KeepSticks undisplays all atoms not in the Endcap draw mode and all bonds not in the Stick draw mode. These draw modes correspond to the stick representation. Interestingly, the draw mode of bonds is also Stick (but the draw mode of atoms is not Endcap) in the ball-and-stick and sphere representations.
KeepSticks is primarily useful when sequence and structure alignments are being examined with MSF Viewer and AlignPlot. Frequently a user will highlight portions of the sequences with the mouse, causing the corresponding regions within the structural alignment to be highlighted as sticks. Using KeepSticks then clears the display of the other portions of the structures so that it is easier to view the highlighted regions.
There are several ways to start KeepSticks, a tool in the Homology category.