PyMol has good tools for this via scripts people have made available.
Simple arbitrary axis if you know where to draw it:
https://pymolwiki.org/index.php/Symmetry_Axis
Crystallographic symmetry tools:
https://pymolwiki.org/index.php/SuperSym
Visualizing the transformation between two selections/objects - I suspect this is the one you want:
https://pymolwiki.org/index.php/RotationAxis
Brian Smith
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IUPAB & EBSA Congress 2017 16-20 July 2017 http://www.iupab2017.org/
Institute of Molecular, Cell and Systems Biology & School of Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
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