<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><font class="Apple-style-span" size="4">Hello all,</font><div><font class="Apple-style-span" size="4"><br></font></div><div><font class="Apple-style-span" size="4">I have a rotation + translation matrix. Let's say</font></div><div><font class="Apple-style-span" size="4"><br></font></div><div><div><font class="Apple-style-span" face="Monaco">py> mtx</font></div><div><font class="Apple-style-span" face="Monaco">array([[ 0.88302225, 0.11697778, 0.45451948, 5. ],</font></div><div><font class="Apple-style-span" face="Monaco"> [ 0.11697778, 0.88302225, -0.45451948, 10. ],</font></div><div><font class="Apple-style-span" face="Monaco"> [ -0.45451948, 0.45451948, 0.76604444, 20. ],</font></div><div><font class="Apple-style-span" face="Monaco"> [ 0. , 0. , 0. , 1. ]])</font></div><div><font class="Apple-style-span" size="4"><br></font></div><div><font class="Apple-style-span" size="4">My usual way of transforming a set of coordinates with a 4x4 matrix is to use numpy:</font></div><div><font class="Apple-style-span" size="4"><br></font></div><div><font class="Apple-style-span" face="Monaco">py> xyz_1</font></div><div><font class="Apple-style-span" face="Monaco">array([[ 5., 10., 15., 1.],</font></div><div><font class="Apple-style-span" face="Monaco"> [ 20., 15., 10., 1.]])</font></div><div><font class="Apple-style-span" face="Monaco"><br></font></div><div><font class="Apple-style-span" face="Monaco"><div>py> numpy.inner(xyz_1, mtx)</div><div>array([[ 17.40268126, 12.59731919, 33.76326397, 1. ],</div><div> [ 28.9603065 , 21.03969455, 25.38784698, 1. ]])</div></font></div></div><div><font class="Apple-style-span" size="4"><br></font></div><div><font class="Apple-style-span" size="4">What is the equivalent in cctbx? Is there a way to avoid converting coordinates back and fourth between numpy arrays with atoms().extract_xyz() & .set_xyz() (as might be used from a iotbx_pdb_hierarchy_ext.root).</font></div><div><font class="Apple-style-span" size="4"><br></font></div><div><font class="Apple-style-span" size="4">Thank you for any help.</font></div><div><font class="Apple-style-span" size="4"><br></font></div><div><font class="Apple-style-span" size="4">James</font></div></body></html>