pre_bunch

• Manual
  • Introduction
  • Running pre_bunch
    • Command-Line Arguments and Options
    • Runtime Output
  • pre_bunch Input Files
  • pre_bunch Output Files
• Examples

Manual

Introduction

Generate an initial approximation for BUNCH. The approximation contains a single CA-chain (even if there are several symmetry related polypeptide chains) with the length equal to the full-length sequence. The gap between the domains in the case of a two-domain protein must be at least four amino acids.

Running pre_bunch

Usage:

$ pre_bunch [OPTIONS] <SEQUENCE> <MODEL(S)>

OPTIONS known by PRE_BUNCH are described in next section, the required arguments SEQUENCE and (one or more) MODELs in the section on input files.

Command-Line Arguments and Options

PRE_BUNCH accepts the following command line arguments:

Argument	Description
SEQUENCE	Exactly one residue sequence data (.seq) file.
MODEL	One or more atomic coordinate files in .pdb or .cif format that (partially) match the provided sequence.

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

Short Option	Long Option	Description
	--seed=<INT>	Set the seed for the random number generator
	--center=<Y|N>	Whether or not to center the final structure (default: yes)
-o	--output=<FILE>	Write output to FILE; writes to stdout if undefined. The output format depends on the FILE extension, supported are PDB and mmCIF format. Output to stdout is written in PDB format for compatibility.
-h	--help	Print a summary of arguments, options, and exit.
-v	--version	Print version information and exit.

Runtime Output

On runtime, PRE_BUNCH reports the found alignments for each input model within the input sequence, or reports an appropriate alignment error if none could be found.

pre_bunch Input Files

PRE_BUNCH expects amino acid residue sequence data (.seq) in FASTA format.

PRE_BUNCH accepts atomic coordinate data in .pdb or .cif format as input. This may be either a relative or absolute file path, or up to one model will be read from stdin (-).

pre_bunch Output Files

PRE_BUNCH may write atomic coordinate data in .pdb or .cif format on output. By default the transformed coordinates are written in .pdb format to stdout, or an output file path my be specified.

Examples

Generate the initial approximation for the example shown in BUNCH

$ pre_bunch gst-dhfr.seq 1gtaz1.pdb 1ra9.pdb -o pre_bunch.cif
 1gtaz1.pdb: alignment found:            1         218
 1ra9.pdb: alignment found:            229         387