Since Jie Liu is talking about coiled coils and heptad repeat, I think what may be needed is the displacement along the bundle axis. So an expression for the best bundle axis line, and then the projection of different C-a's onto that line to measure the difference between them?
Ed Eleanor Dodson wrote: > Jie Liu wrote: > >>Dear CCP4ers: >> >>Does anyone know an existing program to calculate the lateral >>displacement---the vertical offset, measured as a fraction of the >>the heptad repeat---of neighboring helices in coiled coils or helix >>bundles, either parallel or antiparallel? >> >>Your input is greatly appreciated. >> >>Have a nice weekend! >> >>Jie >> >> >> > > > Maybe I dont understand the question.. > > If you know what you want to match to what cant you just superpose the > Cas of helix i onto those of helix j and sort it out from that? > Selecting the match might be tricky but you must have done that? > > You will need to do some geometric fiddling I guess. > The Superpose molecule option from the GUI would give you the centre of > mass of each segment and the direction cosines for the transformation, > which will be those for the helix axes. I think the dot product of the > COM onto the DCs would give you the relative displacements in As > > (X_com1*DC1 + Y_com1*DC2 + Z_com1*DC3) - (X_com2*DC1 + Y_com2*DC2 + > Z_com2*DC3) > > Eleanor
