A computationally elegant and probably faster approach is to use
quaternions, proposed by MacKay in Acta Cryst. A40 165-166. For a recent
description of this method see
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2958452/
George
On 12/27/2012 09:09 PM, Dale Tronrud wrote:
If you just want the mathematics and are willing to roll your own
code, you can use the method of Wolfgang Kabsch. I see this has been
enshrined in a Wikipedia page at
http://en.wikipedia.org/wiki/Kabsch_algorithm
This is what I've used when I've wanted to superimpose points where
the mapping between the points is defined. If the points in your
tetramer aren't pathological, like lying in a common plane, you
shouldn't have to worry about SVD and can just perform the matrix
inversion.
Dale Tronrud
On 12/27/12 11:16, Waugh, David (NIH/NCI) [E] wrote:
Greetings,
I have what seems like a relatively simple problem to solve, but have not been
able to do so using the software tools I know about. I have two sets of 4
points in 3D space (atoms in PDB files). They represent equivalent positions in
two tetrameric proteins. I would like to align these points in one PyMol or
Coot file. I don’t want a NEW set of points representing the LSQ average of the
two sets, which is what I get in Coot’s SuperPose. Instead I am looking for a
way to “superimpose” one atom from each set and then rotate one set for the
best fit. I’m not an intuitive expert on symmetry, but I think there is
probably only one best solution to this problem, right? I also need the atomic
distances to be on the same scale in the two sets of points.
Thanks for any help!
Dave Waugh
--
David S. Waugh, Ph.D.
Macromolecular Crystallography Laboratory
Center for Cancer Research
National Cancer Institute
Bldg. 538, Room 209A
Frederick, MD 21702-1201
+1 (301) 846-1842
[email protected]
http://mcl1.ncifcrf.gov/waugh.html
--
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582
