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BODIES manual

bodies

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© ATSAS Team, 2000-2022

Table of Contents

Manual

The following sections shortly describe how to run Bodies from the command-line, detail the dialog mode as well as the required input and output files.

If you use results from Bodies in your own publication, please cite:

P.V. Konarev, V.V. Volkov, A. V. Sokolova, M.H.J Koch and D. I. Svergun (2003). PRIMUS: a Windows PC-based system for small-angle scattering analysis J Appl Cryst. 36, 1277-1282.

Introduction

BODIES is a program that evaluates the theoretical scattering from geometrical bodies. In addition, it is possible to fit this scattering to experimental curves or to create dummy-atom models of the body in question, as well as generate search volumes, possibly pre-populated, suitable for the use with ab-initio modelling applications like DAMMIN and MONSA.

Input is therefore either experimental data or the dimensions of the body.

The currently supported body types are:

  1. ellipsoid (semiaxes a,b,c)
  2. rotation-ellipsoid (semiaxes, a,c)
  3. cylinder (radius r, height h)
  4. elliptic-cylinder (radii semiaxes a,c, height h)
  5. hollow-cylinder (outer radius ro, inner radius ri, height h)
  6. parallelepiped (sides a,b,c)
  7. hollow-sphere (outer radius ro, inner radius ri)
  8. dumbbell (radius of the first ball, r1, radius of the second ball, r2 and their center-to-center distance d)
  9. liposome (parameters a through f)
  10. membrane protein (rmemb, rtail, rhead, delta, zcorona)

Running bodies

Usage:

$ bodies [OPTIONS] [EXPDATA]

OPTIONS known by BODIES are described in next section, the optional argument 'EXPDATA' in the section on input files.

If EXPDATA is omitted, the interactive configuration is initiated. If no options are provided, default values are used.

Command-Line Arguments and Options

When running BODIES from the command-line only the default mode, fitting, is possible. The remaining modes can be accessed in the interactive configuration.

ArgumentDescription
EXPDATA Experimental data in any of the supported file formats.

BODIES accepts the following command line options:

Short OptionLong OptionDescription
-p --prefix=<PREFIX> The prefix to prepend to output filenames. May include absolute or relative paths, all directory components must exist. Default is the basename of EXPDATA.
--body=<BODY> The type of the geometrical body to fit to the experimental data. If this option is not specified, the fit of all the geometrical bodies will be calculated.
--rg=<X> The expected Rg, by default this is estimated from the data.
--i0=<X> The expected I0, by default this is estimated from the data.
--volume=<X> The expected volume, by default this is estimated from the data.
--first=<N> The first point of the Guinier range, by default this is taken to be 1.
--last=<N> The last point of the Guinier fit range. The default is 4 Shannon channels.
--seed=<N> Allows to specify a random seed. Particularly useful to recalculate previous runs.
-q --quiet Suppress screen output, but still write a .log-file. By default, all runtime information is printed to both, screen and .log file.
-v --version Print version information and exit.
-h --help Print a summary of arguments and options and exit.

Interactive Configuration

Interactively, BODIES may be run in three different modes:

  • fit - fit a geometrical body to experimental data
  • predict - predict the scattering pattern of a geometrical body
  • dam - generate a Dummy Atom Model of a geometrical body
  • search-volume - generate a search volume suitable for use with ab initio modelling programs

Supported body types are listed above.

If started without arguments and options, the mode may be selected, further interactive configuration options depend on the selected mode.

Screen TextDefaultDescription
Operation mode? Select one of: (f) fit, (p) predict, (d) dam, (v) search volume fit Select operation mode, fit, predict, dam or search-volume.

Fit mode

Screen TextDefaultDescription
Experimental data file name? N/A Same as EXPDATA-argument.
Type of Body? 1, ellipsoid The type of the geometrical body to fit to the experimental data.
Expected Radius of Gyration of experimental data? variable Same as rg-option.
Expected Intensity at s=0.0 of experimental data? variable Same as i0-option.
Expected volume at s=0.0 of experimental data? variable Same as volume-option.
First point of fit range? 1 Same as first-option.
Last point of fit range? variable Same as last-option.
Initial random seed? variable Same as seed-option.
Output prefix? N/A Same as p-option.

