A PyMOL plugin to iteratively align the DNA of a probe object (e.g. TF bound to DNA motif) onto the DNA of a target object (e.g. nucleosome) and calculate the clashes between protein atoms of probe and DNA and/or protein atoms of target.

Requires PyMOL with python > 3.x

In the PyMOL console install dependencies pip install pandas pip install matplotlib

Download the scan_factor.py file and install it as a plugin as described under (https://pymolwiki.org/index.php/Plugins).

fetch 6t90, async=0
create NCP, 6t90 and c. A+B+C+D+E+F+G+H+I+J
create OCTSOX, 6t90 and (c. K+L or (c. I and i. 3-24) or (c. J and i. 124-145))
scan_factor NCP, OCTSOX, probe_center=True

Richard D. Bunker and Georg Kempf