CRYSOL manual

Written by D.Svergun, C.Barberato, M.Malfios, V.Volkov, P.Konarev, M.Petoukhov, and A. Shkumatov.
Post all your questions about CRYSOL to the ATSAS Forum.

© ATSAS Team, 1995-2009

• Manual
  • Introduction
  • Running crysol
    • Command-Line Arguments and Options
    • Interactive Configuration
    • Runtime Output
  • crysol Input Files
  • crysol Ouput Files
• Examples
  • Calculating scattering intensity without fitting
  • Processing of PDB file with fitting
  • Processing multiple PDB files with fitting

Manual

The following sections shortly describe the method implemented in CRYSOL, how to run CRYSOL from the command-line on any of the supported platforms, describe the dialog mode as well as the required input and the produced output files.

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

Svergun D.I., Barberato C. & Koch M.H.J. (1995) J. Appl. Cryst. , 28, 768-773.

Introduction

CRYSOL is a program for evaluating the solution scattering from macromolecules with known atomic structure and fitting it to experimental scattering curves from Small-Angle X-ray Scattering (SAXS). 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. Given SAXS experimental data, CRYSOL can fit the theoretical scattering curve by minimizing the discrepancy (chi-square value).

Fitting is done by varying three parameters: (i) average displaced solvent volume per atomic group (ii) contrast of the hydration shell (iii) relative background

Running crysol

Usage:

$> crysol [PDBFILE] [EXPDATA] [OPTIONS] 

CRYSOL accepts absolute as well as relative path to PDBFILE and EXPDATA

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

If no options are provided, default values are used.

Command-Line Arguments and Options

It is possible to provide one or multiple arguments to CRYSOL. Regular expressions, e.g. *.pdb or exp*.dat are supported.

Interactive Configuration

If the optional arguments are omitted, settings available through command-line arguments and options may also be configured interactively as shown in the table below.

CRYSOL offers several options. They can be subdivided into two groups: with and without fitting. The table below shows a list of questions for fitting mode.

Runtime Output

On runtime, the following lines of output will be generated for each PDB file:

  ------------------------------------------------
          Following file names will be used:
 6lyz00.log -- CRYSOL log-file          (ASCII)
 6lyz00.sav -- save CRYSOL information  (binary)
 6lyz00.flm --   multipole coefficients (ASCII)
 6lyz00.int --   scattering intensities (ASCII)
 6lyz00.fit -- fit to experimental data (ASCII)
 6lyz00.alm --   net partial amplitudes (binary)
  ------------------------------------------------

Successive runs for the same PDB file will generate output files with increasing number, e.g. 6lyz01.log, 6lyz01.sav, etc. The size of the output file names is limited to 12 characters. If the PDB file name (without extension) is longer than 5 characters the output file names will be truncated, e.g.: output file names for the PDB file atw2rsta.pdb will be atw2rs00.log, atw2rs00.sav, etc. The program also truncates the string "pdb" at the begining of the PDB files.

 Number of atoms read .................................. : 1001 

Number of atoms read from PDB file.

 Number of discarded waters ............................ : 101 

Number of discarded water molecules.

 Center of the excess electron density:  0.446 -0.004  0.272 

Coordinates of the center of excess electron density.

 Electron   rg   :  13.99       Envelope   Rg      :  14.01
 Shape      Rg   :  13.97       Envelope  volume   : 0.1842E+05
 Shell    volume : 0.1158E+05   Envelope  surface  :  3232.
 Shell      Rg   :  18.89       Envelope  radius   :  25.49
 Shell    width  :  3.000       Envelope  diameter :  49.04
 Molecular weight: 0.1432E+05   Dry volume         : 0.1735E+05
 Displaced volume: 0.1741E+05   Average atomic rad.:  1.607 

Calculated structural parameters (sizes in angstroms)

 Number of residuals :   129 

Number of amino acid residues in PDBFILE

 Title:  02-Oct-2006       (lysB_014.da - 1.000 *Avrag05.dat) /  4.1300 

The first line of EXPDATA file

 Maximum angle in the data file ........................ : 4.861 

Maximum value of scattering vector in the data file

 Number of experimental points ......................... : 2048 

Total number of experimental points found

 Angular units multiplied by ........................... : 0.1000 

See un-option

 Number of points after regriding ...................... : 204 

Experimental curve is divided into bins. Number of bins depends on the number of experimental points. For each bin (point) scattering intensity and error is calculated. This allows to speed up fitting step.

 Number of experimental points used .................... : 204 

Number of experimental points used for fitting.

 6lyz.pdb  Dro:0.015  Ra:1.560  RGE:15.11  RGT:14.91  Vol: 17322.  Chi:1.311 

Results of fitting '6lyz.pdb' to experimental data:

Field	Description
Dro	Optimal contrast of hydration shell.
Ra	Optimal radius of atomic group.
RGE	Radius of gyration estimated from experimental curve.
RGT	Radius of gyration estimated from theoretical curve.
Vol	Optimal excluded volume.
Chi	Disrepancy between theoretical and experimental curves.

 Rg from the slope of net intensity ..................... : 14.94 

Radius of gyration calculated from the slope of net intensity

 Average electron density ............................... : 0.4714 

Calculated average of electron density

crysol Input Files

CRYSOL reads the atomic coordinates of the structure in Protein Data Bank format

Optionally an experimental curve can be supplied. See EXPDATA-argument.

crysol Output Files

Examples

All examples use 6lyz.pdb, lyz_014.dat and lyzexp.dat. They are included in the documentation directory of the installation package

Calculating scattering intensity without fitting

 $> crysol 6lyz.pdb /lm 18 

Use CRYSOL to calculate the scattering intensity from the PDB file. Maximum order of harmonics = 18

Processing of PDB file with fitting.

 $> crysol 6lyz.pdb *.dat /cs y  

Use CRYSOL to calculate the scattering intensity from the PDB file, fit to all available experimental data, use constant subtraction to improve fit.

Processing multiple PDB files with fitting.

 $> crysol 6lyz?.pdb lyzexp.dat /cs y  

Use CRYSOL to calculate the scattering intensities from PDB files: 6lyz1.pdb, 6lyz2.pdb, 6lyz3, etc and fit to all experimental data, use constant subtraction to improve fit.

 $> crysol all lyzexp.dat /sm 0.25 

Use CRYSOL to process all PDB files in current directory, calculate scattering intensity till 0.25 and fit to experimental data

For more examples, try

crysol -help