When you are selecting a region of a sequence e.g in the Sequence zoom view the corresponding region on the 3D structure is being highlighted while the rest regions of the 3D structure are being shaded.
To configure the color of a region selected open the Settings dialog (press the Settings item in the 3D Structure Viewer context menu or in the Display menu on the toolbar to do it), press the Set selection color button and select a color in the dialog appeared.
To adjust the shading drag the Unselected regions shading slider in the Settings dialog.
