CIFSUP manual

Written by D. Franke
Post all your questions about CIFSUP to the ATSAS Forum.

© ATSAS Team, 2021-2022

Table of Contents

• 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 shortly describe the method implemented in CIFSUP, how to run CIFSUP from the command-line and describe the required input and the produced output files.

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 mmCIF format.

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

Command-Line Arguments and Options

CIFSUP requires the following command line arguments:

CIFSUP recognizes the following command-line options.

Runtime Output

CIFSUP does not have any runtime output. If the output file is undefined, the transformed coordinates will be written to a (new) file path created from the basename of the MOVABLE argument plus r.cif.

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 mmCIF format.

CIFSUP Output Files

CIFSUP creates a single output file for the superimposed target structure. By default the output filename is taken from the input MOVABLE structure but is appended with 'r', eg.

$ CIFSUP file1.pdb file2.pdb

yields file2r.cif as output. A different filename, and file format, can be specified with the --output option.

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.