cifop

• Manual
  • Introduction
  • Running cifop
    • Command-Line Arguments and Options
    • Runtime Output
  • cifop Input Files
  • cifop Ouput Files
• Examples
  • cifop as replacement of ALPRAXIN
  • cifop as replacement of DAM2EN
  • cifop as replacement of DAM2DAM

Manual

The following sections briefly describe the method implemented in CIFOP, how to run CIFOP from the command-line, as well as the required input and the produced output file.

Introduction

CIFOP applies linear operations on atomic coordinates files in .pdb or .cif format. Operations include any combination of translation, rotation and reflection, as well as derived operations like translation to origin or alignment of principle axes to coordinate directions.

Running CIFOP

Usage:

$> CIFOP [OPTIONS] [MODEL]

CIFOP accepts absolute as well as relative paths to the atomic coordinate MODEL in .pdb or .cif format. If no path to a MODEL is provided, CIFOP reads from stdin. Input format on stdin is .pdb for historic reasons.

The OPTIONS known by CIFOP are described in the next section.

Command-Line Arguments and Options

CIFOP requires the following command line arguments:

Argument	Description
MODEL	Optional. The atomic coordinate file in .pdb or .cif format. If no MODEL path is specified, input is read from stdin.

CIFOP recognizes the following command-line options.

Short option	Long option	Description
	--model <ARG>	model number or ID in the atomic coordinates data to transform (default: all)
	--shift-x <ARG>	offset to apply in X direction; default: 0.0
	--shift-y <ARG>	offset to apply in Y direction; default: 0.0
	--shift-z <ARG>	offset to apply in Z direction; default: 0.0
	--alpha <ARG>	Euler rotation angle alpha; default: 0.0
	--beta <ARG>	Euler rotation angle beta; default: 0.0
	--gamma <ARG>	Euler rotation angle gamma; default: 0.0
	--reflect-x	If set, all X coordinates are replaced with -X; default: no reflection
	--reflect-y	If set, all Y coordinates are replaced with -Y; default: no reflection
	--reflect-z	If set, all Z coordinates are replaced with -Z; default: no reflection
	--shift-to-origin	shift geometric center of each selected model to the origin
	--align-axis	align eigenvectors with coordinate axes
	--dam <R>	convert to dummy atom model with bead radius R
-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.
-v	--version	Print version information and exit.
-h	--help	Print a summary of arguments, options, and exit.

Runtime Output

CIFOP does not have any runtime output. If the output file is undefined, the transformed coordinates will be written to stdout.

CIFOP Input Files

CIFOP accepts atomic coordinate data in .pdb or .cif format as input. This may be either a relative or absolute file path, or data will be read from stdin.

CIFOP Output Files

CIFOP 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

CIFOP as replacement of ALPRAXIN

Use CIFOP to align 6lyz.cif and write the result to 6lyz-aligned.pdb:

$ cifop --align-axis 6lyz.cif -o 6lyz-aligned.pdb

CIFOP as replacement of DAM2EN

Use CIFOP to create an enantiomorph of 6lyz.cif and write the result to 6lyz- en.cif:

$ cifop --reflext-z 6lyz.cif -o 6lyz-en.cif

CIFOP as replacement of DAM2DAM

Use CIFOP to create a DAM representation of 6lyz.cif and write the result to 6lyz-dam.pdb:

$ cifop --dam=2.0 6lyz.cif -o 6lyz-dam.pdb