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The idea of the panel design tool is to select sequences from the alignment such that the selected sequences are maximally distributed over the superfamily. This is done in two steps: First the sequences of the superfamily are grouped. This can simply be based on sequence similarity (similar sequences are within the same group), but groups can also be based on sequence motifs found at user selected positions. The last option is used to group sequences based on a protein feature. For instance, the user can pick positions important for specificity. The idea is that sequences that have the exact same residues (the same motif) at those positions they are likely to have the same specificity. Both methods can be combined. In the second step a user defined number of sequences (usually one or two) are selected from each group. The selection step contains all kinds of options to maximize the chance that these proteins are likely to express. Lets Let's see how it works.
Select the "panel design" option in 3DM. First we will divide the super-family based on sequence motifs. Because we want maximize the specificity range in the panel, we will use the "specificity hotspot" basket you have generated in question 30. This way all sequences with the same motif at our specificity hotspots (thus will likely have the same specificity) will be in one group. Use the "add hotspots" button to select the hotspot basket you made in Q30 (it should contain 9 positions).
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