Choosing Edit... Realign Sequences from the Multalign Viewer menu opens a dialog for generating a new multiple sequence alignment (MSA) from all of the sequences in the current alignment. The current alignment is not used; the sequences are submitted in a dealigned state to a Clustal Omega or MUSCLE web service provided by the UCSF RBVI. The MSA web service is also used by Align Chain Sequences to align the sequences of structure chains in Chimera. See also: alignment editing, Match -> AlignClustal 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.
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. Close dismisses the dialog, and Help opens this manual page in a browser window.