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Command: align

align  matchatoms  toAtoms  refatoms  [ cutoffDistance  d ] [ move  what ] [ each  level ] [ 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:

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

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, regardless of their order. Using matchAtomNames true is not recommended for matching atoms from multiple residues per model unless matchNumbering true can also be used.
matchNumbering  true | false
Only pair atoms with the same residue numbers. Atoms are assumed to be in residue-number order. Using matchNumbering true is not recommended when matching atoms from multiple chains per model unless matchChainIds true can also be used.
matchChainIds  true | false
Only pair atoms with the same chain identifiers.

UCSF Resource for Biocomputing, Visualization, and Informatics / May 2024