Predict mode

Screen TextDefaultDescription
Type of Body? 1, ellipsoid The type of the geometrical body to predict scattering pattern of.
Value of parameter ...? N/A The dimensions of the selected geometrical body.
Value of parameter scale? N/A Intensity scaling factor, usually 1.0 in predict mode.
Minimum s [Angstrom^-1]? 0 The minimum scattering vector in reverse angstroms.
Maximum s [Angstrom^-1]? 0.5 The maximum scattering vector in reverse angstroms.
Number of points in s-range? 201 The number of points in the theoretical curve.
Output filename? N/A Output file name. Output format depends on extension, supported are PDB and mmCIF format.

DAM mode

Screen TextDefaultDescription
Type of Body? 1, ellipsoid The type of the geometrical body to create Dummy Atom Model of.
Value of parameter ...? N/A The dimensions of the selected geometrical body.
Value of parameter scale? N/A Unused; set 1.
Dummy atom radius [A]? 3.00 The radius of the dummy atom to be used in the model.
DAM output file name? N/A Output file name. Output format depends on extension, supported are PDB and mmCIF format.

Search Volume mode

Screen TextDefaultDescription
Search volume shape? 1, ellipsoid The outer shape of the geometrical body to use as a search volume.
Value of parameter ...? N/A The dimensions of the selected geometrical body.
Value of parameter scale? N/A Unused; set 1.
Shall the search volume include a start model? Y If yes, the shape and shape parameters of the start model will be queried.
Search volume symmetry? P1 The overall symmetry of the search volume. Possible options depend on the included start model.
Number of phases in the search volume? 1 The number of phases that are allowed in this start model, usually between 1 and 4.
Number of dummy atoms? 2000 The approximate number of total dummy atoms in this start model.
DAM output file name? N/A Output file name. Output format depends on extension, supported are PDB and mmCIF format.

Runtime Output

On runtime in fit-mode, the following lines will be generated for each geometrical body.

  Initial random seed .................................... : 0
  Input file name ........................................ : adh_136.dat
  First point of fit region .............................. : 1
  Last point of fit region ............................... : 447
  Expected Radius of Gyration ............................ : 3.050
  Expected I0 ............................................ : 75.00
  Expected Volume ........................................ : 188.0

A statement of parameters used by BODIES to perform the calculation (see above)

  Body type .............................................. : ellipsoid
  Parameter 'a' .......................................... : 2.745
  Parameter 'b' .......................................... : 4.595
  Parameter 'c' .......................................... : 4.596

Type of geometrical body, and its dimensions.

  Parameter 'scale' ...................................... : 1.294e-30

The scaling factor used to scale the theoretical intensities to the experimental data.

 
  Fit Radius of Gyration ................................. : 3.199
  Fit I0 ................................................. : 76.54
  Fit Volume ............................................. : 229.1
  Goodness of Fit (Chi^2) ................................ : 13.16

The evaluated Rg, I(0), Volume and Chi for the submitted experimental data.

bodies Input Files

BODIES fits the scattering of a geometrical body to an experimental curve. See EXPDATA-argument. In predict/dam mode only the dimensions of the body needs to be supplied.

bodies Output Files

Depending on the selected mode, BODIES may create one or more output files. Existing files will be overwritten without further notice.

Fit mode

For each body type, three output files are created:

ExtensionDescription
.log A copy of the screen output
.fir Fit of the simulated scattering curve versus the experimental data. Columns in the output file are: 's', 'Iexp', 'Errexp' and 'Isim'.
.cif A DAM representation of the body.

Predict mode

ExtensionDescription
.dat The theoretical scattering from a geometrical body created in predict mode is written to a .dat file, with the following columns: 's','Iexp'. First line contains the name and dimensions of the geometrical body.

DAM mode

ExtensionDescription
.pdb/.cif The dummy atom model is written in either PDB or mmCIF file format, depending on the extension provided. The header contains the name and dimensions of the geometrical body.

Search Volume mode

ExtensionDescription
.pdb/.cif The search volume is written in either PDB or mmCIF file format, depending on the extension provided. The header contains the name and dimensions of the geometrical body.

  Last modified: February 25, 2015
© BioSAXS group 2015