<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Yen,<div><a href="https://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/wiki/Scripts/changeaxes.py"></a><a href="https://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/wiki/Scripts/changeaxes.py"></a><a href="https://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/wiki/Scripts/changeaxes.py"></a><a href="https://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/wiki/Scripts/changeaxes.py"></a><a href="https://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/wiki/Scripts/changeaxes.py"></a><a href="https://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/wiki/Scripts/changeaxes.py"></a><a href="https://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/wiki/Scripts/changeaxes.py"></a><a href="https://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/wiki/Scripts/changeaxes.py"></a><a href="https://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/wiki/Scripts/changeaxes.py"></a><a href="https://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/wiki/Scripts/changeaxes.py"></a><a href="https://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/wiki/Scripts/changeaxes.py"></a><a href="https://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/wiki/Scripts/changeaxes.py"></a><a href="https://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/wiki/Scripts/changeaxes.py"></a><a href="https://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/wiki/Scripts/changeaxes.py"></a></div><div> Here is a Python script that will change your atom coordinates to rotate a given vector to the z axis, and another given vector into the yz plane with y > 0, and a given point is moved to 0,0,0. The vectors and point are specified each as 3 numbers separated by commas. For example, Chimera command</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>runscript ~/Desktop/changeaxes.py #1 .7,.2,0 0,-.5,.5 16,7,-5</div><div><br></div><div>will change the coordinates of atoms to make the new z-axis in direction .7,.2,0 from the original coords, with 0,-.5,.5 from original coords pointing in the new yz plane with y>0 and the original point 16,7,-5 will move to the origin 0,0,0. Notice the first two vectors need not have unit length. They will be normalized by the code. This should allow you to specify your 5-fold symmetry axis as z and put the 2-fold symmetry axis in the yz plane. I only did one test so if the results look wrong, tell me. The script is attached and is also available on the Chimera Python scripts web page, called changeaxes.py</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts">http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a></div><div><br></div><div>I hope this lets you take vacation for a week!</div><div><br></div><div> Tom</div><div><br></div><div></div></body></html>