Hi Graeme,<div><br></div><div>You can make it work like this:</div><div><br></div><div><div><font class="Apple-style-span" face="'courier new', monospace">def symop_to_mat(symop):</font></div><div><font class="Apple-style-span" face="'courier new', monospace"> return matrix.sqr(sgtbx.rt_mx(</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"> sgtbx.parse_string(symop)<font class="Apple-style-span" color="#ff0000">, r_den=12, t_den=144</font>).as_double_array()[:9]).transpose().elems</font></div>
<div><br></div><div>But I suggest using the change_of_basis_op type instead. See the complete script below.</div><div><br></div><div>Ralf</div><div><br></div><div><br></div><div><div><font class="Apple-style-span" face="'courier new', monospace">from cctbx import sgtbx</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">from cctbx.array_family import flex</font></div><div><font class="Apple-style-span" face="'courier new', monospace">from scitbx import matrix</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace">def symop_to_mat(symop):</font></div><div><font class="Apple-style-span" face="'courier new', monospace"> return matrix.sqr(sgtbx.rt_mx(</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"> sgtbx.parse_string(symop), r_den=12, t_den=144).as_double_array()[:9]).transpose().elems</font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br>
</font></div><div><font class="Apple-style-span" face="'courier new', monospace">def run(args):</font></div><div><font class="Apple-style-span" face="'courier new', monospace"> assert len(args) == 0</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"> print symop_to_mat("1/2*z,-y+1/2*z,x")</font></div><div><font class="Apple-style-span" face="'courier new', monospace"> cb_op = sgtbx.change_of_basis_op("1/2*z,-y+1/2*z,x").inverse()</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"> print cb_op.as_hkl()</font></div><div><font class="Apple-style-span" face="'courier new', monospace"> miller_indices = flex.miller_index([(2,4,1)])</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"> print list(cb_op.apply(miller_indices))</font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">if (__name__ == "__main__"):</font></div><div><font class="Apple-style-span" face="'courier new', monospace"> import sys</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"> run(args=sys.argv[1:])</font></div></div><div><br></div><br><div class="gmail_quote">On Tue, Jul 12, 2011 at 7:06 AM, <span dir="ltr"><<a href="mailto:Graeme.Winter@diamond.ac.uk">Graeme.Winter@diamond.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div lang="EN-GB" link="blue" vlink="purple">
<div>
<p class="MsoNormal">Dear All,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">def symop_to_mat(symop):<u></u><u></u></p>
<p class="MsoNormal"> return matrix.sqr(sgtbx.rt_mx(<u></u><u></u></p>
<p class="MsoNormal"> sgtbx.parse_string(symop)).as_double_array()[:9]).transpose().elems<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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…<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Many thanks in advance,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Graeme<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Dr. Graeme Winter<u></u><u></u></p>
<p class="MsoNormal">Senior Software Scientist<u></u><u></u></p>
<p class="MsoNormal">Diamond Light Source<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"><a href="tel:%2B44%201235%20778091" value="+441235778091" target="_blank">+44 1235 778091</a> (work)<u></u><u></u></p>
<p class="MsoNormal"><a href="tel:%2B44%207786%20662784" value="+447786662784" target="_blank">+44 7786 662784</a> (work mobile)<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
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