CRYSON manual

Written by D.Svergun, M.Malfois, M. Petoukhov and A. Shkumatov.
Post all your questions about CRYSON to the ATSAS Forum.

© ATSAS Team, 1998-2009

Table of Contents

• Manual
  • Introduction
  • Running cryson
    • Command-Line Arguments and Options Unique to cryson
    • Interactive Configuration Different from crysol
    • Runtime Output
  • Input Files Unique to cryson
  • cryson Ouput Files
• Examples
  • Calculating scattering intensity without fitting
  • Processing PDB files with fitting

Manual

CRYSON is a reimplementation of CRYSOL, adopted to work with Small-Angle Neutron Scattering (SANS) data. The following shortly describes the main differences between CRYSON and CRYSOL. For detailed description, see CRYSOL manual.

If you use results from CRYSON in your own publication, please cite:
Svergun D.I., Richard S., Koch M.H.J., Sayers Z., Kuprin S. & Zaccai G. (1998) Protein hydration in solution: experimental observation by X-ray and neutron scattering. Proc. Natl. Acad. Sci. USA 95, 2267-2272.

Introduction

CRYSON is a program for evaluating the solution scattering from macromolecules with known atomic structure and fitting it to experimental scattering curves from Small-Angle Neutron Scattering (SANS). As an input one can use a PDB file with an X-ray or NMR structure of a protein or a protein-DNA(RNA) complex.

The program uses multipole expansion of the scattering amplitudes to calculate the spherically averaged scattering pattern and takes into account the hydration shell, D₂O fraction as well as perdeuteration fraction for individual molecule. Given SANS experimental data, CRYSON can fit the theoretical scattering curve by minimizing the discrepancy (chi-square value).

CRYSON smears the theoretical curves using the resolution function to take the instrumental distortion into account.

Running cryson

Usage:

$> cryson [PDBFILE] [EXPDATA] [ILLRES] [OPTIONS] 

CRYSON accepts absolute as well as relative path to PDBFILE, EXPDATA or ILLRES.

If no input files are given, the configuration is done in interactive mode.

Generally, CRYSON uses same command line arguments and interactive configuration as CRYSOL. Here the main differences are outlined:

Command-Line Arguments and Options Unique to cryson

Interactive Configuration Different from crysol

If no input files are given, interactive mode with same questions as in CRYSOL is started. Differences include:

Runtime Output

See CRYSOL manual

Input Files Unique to cryson

CRYSON uses both PDB file and SANS experimental data as input. An additional file (ill.res) required for smearing the theoretical curve has the following format (the numbers describe a setting at RISOE SANS instrument):

cryson Output Files

See CRYSOL manual.

Examples

All examples use tr.pdb, trd2o.dat and ill.res. They are included in the documentation directory of the installation package.

Calculating scattering intensity without fitting

$ cryson tr.pdb /lm 20 /D2O 0.5 

Use CRYSON to calculate the scattering intensity from the PDB file. Maximum order of harmonics = 20 and D₂O fraction = 0.5

Processing PDB files with fitting

$ cryson "tr*.pdb" trd2o.dat /res ill.res 

Use CRYSON to calculate the scattering intensity from all PDB files, starting with 'tr' and ending with '.pdb'. Calculated theoretical curve is smeared using parameters in resolution file ill.res and fitted to experimental data trd2o.dat