Hi Mike, There is just one Xform per Chimera model that you access using model.openState.xform You can set the transform of one model to be the same as another with model2.openState.xform = model1.openState.xform The assignment copies the xform so each model will have its own copy. The xform first applies the rotation matrix and then a translation. You probably see the translation changing when you rotate the molecule because the center of rotation when using the mouse is not at the origin (0,0,0). (The center of rotation for mouse rotations can be controlled -- see the Rotation tab of the Side View dialog.) When you get atom coordinates with atom.coord() you get the original xyz values from say a PDB file. The m.openState.xform applied to those coordinates gives you the displayed xyz Chimera coordinates of the atom taking into account the rotation and translation. So you should apply the xform before comparing distances between atoms in different molecules. Tom