On Fri, Aug 26, 2011 at 8:49 AM, Bryan Lepore <span dir="ltr">&lt;<a href="mailto:bryanlepore@gmail.com">bryanlepore@gmail.com</a>&gt;</span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
[ dev-837 ]<br>
<br>
I am trying to understand a symmetry operation from coot as it bears<br>
on phenix bond in the geometry restraints. in essence:<br>
<br>
in coot, origin-pre-shift is (-1 0 0) and the symmetry-related atom I want is<br>
<br>
Y,X,-Z + (0 1 1)<br>
<br>
however, the correct operation in phenix is<br>
<br>
Y,X,-Z+1<br>
<br>
... I suspect I simply do not understand the transformation. if i<br>
could at least confirm this math is correct, i&#39;d appreciate it.<br></blockquote><div><br></div><div>Yes, correct:</div><div><br></div><div>  from cctbx import sgtbx</div><div>  p = sgtbx.rt_mx(&quot;x-1,y,z&quot;)</div>
<div>  s = sgtbx.rt_mx(&quot;Y,X+1,-Z+1&quot;)</div><div>  print s.multiply(p)</div><div><br></div><div>You have two rotation-translation matrices, which you have to multiply in the correct order: first you shift the structure</div>
<div><br></div><div>  p * x</div><div><br></div><div> then you apply the symmetry operation</div><div><br></div><div>  s * p * x</div><div><br></div><div>Ralf</div><div><br></div></div>