[Chimera-users] centering a volume to an atom's coordinate

Hi, I am trying to center volumes (cylinders and spheres that I created using spider) to an atom from a pdb file. When I created the volumes I made sure that their center is in the middle of the box containing the volume. I tried to set the coordinate of the volume to the atom's coordinate (in the coordinate tab under volume viewer) but the position of the volume was not centered to the coordinates provided. Any idea on how to do that? Thank you Roni