Dear all, Based on early queries, I am now using xform coord for most of my scripts. However, now I have a problem because I have mixture between xforms and coord. For example, I want to place a helium at the center of mass of the molecular and having previously calculated it using xform coordinates... The center of mass is therefore located at another part of the space. How could I transform on set of coords to the other? Thanks for any help! JD Here is the script from chimera import selection from chimera import Point, Vector, Xform import BuildStructure def com(sub): for i in range(len(sub.atoms)): sumi=0 center = Vector(0, 0, 0) for a in sub.atoms: sumi += a.element.mass center += a.element.mass * Vector(*a.xformCoord().data()) center_point=Point(center[0]/sumi,center[1]/sumi,center[2]/sumi) return center_point def placing_points(center): #pt=Point(center[0]/sum,center[1]/sum,center[2]/sum) #print pt BuildStructure.placeHelium('com', model='scratch', position=center) ligand = selection.currentResidues()[0] center=com(ligand) placing_points(center)