To use Sequence Logo, select the tab for your Design or Flex Design job (or open a new tab). The Structure Viewer should load your protein structure shortly in the workspace at the lower part of the screen. On the bottom right, click the arrow button next to Structure Viewer to switch to Sequence Logo. On the x-axis, you can slide though sequence positions to focus on a region of interest. The y-axis displays the relative frequency (in the final sequences) of each mutation at a position.
Above, this Sequence Logo is shown for all the poses for this design case. The y-axis is in bits. In information theory, a bit is a log scale measure of frequency. Often the less frequent residues are hard to see so switch to % mode.
Above, this Sequence Logo is shown for selected poses for this design case. This image shows the y-axis in % mode. As you can see, positions like 137 are much easier to read in this mode.
For more information about how Sequence Logo is calculated, visit: