Manual

The following sections briefly describe the method implemented in NMATOR, how to run NMATOR from the command line, the required input and the produced output files.

Introduction

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 for 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.

Running nmator

Usage:

$ nmator <MODEL> [DATA]

Command-Line Arguments and Options

NMATOR recognizes the following command-line arguments.

Argument	Description
MODEL	Required. The atomic coordinate file in .pdb or .cif format.
DATA	Optional, used only when fitting. Exactly one experimental SAS data (.dat) file.

Absolute as well as relative paths to data files are accepted. Instead of a file name, one of the arguments may be given as ‘-‘ to read data from stdin.

NMATOR recognizes the following command-line options. Mandatory arguments to long options are mandatory for short options too.

Short Option	Long Option	Description
-P	--pool <N>	Specify maximum number of conformers to generate from initial structure. Skip the refinement against experimental data.
	--explicit-hydrogens	Use explicit hydrogens provided in the atomic structure file; default: use implicit hydrogen groups determined by looking up the number of hydrogens in components.cif.
	--lm <N>	Maximum order of harmonics; default: 20, minimum: 1, maximum: 100. This defines the resolution of the calculated curve. The default value should be sufficient in most use cases. For large or extended particles higher orders could improve the results, at the cost of an increased run time. This value must be increased whenever the maximum scattering angle is increased (smax).
	--fb <N>	Order of Fibonacci grid; default: 17, minimum: 10, maximum: 18 The order of Fibonacci grid defines the number of points describing the surface of the macromolecule. Higher grid orders give a more accurate surface representation, but more CPU expensive. Only used if option shell=directional (the default).
	--ns <N>	Number of calculated data points; default: 101, maximum = 10001.
	--smax <SM>	Maximum scattering angle in inverse angstroms, either for calculating the theoretical curve up to SM or for fitting to SM; default: 0.5\(\AA^{-1}\), maximum: 2.0\(\AA^{-1}\)
	--units <N>	Angular units of the experimental data: 1 = \(\AA^{-1}\), \(s = 4\pi sin(\theta)/\lambda\); 2 = \(\mathrm{nm}^{-1}\), \(s = 4 \pi sin(\theta)/\lambda\); 3 = \(\AA^{-1}\), \(s = 2 sin(\theta)/\lambda\); 4 = \(\mathrm{nm}^{-1}\), \(s = 2 sin(\theta)/\lambda\). By default, an attempt is made to estimate the unit scale.
	--dns <VALUE>	Solvent density; default: \(0.334 \mathrm{e}/\AA^3\), the electron density of pure water. Solvents with high salt concentration may have a somewhat higher electron density.
	--dro <VALUE>	Contrast of hydration shell, default: \(0.03 \mathrm{e}/\AA^3\)
	--constant	Enables constant subtraction. This operation accounts for possible systematic errors due to mismatched buffers in the experimental data.
	--energy <eV>	X-ray energy in eV, required for energy correction in anomalous SAXS only.
	--shell <VALUE>	Shell kind, one of ‘directional’ (classic CRYSOL) or ‘water’ (previously CRYSOL3)
	--alternative-names	Enable alternative (old) atom naming for all atomic structure files; default: disabled. See also:components.cif
	--implicit-hydrogen <N>	Set this to a value N>=0 to override ‘unable to determine number of hydrogens’ errors.
	--sub-element <NAME>	Set this to a valid element to override ‘unable to determine element’ errors.
-v	--version	Print version information and exit.
-h	--help	Print a summary of arguments, options, and exit.

nmator Input Files

NMATOR requires atomic coordinates in .pdb or .cif format. 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.

Optionally, NMATOR accepts experimental SAS data (.dat) files.

nmator Output Files

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:

Output	Description
log.txt	A copy of the screen output
modX_chY/.pdb or modX_chY/.cif	Output models derived from model X, chain Y of the given atomic coordinate file.
modX_chY/*.fit	Fit of the calculated scattering curve versus the experimental data.
modX_chY/report.txt	Summary of information on the resulting models
modX_chY.tnm	in tnm mode only; The first 20 torsional normal modes for model X, chain Y of the given atomic coordinate file; Each TNM is defined by a first line”Eigenvalue<mode number><frequency of motion>”, followed by the TNM specified as new-line delimited values.

Examples

Here we use two solution NMR models of the single-chain RNA U65 Box H/ACA snoRNA (PDB ID: 2PCV, models 3 and 4).

Computing normal modes

NMATOR can compute TNMs that specify the 20 lowest frequency motions for 2PCV model 4:

$ nmator 2PCV_4.pdb

The normal modes are written in the text file modX_chY.tnm in the output directory.

Modeling conformational change

The conformation of 2PCV model 3 can be reconstructed from the structure of 2PCV model 4, and SAXS data from 2PCV model 3, as follows:

$ nmator 2PCV_4.pdb 2PCV_3.dat

The resulting models and fits can be found in the output directory nma_odir/modX_chY/

Generating a pool of models

The three lowest frequency TNMs can be used to generate a set of around 300 models from 2PCV model 4, as follows:

$ nmator 2PCV_4.pdb --pool=300

The resulting models can be found in the output directory nma_odir/modX_chY/