The msa3d command 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. See also: 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.
cutoffDistance d
The maximum CA-CA distance (C4'-C4' for nucleic acids) for defining membership in a column of the output sequence alignment (default 5.0 Å).
columnCriterion any | all
A residue can be aligned in a column if it is within the cutoff distance of:
- any (default) – at least one other residue in the column
- all – all other residues in the column
showAlignment true | false
Whether to show the resulting multiple sequence alignment in the Sequence Viewer. An RMSD header is automatically shown above the sequences, with histogram bar heights representing the spatial variation among residues associated with a column.
alignmentId alignment-ID
Specify the alignment-ID of the output sequence alignment (i.e., the text string to be shown in the title bar of the Sequence Viewer window and that can be used to specify the sequence alignment in commands such as sequence).
gapChar char
What character to use for gaps in the output sequence alignment (default .).
circular true | false *not yet implemented*
Whether to allow for circular permutation by doubling sequences as needed to simultaneously align the N-terminal region of one protein with the C-terminal region of the other and vice versa. Information on any permutations will be sent to the Log.
maxIterations N | none [ refChain chain-spec ] [ minStretch L ]
Maximum number of times to refit the structures based on the output sequence alignment and generate a new sequence alignment, either an integer N ≥ 0 (default 3) or the word none. (no maximum, continue to convergence). Regardless of N, iteration will stop at convergence, or will not occur at all if there are no fully populated columns in the sequence alignment. Suboptions:
- A reference chain is needed to refit the structures; if not specified with refChain, the first chain listed among those to include in the alignment (the first chain-spec in the command) will be used.
- Only stretches of minStretch L fully populated columns or longer will be used during iteration, where L is a positive integer (default 3).