NMATOR uses normal mode analysis (NMA) in dihedral/torsion angle space to approximate the flexible motions of biological macromolecules, and generate conformations that account for the experimental small-angle X-ray scattering (SAXS) data. Torsional normal modes (TNMs) are first computed based on an initial set of atomic coordinates. If a SAXS data profile is provided, the initial coordinates are modified along the TNMs such that the resulting models have improved correspondence to the SAXS data. NMATOR has been developed and optimized on single-chain RNA structures, but also functions for protein and DNA structures.
NMATOR can also be used to derive a pool of models from an initial structure. The pool consists of conformers that have been modified from the initial structure along different combinations of the first three TNMs.
NMATOR can read atomic coordinates in both Protein Data Bank (PDB) and Macromolecular
Crystallographic Information File (mmCIF) formats. Both atom name and element name fields
are required, as well as the standard ordering of the atoms to correctly establish bond
conectivity. Best results are achieved with a complete backbone structure. Multichain
structures and non-solvent HETATM entries are currently not supported.
NMATOR reads experimental SAXS data files (*.dat) in ascii format containing 3 columns:
(1) scattering vector, (2) intensity and (3) experimental errors.
Upon execution, NMATOR creates an directory named nma_odir to store the resulting
output files. If the directory already exists, a number will be appended to create
a new directory (e.g. nma_odir2). The output directory contains the following files:
in fit mode only; Fit of the corresponding model's theoretical scattering to the
experimental scattering. Columns in the output file are (1) experimental scattering vector
in Angstroms, (2) experimental intensity, (3) experimental errors, and (4) theoretical
scattering of model
in tnm mode only; The first 20 torsional normal modes for model X, chain Y
of the given PDB/mmCIF structure; Each TNM is defined by a first line
followed by the TNM specified as new-line delimited values.