On 11/17/16 5:14 PM, Parker de Waal wrote: > Does anyone know if it is possible to perform a 3d alignment between > two proteins while only moving the selected atoms? (i.e. leaving the > unselected atoms for the alignment unmoved?)

Modeller's 3D alignment (superpose) does a rigid rotation and translation of the entire protein. It doesn't really make sense to not move the unselected part of the protein because that would distort the structure. But you could certainly do the superposition and then combine the moved selected atoms with the unmoved unselected atoms from the original PDB file, either manually or with some simple scripting.

Ben Webb, Modeller Caretaker