Jonathan, this is called the quaternion difference, but I don't know how you get access to quaternions in PyMOL. If you could, you would just take the difference between the two quaternion representations of the views and get it's angle for the corresponding axis-angle.

Jason, are there standard Python utilities that one can use to get the quaternion equivalents of PyMOL matrices?


On Mon, Nov 25, 2013 at 9:14 AM, Jonathan Grimes <> wrote:

   is there a script available to calculate the min rotation about a vector
   that describes the relationship between 2 views……

   i am happy to ignore any translational component but i have 2 views
   of a molecule and want to say that theres a *** deg rotation between the


Dr. Jonathan M. Grimes,
NDM Senior Reseach Fellow
University Research Lecturer
DIAMOND Research Fellow

Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive,
Oxford OX3 7BN, UK

Email:, Web:
Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

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Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900