Biological
Small Angle Scattering

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CRYSON manual

cryson

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

Manual
Examples

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] [RESFILE] [OPTIONS]

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

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

Argument	Description
`*.res`	Resolution file name. It can be used as a third argument in order to smear the theoretical curve. If '`*.res`' file is corrupted or not provided, no smearing is performed.

Option	Default	Description
`-D2O`	1.0	Fraction of D₂O in solution.
`-per`	0.0	Perdeuteration of all chains.
`-res`	N/A	Resolution file name.

Interactive Configuration Different from crysol

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

Screen Text Default Description

Enter perdeuteration for individual chain? 0.0 CRYSON checks how many chains (molecules different by chain identifier) are in the PDB file. For each chain found, it is possible to provide fraction of perdeuteration.

D2O fraction in solvent?

1.0

D₂O content in the solution (ranges from 0 to 1). It is used to evaluate solvent density SD:

SD = ROH₂O*(1.-Y) + ROD₂O*Y

where Y is D₂O content

ROH₂O = -0.562 is the H₂O scattering length density (10¹⁰ cm^-2)

ROD₂O = 6.404 is the D₂O scattering length density (10¹⁰ cm^-2)

Fraction of nonexchanged NH peptide? 0.1 If D₂O content is not zero, CRYSON prompts for the fraction of nonexchanged NH peptide (DNEXCH). It is assumed that all exchangeable hydrogens (which belong to NH, NH₂, NH₃, OH and SH groups) are replaced by deuteriums proportional to D₂O content, except for the main-chain NH groups, for which the probability is D₂O*(1-DNEXCH). Default value DNEXCH = 0.1 is generally accepted.

Runtime Output

See CRYSOL manual

Input Files Unique to cryson

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

Row	Value	Description
1	`0.8`	Effective collimation slit diameter in cm.
2	`0.35`	Effective sample diameter in cm.
3	`300`	Collimation distance in cm.
4	`105`	Sample-detector distance in cm.
5	`3`	λ in Å
6	`0.18`	δ(λ)/λ
7	`1.1`	Pixel size in cm.
8	`0.0000`	Averaging error (accounted for in Pixel size).

Diagram of a SANS instrument showing the various distances needed for the ill.res file

cryson Output Files

See CRYSOL manual.

Pecularity using cryson with eh option

If -eh option is used, the program reads the position of H/D atom from the PDB file, whereby the H/D atom is considered exchangable if the position 73 of the PDB file contains "Y".

Examples

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

Processing PDB files with fitting in interactive mode

Use CRYSON to calculate the scattering intensity from tr.pdb. Calculated theoretical curve is smeared using parameters in resolution file ill.res and fitted to experimental data trd2o.dat


  ***  ------------------------------------------------  ***
  ***    C R Y S O N  W95/98/NT/UNIX version 2.7         ***
  ***    Please reference: D.Svergun et al. (1998)       ***
  ***    Proc. Natl. Acad. Sci. USA, 95, 2267-2272.      ***
  ***    Version (LMAX=50) for small and wide angles     ***
  ***        Last revised  ---  13/03/2015               ***
  ***    Copyright (c) ATSAS Team                        ***
  ***    EMBL, Hamburg Outstation, 1998 - 2015           ***
  ***  ------------------------------------------------  ***

  ------------------------------------------------
                  Program options :
  0 - evaluate scattering amplitudes and envelope
  1 - evaluate only envelope and Flms
  2 - read CRYSON information from a .sav file
   Type cryson --help for batch mode use
  ------------------------------------------------

