cifsup

• Manual
  • Introduction
  • Running cifsup
    • Command-Line Arguments and Options
    • Runtime Output
  • cifsup Input Files
  • cifsup Ouput Files
• Examples
  • cifsup as replacement of supcomb
  • cifsup as replacement of supalm
  • cifsup as replacement of suppdb
  • Running cifsup multiple times

Manual

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

Introduction

CIFSUP, is a program to superimpose one set of atomic coordinates onto another. These coordinates may be low-resolution bead models and/or high resolution NMR or x-ray crystal structures.

The program represents each input structure as an ensemble of points, then minimised the distance between them, where the distance measure is defined by the selected method. The following methods are implemented:

• ICP - Iterative Closest Point (point cloud in real space)
• NSD - Normalised Spacial Discrepancy (point cloud in real space)
• NCC - Normalised Cross Correlation (amplitudes in reciprocal space)
• RMSD - Root Mean Square Deviation (rigid transformation in real space, requires a one-to-one correspondence of ATOMs)

Running CIFSUP

Usage:

$ cifsup [OPTIONS] <STATIC> <MOVABLE>

CIFSUP accepts absolute as well as relative paths to the atomic coordinate files STATIC and MOVABLE. Both inputs may be either in .pdb or .cif format. The OPTIONS known by CIFSUP are described in the next section.

Command-Line Arguments and Options

CIFSUP requires the following command line arguments:

Argument	Description
STATIC	Atomic coordinates in .pdb or .cif format.
MOVABLE	Atomic coordinates in .pdb or .cif format.

CIFSUP recognizes the following command-line options.

Short Option	Long Option	Description
	--template-model <ID>	Model ID in the template file; default: 1
	--movable-model <ID>	Model ID in the movable file; default: 1
	--selection <S>	One of ALL (all atoms), BACKBONE (only the backbone/CA atoms), REGRID (convert both inputs to DAM) or SHELL (use only the outermost atoms); default: ALL
	--method <NAME>	One of NSD, NCC, ICP or RMSD; default: ICP
-e	--enantiomorphs <Y|N>	Search enantiomorphs, this is enabled by default
	--lm <N>	Only used with method=NCC. Maximum order of harmonics; range \(1 \leq \text{lm} \leq 100\), default: 5. See CRYSOL for details.
	--ns <N>	Only used with method=NCC. Number of calculated data points; range: \(51 \leq \text{ns} \leq 10001\), default: 101. See CRYSOLfor details.
	--smax <SM>	Only used with method=NCC. Maximum scattering angle, range: \(0.0 < s_{max} \leq 2.0\) \(\AA^{-1}\), default: 0.5 \(\AA^{-1}\). See CRYSOL for details.
	--beads <N>	Only used when selection=REGRID. Approximate number of beads for REGRID models; default: 2000
-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

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

CIFSUP Input Files

CIFSUP requires two atomic coordinate files as input, a template structure and a target structure for alignment/superposition. Both may be either in .pdb or .cif format.

CIFSUP Output Files

CIFSUP creates a single output file for the superimposed target structure. By default the transformed coordinates are written in .pdb format to stdout, or an output file path my be specified.

Examples

CIFSUP as replacement of SUPCOMB

Use CIFSUP to align a dummy atom model on a crystal structure, using the options to select the method that corresponds to slow mode in SUPCOMB and writing the output in .pdb format:

$ cifsup --method=nsd 6lyz.pdb ly01-1.pdb -o ly0r.pdb

As above, but equivalent to fast mode:

$ cifsup --method=nsd --selection=regrid 6lyz.pdb ly01-1.pdb -o ly0r.pdb

CIFSUP as replacement of SUPALM

Use CIFSUP to align a dummy atom model on a crystal structure, using the options to select the method that corresponds to slow mode in SUPALM and writing the output in .pdb format:

$ cifsup --method=ncc 6lyz.pdb ly01-1.pdb -o ly0r.pdb

CIFSUP as replacement of SUPPDB

As above, but use –method=rmsd. Note that this requires a one-to-one correspondence of ATOMs. This is generally not the case for dummy atom or dummy residue models.

Running CIFSUP Multiple Times

To superimpose 10 structures onto a single template, on linux, in bash syntax:

$ for i in `seq 1 10` ; do CIFSUP template.pdb file-$i.pdb; done

If one has unnumbered files to superimpose, on linux, in bash syntax:

$ for file in  "a.pdb b.pdb c.pdb d.pdb" ; do CIFSUP template.pdb $file; done

where template.pdb is the reference/template structure. Note that when one has a large collection of structures for superposition, the program DAMAVER is optimised for a fast superposition of multiple structures, automatically choosing the most representative structure.