Align Chain Sequences generates a multiple sequence alignment (MSA) of structure chains in Chimera using a Clustal Omega or MUSCLE web service provided by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI). The MSA web service can also be called from Multalign Viewer to realign an existing alignment. The coordinates of the structures are not used, only the sequences. By contrast, the Match -> Align tool generates an MSA using only the α-carbon proximities in a 3D superposition. See also: MatchMakerClustal Omega users should cite:
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG. Mol Syst Biol. 2011 Oct 11;7:539.MUSCLE users should cite:
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Edgar RC. Nucleic Acids Res. 2004 Mar 19;32(5):1792-7.
There are several ways to start Align Chain Sequences, a tool in the Sequence category.
Two or more Chains to align should be chosen from the list of structure chains currently open in Chimera. A contiguous block can be chosen by click-and-drag, or by clicking on the first (or last) line in the block and then Shift-clicking on its last (or first) line. Ctrl-click toggles the status of a single line.Options (default settings bold):
OK initiates the calculation and dismisses the dialog, whereas Apply initiates the calculation without dismissing the dialog. The job will be run in the background; clicking the information icon in the Chimera status line will bring up the Task Panel, in which the job can be canceled if desired. Cancel dismisses the dialog, and Help opens this manual page in a browser window.
The output sequence alignment will be opened automatically in Multalign Viewer.