Dear Tarique,
The elbow angle in a Fab is just the angle between two pseudo-twofold axes:
one relating VL to VH and one relating CL to CH. You can find the
pseudo-twofold axes using many different least-squares alignment programs, just
pick your favorite. Then, just take the dot product of
This is not an ERROR message. It is a WARNING: Once the principal
Euler angle (or kappa) of the rotation angle relating the domains
deviates significantly from a (pseudo)dyad, the interpretation of the
kappa angle becomes somewhat obscure. The program kindly advises you
of that fact and places
Inherently you want to calculate:
1. the approximately two-fold relationship between VH and VL
2. the approximately two-fold relationship between CL and CH1
You can use many programs for that (e.g. LSQMAN) but ideally you want a
program that will report Direction Cosines for the rotation axis
