Article ID: 1503 - Last Modified: June 9, 2011
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.
- Import the PDB files into Maestro. Sequence manipulation will be faster if you only load a representative chain from each PDB file.
- Choose Tools → Multiple Sequence Viewer.
- Perform a multiple alignment. Lock gaps when you are satisfied with the alignment.
- Select the binding site residues in the Workspace.
- In the MSV, from the Alignment menu, choose Expand Selection, then choose Invert Selection, then choose Fill with Gaps.
- Click in the MSV to clear the selection
- Choose File → Save Image
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