I want to create an image that shows the sequence alignment of just the binding site resiudes for several receptors. How do I do this?

You can do this in the Multiple Sequence Viewer, as of Suite 2010.

1. Import the PDB files into Maestro. Sequence manipulation will be faster if you only load a representative chain from each PDB file.
2. Choose Tools → Multiple Sequence Viewer.
3. Perform a multiple alignment. Lock gaps when you are satisfied with the alignment.
4. Select the binding site residues in the Workspace.
5. In the MSV, from the Alignment menu, choose Expand Selection, then choose Invert Selection, then choose Fill with Gaps.
6. Click in the MSV to clear the selection
7. Choose File → Save Image

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