PARCOOR manual

Written by A. Panjkovich.
Post all your questions about PARCOOR to the ATSAS Forum.

© ATSAS Team, 2016

Table of Contents

• Manual
  • Introduction
  • Running parcoor
  • parcoor Input Files
  • parcoor Output Files

Manual

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

If you use PARCOOR in your work, please cite:
Panjkovich A. and Svergun D.I. (2016) Deciphering conformational transitions of proteins by small angle X-ray scattering and normal mode analysis. Phys. Chem. Chem. Phys., 18, 5707-5719 DOI:10.1039/c5cp04540a

Introduction

PARCOOR will partition a high-resolution structural model into pseudo-domains that are expected to show partially independent dynamics, as predicted using normal mode analysis (NMA). The output consists in a set of structures corresponding to subdomains.

The structural partitioning algorithm is described in detail in the paper cited above.

Running parcoor

Usage:

$ parcoor [OPTIONS] <COORD FILE>

PARCOOR expects the following command line arguments:

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

parcoor Input Files

PARCOOR expects atomic coordinates in Protein Data Bank (PDB) format. NMA calculations are based on backbone atoms (centroids): alpha carbons (CA) for proteins and sugar C1' for nucleotides. Please note that PARCOOR parses centroid atoms from the ATOM record. The program will not work properly if input coordinates lack backbone atoms. Non-solvent HETATM entries are grouped by residue identifier and number. These are then associated to the closest ATOM centroid in the structure for the application of rotations and translations.

To skip the NMA calculation, normal modes vectors can be precomputed and saved to file using the NMAWRAPPER program.

parcoor Output Files

Upon execution, PARCOOR will create a set of PDB files, each corresponding to one of the subdomains into which the input structure was partitioned.