Objects in the notebook can be aligned with each other to provide better ways of comparing and presenting results.

1. This tutorial will describe how to align and automatically resize objects. To do this you must first generate some output objects to be aligned. For this tutorial, choose to do the “Accessible Surface Area” analysis on lamprey, octopus, and xenopus rhodopsins (they are in the peptide sequences folder). Accept all the default parameters and choose Run as described earlier in this chapter.
2. Click on the top output object and make it wide and short as shown in the top analysis in Figure 24.

   Figure 24: Output Objects Before Alignment

3. Select all of the analysis objects by clicking on one of them once and then choosing Edit ➧ Select All. This will select all GI Notebook objects (two in this case). Choose Notebook ➧ Arrangement ➧ Align Objects…. You will see the alignment dialog shown in Figure 25. The ability to adjust sizes and align objects as shown in the figure is very useful for making all analyses have the same width, for example, so that the X-axes align and graph results can be compared. Set the items in the window to match what is shown in Figure 25. This will cause the objects to line up along their left edges and to be as wide as the widest object and as short as the shortest object. Press the OK button.

   Figure 25: Notebook Object Alignment

4. After alignment, the analysis objects will look like Figure 26. Note that the objects are all aligned on the left as defined in the object alignment dialog. Since we did not specify any vertical alignment, the tops of each object remain the same as they were before the alignment. This results in vertical space between the object.

   Figure 26: Output Objects After Alignment

5. This same alignment dialog can be used to superimpose graphs to see how different plots compare. One use might to make one protein plot red and another blue – then superimpose them for a direct comparison. To superimpose the plots, one needs to align objects at their tops and at their left edges while defining the same widths and heights for all objects.
6. Save the notebook using File ➧ Save . You will need the notebook for a later tutorial (Tutorial 9: Taking Notes Using Background Text).

This concludes this tutorial. If you choose to continue to the next tutorial, close all open windows now.