### Usage: alignmatchatomstoAtomsrefatoms  [ cutoffDistanced ] [ movewhat ] [ eachlevel ] [ reportMatrix  true | false ]  pairing-options

The align command performs least-squares fitting of the matchatoms onto the refatoms. It can also report least-squares-fit root-mean-square deviations (RMSDs) as if the atoms had been moved, but without actually moving the atoms. The number of atom pairs used and the RMSD are reported in the Log.

To calculate RMSDs using the current atomic positions without any fitting, see the rmsd command. See also: matchmaker, fitmap, view, measure rotation, save PDB

Only equal numbers of matchatoms and refatoms can be used in the calculation, but the pairing options may help to restrict broader specifications to only the relevant pairs.

If a cutoffDistance d is supplied, the fit will be iterated. 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 d 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.

The move option indicates what to move, which can be:

• atoms – move the specified atoms (matchatoms)
• residues – move the residues containing the specified atoms
• chains – move the chains containing the specified atoms
• structures (default unless each is used) – move the models containing the specified atoms by overall rotation/translation (transform the models)
• structure atoms – move all atoms in the models by changing their coordinates instead of transforming the overall models
• nothing – do not move anything, but report the RMSD as if the atoms had been fitted

The each option indicates dividing matchatoms into subsets for matching independently rather than collectively, where the level can be:

• chain – match each chain separately (implies move chains)
• structure – match each atomic model separately
• coordset – match each coordinate set in matchatoms (which must specify a trajectory model) separately

The reportMatrix option (default false) indicates whether to show the transformation matrix or matrices in the Log.

### Pairing Options

The options below restrict how matchatoms are paired with refatoms. Unpaired atoms are ignored, so these options may help to limit broader specifications to the equal numbers of atoms required for the calculation.

matchAtomNames  true | false
Only pair atoms with the same atom names.
matchNumbering  true | false
Only pair atoms with the same residue numbers. Atoms are assumed to be in residue-number order.
matchChainIds  true | false
Only pair atoms with the same chain identifiers.

UCSF Resource for Biocomputing, Visualization, and Informatics / September 2020