parcoor
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.
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.
Running parcoor
Command-Line
Usage:
$ parcoor [OPTIONS] <COORD FILE>
PARCOOR expects the following command line arguments:
Arguments and Options
| 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 accepts atomic coordinate data in .pdb format as input. This may be either a relative or absolute file path, or data will be read from stdin.
parcoor Output Files
Upon execution, PARCOOR will create a set of atomic model files in .pdb format, each corresponding to one of the subdomains into which the input structure was partitioned.
Examples
Splitting an atomic model into domains
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.