week 3 but a bit late!

Well I am beginning to feel more confident in python and decided to implement the alignment of two structures as was done by W. Kabsch (1976). Nice bit of maths and also a fun introduction to eigenvectors! Though wasted two days on learning that np.eig wont work on symmetric matrices and one should use .eigh,.

Well at least I now have my alignments for the ILE rotamers  and calculated all my RSMDs to compare the geometry optimized structures against the ones I produced earlier.

So I found the alignment looked best (example shown below made using Pymol) when the alignment was done using only the fixed atoms to generate the rotation matrix.