Hi Katherine, Just reporting the translation vector is not very useful, since it depends on how far your protein molecule is away from the origin (rotation center). I do have an ancient program which reports the translation vector when rotation axis through centroid and the component of the translation vector parallel to the rotation axis.
However, in your case, I would critically examine the structures. Usually, most of the movements can be explained by rotations and in this case I would only report rotations. However, if it looks like there is a significant translation component, or the center of rotation is away from the hinge, I would try to quantify this translational component as well. My 2 cents, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Katherine Sippel Gesendet: Montag, 4. August 2014 19:02 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] reporting rotational and translational interface shifts Hi all, I am trying to figure out the best way of reporting changes in dimer orientations between three structures. I have an apo, a drug-bound, and a homolog dimer structure. I had originally decided to calculate the angle from the rotation matrix generated by LSQKAB, but the translational component is oriented in opposite directions (translation vector of -22.9, 3.2, 10.8 versus 22.4, -3.4, -17.1). I've only ever seen these types of orientation shifts reported in degrees, so I was wondering how other people dealt with accurately reporting these numbers in their manuscripts. Did you include the translation vectors in the text or just rely on figures and arrow to make your point? Thanks for your time, Katherine -- "Nil illegitimo carborundum" - Didactylos
