Chimera Commands Index

match  atom-spec1  atom-spec2  options

The match command performs least-squares fitting of specified atoms, moving the first set of atoms (by default, the entire models containing them) onto the second. It can also report least-squares-fit root-mean-square deviations (RMSDs) without actually performing the fits, i.e., without moving the atoms. The related command rmsd calculates RMSDs without any fitting, using the current positions of atoms. See also: matchmaker, measure rotation, matrixcopy, Ensemble Match, superimposing structures

Atom-spec1 and atom-spec2 must specify equal numbers of atoms. Options may precede and/or follow the atom specifications.

Atoms are paired in the order specified, i.e., the first atom in the first specification is matched to the first atom in the second specification, the second atom to the second atom, and so on. At least three pairs of atoms are needed to define a unique transformation, although fewer pairs can be used. If atom order is not specified, for example,

match #1:fad #0:fad
match #2:246,295 #0:195,221
the atoms within a residue are ordered first by name, and where these are identical, by alternate location identifier, and where these are also identical, by serial number.

The two sets of atoms can be specified collectively as a selection using the word selected, sel, or picked. An ordered selection can be created by picking atoms one by one, first the atoms of the first set, then those of the second in the corresponding order.

The fit can be iterated. The number of atom pairs in the final fit and their RMSD are reported in the status line and Reply Log. The transformation matrix can also be reported.


A vertical bar “|” designates mutually exclusive options, of which the default values are indicated with bold.

iterate cutoff
Perform successive rounds of matching to the indicated stringency (default is no iteration). In each cycle of iteration, atom pairs are removed from the match list and the remaining pairs are fitted, until no matched pair is more than cutoff Å apart. The atom pairs removed are either the 10% farthest apart of all pairs or the 50% farthest apart of all pairs exceeding the cutoff, whichever is the lesser number of pairs. This excludes conformationally dissimilar regions from the final fit and allows the best-matching regions to be well superimposed.
move  true | false | molecules | chains | residues | atoms | atom-spec3
Whether to move atoms as a result of the fitting calculation, and if so, whether to move the entire molecule models containing the atoms in atom-spec1 (default true, equivalent to molecules), only the chains containing them, only the residues containing them, only the atoms themselves, or a different set of atoms (atom-spec3). If false, no atoms will be moved, but the reported RMSD and matrix will still reflect the movement that would have occurred.

** Movements of chains, residues, atoms, or atom-spec3 cannot be undone except by reopening the original structure. **

showMatrix true | false
– or –
show true | false
Whether to report the transformation matrix in the Reply Log. If the model was previously moved relative to the reference coordinate system (before the current command), matrices for both the change in position from the current command and the overall change in position relative to the reference since file opening will be reported.
In addition to what would otherwise move, apply the same transformation to any other models that are activated for motion (except the reference model(s), i.e., those containing the second set of atoms).