</a> (work mobile)</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<p class="MsoNormal"><span style="color:#888888"><o:p> </o:p></span></p>
<p><span style="color:#888888"> <o:p></o:p></span></p>
<p><span style="color:#888888">-- <o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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