parcoor

• Manual
  • Introduction
  • Running parcoor
  • parcoor Input Files
  • parcoor Output Files
• Examples
  • Splittin a pdb file into domains

Manual

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

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:

Argument	Description
COORD FILE	High-resolution atomic model in PDB format.

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

Short Option	Long Option	Description
-p	--prefix=<PREFIX>	Prefix to prepend to the output directory, the default iswd_parcoor.
-e	--vectors	Skip NMA and use provided vectors file.
-v	--version	Print version information and exit.
-h	--help	Print a summary of arguments, options, and exit.

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.

Examples

Sample run

Here we use the model 1IRA_r_u.pdb to split it into domains.

$ parcoor 1IRA_r_u.pdb 

The individual domains are written to the files 0?.pdb in the output directory.