1. Choose Analysis ➧ New Analysis... and create a new protein analysis. Select Helical Wheel and choose OK. Each new analysis you add will have parameters associated with it. With Helical Wheel icon selected in the left list, choose the Kyte & Doolittle table from the Table popup menu on the right.
2. Click on Input Sequences icon on the left, open the peptide rhodopsins file and select the sequence Lamprey rhodopsin. Click on the Lamprey rhodopsin sequence as shown in Figure 31. Press the Segment button on the bottom right of this panel and specify that you want to analyze residues 75-100 as shown in the figure. The segment selector always refers to the sequence that is highlighted in the list in the top part of the panel. Run the Analysis Setup.

   Figure 31: Selecting a Sequence Segment for Analysis

    

3. Double-click on the resulting Helical Wheel output object in the notebook to make it the target and try some of the options under the Object menu. This analysis shows how the amino acid side chains would be distributed if you were to look down the central axis of an alpha helical segment of a peptide. Functions that are specific to each analysis output object will always be found under the Object menu.
4. Choose Object ➧ Recalculate... and rerun the analysis using a different table (Sweet and Eisenberg). Note that you can also create your own tables for use in any appropriate analysis (Use the Analysis ➧ Tables... option to create your own tables). Creating tables is discussed in the Tutorial 20: Creating Your Own Analysis Tables.
5. Double-click on the Helical Wheel output object and choose Object ➧ Recalculate again. Remove the Helical Wheel analysis from the Analysis Setup by clicking on the Helical Wheel icon in the list on the left and then choosing Analysis ➧ Remove Analysis.
6. Choose Analysis ➧ Add Another Analysis.... Add the Amino Acid Composition analysis and then add the analysis called pH/pI . Notice that the top of the pane now shows two analyses, as shown in Figure 32.

   Figure 32: Adding Analyses

    

7. You can add and remove analyses from any Analysis Setup using the approach described in this tutorial. It does not matter how the Analysis Setup was opened - as a new analysis, from a recalculation, or from the Setup Menu option.
8. Press the Run button to start the analyses.

This concludes this tutorial. You may quit or continue on to the next tutorial. If you choose to continue, close all open windows now.