Editing Kabsch (section)

== Notes ==
<ol><li>Windows users are having problems running the script.  Python tells them first off "TypeError: Can't convert rank-0 arrays to Python scalars."  The fix to that breaks some code in Numeric -- which I don't maintain.</li><br>
<li>However, to make this work, you can change the code in <b>Numeric.py</b> supplied with Pymol, located in the folder "<Pymol Home>\modules\Numeric\" (for example:  "C:\Program Files\DeLano Scientific\PyMOL\modules\Numeric").<br><br>
Essentially, you need to search for the line: <source lang="python"> if axis2 < 0: axis2 = axis1 + n  # (should be around line 250) </source> and replace it with: <source lang="python">if axis2 < 0: axis2 = axis2 + n </source></li></ol>

===Examples===
 optAlign 1cll and n. CA and i. 4-20+30-60, 1ggz and n. CA and i. 4-20+30-60

 optAlign 1kao and n. CA and i. 20-50, 1ctq and n. CA and i. 20-50

<gallery>
Image:OptAlign1.png|1cll and 1ggz loaded
Image:OptAlign2.png|1cll and 1ggz aligned to residues 5-50+55-80 shown in red
</gallery>

Kabsch can also align hetero-atoms:
<source lang="python">
load 1cll.pdb
load 1ggz.pdb
optAlign 1cll and e. CA, 1ggz and e. CA
</source>
The above aligns the 4 Calciums in each structure.