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EMBL Hamburg Biological
Small Angle Scattering
BioSAXS

NMATOR manual

NMATOR

Written by K. Manalastas-Cantos.
Post all your questions about NMATOR to the ATSAS Forum.

© ATSAS Team, 2019-2020

Table of Contents

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 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.

Running nmator

Usage:

$ nmator <COORD FILE> <RUN MODE> [SAXS FILE]

NMATOR expects the following command line arguments:

ArgumentDescription
COORD FILE Atomic model in standard PDB/mmCIF format.
RUN MODE Specifies nmator output: 'tnm' to compute TNMs only, 'fit' to output models that fit a given SAXS curve, 'pool' to generate a set of related models
SAXS FILE SAXS data file; for fit mode only

nmator Input Files

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.

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:

OutputDescription
log.txt Contains real-time updates of the run, as reflected on the screen output
modX_chY/*.pdb Output models derived from model X, chain Y of the given PDB/mmCIF structure.
modX_chY/*.fit 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
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 PDB/mmCIF structure; Each TNM is defined by a first line "Eigenvalue ", 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 tnm

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 fit 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

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


  Last modified: May 15, 2020

© BioSAXS group 2020