Match -> Align

Match -> Align creates a sequence alignment based on a structural superposition in Chimera. Residue types are not used, only their spatial proximities. The output sequence alignment is automatically shown in Multalign Viewer.

For an informal introduction, see the Superpositions and Alignments tutorial. See also: MatchMaker, Multalign Viewer, and

Meng, E.C., Pettersen, E.F., Couch, G.S., Huang, C.C., and Ferrin, T.E. "Tools for integrated sequence-structure analysis with UCSF Chimera." BMC Bioinformatics 7(1):339 (2006).

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

The Residue-residue distance cutoff (angstroms) (default 5.0) determines which residues can be aligned in the output sequence alignment. Distances are measured between the CA atoms of amino acid residues and the C4' atoms of nucleic acid residues. The cutoff can be enforced in two ways, Residue aligned in column if within cutoff of:

• at least one other
• all others (default)

The Gap character in the output sequence alignment can be a period (.), dash (-), or tilde (~).

A pair of proteins may be related by circular permutation, where the N-terminal region of one protein resembles the C-terminal region of the other and vice versa. Although Match->Align enforces N → C chain directionality, the option to Allow for circular permutation doubles sequences as needed. Information on any permutations is written to the Reply Log.

When aligning two chains without allowing for circular permutation:

A modified Needleman-Wunsch procedure (dynamic programming) is used to determine the sequence alignment that best represents the structural alignment. The score for aligning a pair of residues is:

• (cutoff – distance) for distances no greater than the cutoff
• –1 for distances greater than the cutoff

The gap penalty is zero, since for this application the spatial proximity should be more important than adjacency in sequence; that is, residues farther apart than the distance cutoff should not be aligned. The number of residue pairs aligned is reported in the status line and Reply Log.

Save settings writes the current Match -> Align parameters to the preferences file. Reset to defaults resets the dialog to the factory default parameter settings without changing any preferences.

OK initiates calculating the alignment and dismisses the dialog, whereas Apply initiates the calculation without dismissing the dialog. The resulting sequence alignment is automatically shown in Multalign Viewer and can be saved to a file from that tool.

Close simply dismisses the dialog. Help opens this manual page in a browser window.