Hi Jonathan - 

There is a script by Christoph Gohlke on the PyMOL Wiki called transformations.py  which may be useful.  It provides several functions that can be used to manipulate quaternions.  I used it to calculate pseudo-twofold axes for my Fab elbow angle script last year.  The implementation would be different, using camera matrices instead of object matrices, but the general idea would be similar.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/






On Nov 25, 2013, at 11:20 AM, Robert Hanson <hansonr@stolaf.edu>
 wrote:

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?

Bob
 


On Mon, Nov 25, 2013 at 9:14 AM, Jonathan Grimes <jonathan@strubi.ox.ac.uk> 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
    2 views ?

   thanks
    jon


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: Jonathan@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk
Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547


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--
Robert M. Hanson
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St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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

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