Hi Katherine, in this case, I would specify the polar rotation parameters, which give you the direction of the rotation axis (specified by two angles) and the rotation around this axis (the angle you already calculated). As I said, if DynDom 3D or your superposition program do not print these values, I could provide you with an old program that prints them.
Best, Herman Von: Katherine Sippel [mailto:katherine.sip...@gmail.com] Gesendet: Dienstag, 5. August 2014 23:23 An: Schreuder, Herman R&D/DE Cc: ccp4bb Betreff: Re: [ccp4bb] AW: [ccp4bb] reporting rotational and translational interface shifts Hi Herman, I have done a categorically awful job at explaining the problem. I'll just copy and paste my explanation from an off-board conversation. Normally I would use the angle = cos^-1((a11+a22+a33-1)/2) formula on the rotation matrix to get the shift angle. My problem is that the shift is occurring in not quite opposite directions between the three different models (see attached). Saying that "the dimer orientation shifted 15 degrees between apo and the homolog versus 11 degrees between the apo and bound" is misleading because there is a directional component that isn't being accounted for in that statement. I'm trying to figure the best way to express the dimer orientation changes in a results section so that it won't be confusing for the reader. At the moment I'm attempting to co-opt DynDom 3D into identify a rotation axis, but I am open for suggestions. On Tue, Aug 5, 2014 at 1:50 AM, <herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com>> wrote: 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<mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag von Katherine Sippel Gesendet: Montag, 4. August 2014 19:02 An: CCP4BB@JISCMAIL.AC.UK<mailto: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 -- "Nil illegitimo carborundum" - Didactylos
