LSQKAB gives something of what you want..
If you fit domain_open to domain_closed after the rest of the structure
is aligned.
you get
the COM of the two domains.
the rotation angles in euler and polar form
I would say the rotation angle was the omega angle and the translation
the difference between the COMs
Eleanor
peter hudson wrote:
Hi all
I am working with a multidomain protein whcih binds to a ligand. This
protein exist in two different states, a) apo form of the protein is closed
state and b) holo protein is an open state. One of the domain is mobile and
have different conformation compared to its closed conformation. This
domain have rotated by an angle of 15 degree and also translated with some
Angstrom. Can any one explain me how to calculate the Translation distance
as well as the rotation angle of the domain in the different states? I would
appreciate the suggestions.
Thanks in advance
Peter
