Tool: Match→Align

The Match→Align tool creates a multiple sequence alignment from a structural superposition of the specified chains (either all protein or all nucleic acid). Residue types are not used, only their spatial proximities. Iterations of refitting the structures using the sequence alignment and generating a new sequence alignment can be performed. The corresponding command is msa3d. See also: Sequence Viewer, Matchmaker, align, sequence align, sequence match, rmsd

The method was originally implemented in Chimera, as described in:

Tools for integrated sequence-structure analysis with UCSF Chimera. Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. BMC Bioinformatics. 2006 Jul 12;7:339.

Match→Align can be opened from the Sequence or Structure Analysis section of the Tools menu and manipulated like other panels (more...).

Chains to be included in the sequence alignment should be chosen from the top section of the panel.

• Residue-residue distance cutoff (angstroms) (default 5.0) – maximum CA-CA distance (C4'-C4' for nucleic acids) for defining membership in a column of the output sequence alignment
• Residue aligned in column if within cutoff of:
  • at least one other (default)
  • all others
  – how the cutoff should be applied; equivalent for alignments of only two chains
• Gap character – how to show gaps in the output sequence alignment
  • . (period)
  • - (dash)
  • ~ (tilde)
• *not yet implemented* Allow for circular permutation – whether to double sequences as needed to simultaneously align the N-terminal region of one protein with the C-terminal region of the other and vice versa. Doubling the sequence of one of a pair of proteins related by circular permutation is required because Match→Align enforces N → C chain directionality. Information on any permutations will be sent to the Log.
• Iterate superposition/alignment... whether to perform one or more cycles of refitting the structures using the sequence alignment and generating a new sequence alignment from the adjusted superposition. Superpositions will not be adjusted unless iteration is turned on. Only the final superposition and final sequence alignment will be shown. The number of fully populated columns in any intermediate sequence alignments and corresponding match statistics will be reported in the Log. When this option is turned on, the Iteration Parameters are shown:

  • Iterate alignment:
    • at most [N] times (default 3) – refit and then generate a new sequence alignment N times (or fewer, if convergence is reached)
    • until convergence – refit and then generate a new sequence alignment until the number of fully populated columns no longer increases
  • Superimpose full columns:
    • across entire alignment – refit the structures using all fully populated columns of the sequence alignment
    • in stretches of at least [L] consecutive columns (default 3) – refit the structures using only the fully populated columns in consecutive stretches of L or more
  • Reference chain for matching [chain] – which structure should remain fixed as the others are matched to it

Save saves the current Match→Align settings as user preferences. Reset restores the factory defaults without changing what was saved, whereas Restore populates the dialog with the last-saved settings.

Clicking OK or Apply will start the calculation with or without closing the dialog, respectively. Close simply closes the dialog, while Help opens this page in the Help Viewer. The output multiple sequence alignment is automatically shown in the Sequence Viewer.