 Enter your option ...................... <            0 >:
 Brookhaven file name ................... <         .pdb >: tr
  ------------------------------------------------
          Following file names will be used:
 tr00.log -- CRYSON log-file          (ASCII)
 tr00.sav -- save CRYSON information  (binary)
 tr00.flm --   multipole coefficients (ASCII)
 tr00.int --   scattering intensities (ASCII)
 tr00.fit -- fit to experimental data (ASCII)
 tr00.alm --   net partial amplitudes (binary)
  ------------------------------------------------
  Maximum order of  harmonics ........... <           15 >:
  Order of Fibonacci grid ............... <           17 >:
  ----------  Reciprocal space grid  -------------
   ( in s = 4*pi*sin(theta)/lambda [1/angstrom] )
 Maximum s value ........................ <       0.5000 >:
  Number of points ...................... <           51 >:
  Enter perdeuteration for individual chains
  Typing negative number indicates that the
  rest of the molecule is protonated
 Perdeuteration, chain [A] (0 y 1) ...... <        0.000 >:
 D2O fraction in solvent (0 y 1) ........ <        1.000 >:
 Account for explicit hydrogens? [ Y / N ] <           No >:
 Fraction of nonexchanged NH peptide .... <       0.1000 >:
 Read atoms and evaluate geometrical center ...
  Number of atoms read .................................. : 4788
 Percent processed      10  20  30  40  50  60  70  80  90 100
 Processing atoms   :>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 Processing envelope:>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 Coefficients   saved to file tr00.flm
 CRYSON data    saved to file tr00.sav
 --- Structural parameters (sizes in angstroms) ---
 Atomic     Rg   :  27.80       Envelope   Rg      :  27.47
 Shape      Rg   :  27.34       Envelope  volume   : 0.1040E+06
 Shell    volume : 0.3268E+05   Envelope  surface  :  9844.
 Shell      Rg   :  34.20       Envelope  radius   :  51.26
 Shell    width  :  3.000       Envelope  diameter :  101.0
 Solvent density [10**10 cm**-2] ........ <        6.404 >:
 Molecular weight: 0.6812E+05   Dry volume         : 0.8256E+05
 Displaced volume: 0.8436E+05   Average atomic rad.:  1.614
 Solvent density :  6.404       Particle contrast  : -3.301
 Number of residuals :             632
  Fit the experimental curve [ Y / N ] .. <          Yes >:
 File name (experimental data) .......... <         .dat >: trd2o
  Number of data points read ............................ : 122
  Maximum angle in the data file ........................ : 0.5223
 Angular units in the input file:
 4*pi*sin(theta)/lambda [1/angstrom] (1)
 4*pi*sin(theta)/lambda [1/nm]       (2)
 2 *  sin(theta)/lambda [1/angstrom] (3)
 2 *  sin(theta)/lambda [1/nm]  (4) ..... <            1 >:
  Angular units multiplied by ........................... : 1.000
  Resolution file, CR for none .......... <         .res >: ill
  Warning: current Smax is to small to obtain
  the smeared curve in the experimental range.
  Smax for the entire range would be .................... : 0.5855
  The fitting range will be reduced.
  Number of experimental points taken ................... : 99
 Number of experimental points used ..................... : 99
  ------  Fitting the experimental data ...    ---
 Plot the fit to experimental data [ Y /N ] .................................... <          Yes >: n
 tr.pdb    Dro: 0.521 Bck:0.50  RgE:27.43  RgT:25.38  Vol: 78035.  Chi^2: 8.475
 Another set of parameters [ Y / N ] .... <           No >:
 Rg from the slope of net intensity ..................... : 25.74
 Data fit       saved to file tr00.fit
 Intensities    saved to file tr00.int
 Net amplitudes saved to file tr00.alm

Processing PDB files with multiple chains and perdeuteration

Use CRYSON to calculate the scattering intensity from Arp23_Active_WC_Actin.pdb in which the second chain is 50% perdeuterated and the third chain is 100% perdeuterated.


  ***  ------------------------------------------------  ***
  ***    C R Y S O N  W95/98/NT/UNIX version 2.7         ***
  ***    Please reference: D.Svergun et al. (1998)       ***
  ***    Proc. Natl. Acad. Sci. USA, 95, 2267-2272.      ***
  ***    Version (LMAX=50) for small and wide angles     ***
  ***        Last revised  ---  13/03/2015               ***
  ***    Copyright (c) ATSAS Team                        ***
  ***    EMBL, Hamburg Outstation, 1998 - 2015           ***
  ***  ------------------------------------------------  ***

  ------------------------------------------------
                  Program options :
  0 - evaluate scattering amplitudes and envelope
  1 - evaluate only envelope and Flms
  2 - read CRYSON information from a .sav file
   Type cryson --help for batch mode use
  ------------------------------------------------

 Enter your option ...................... <            0 >:
 Brookhaven file name ................... <         .pdb >: Arp23_Active_WC_Actin.pdb
  ------------------------------------------------
          Following file names will be used:
 Arp23_Active_WC_Actin00.log -- CRYSON log-file          (ASCII)
 Arp23_Active_WC_Actin00.sav -- save CRYSON information  (binary)
 Arp23_Active_WC_Actin00.flm --   multipole coefficients (ASCII)
 Arp23_Active_WC_Actin00.int --   scattering intensities (ASCII)
 Arp23_Active_WC_Actin00.fit -- fit to experimental data (ASCII)
 Arp23_Active_WC_Actin00.alm --   net partial amplitudes (binary)
  ------------------------------------------------
  Maximum order of  harmonics ........... <           15 >:
  Order of Fibonacci grid ............... <           17 >:
  ----------  Reciprocal space grid  -------------
   ( in s = 4*pi*sin(theta)/lambda [1/angstrom] )
 Maximum s value ........................ <       0.5000 >:
  Number of points ...................... <           51 >:
  Enter perdeuteration for individual chains
  Typing negative number indicates that the
  rest of the molecule is protonated
 Perdeuteration, chain [A] (0 y 1) ...... <        0.000 >:
 Perdeuteration, chain [B] (0 y 1) ...... <        0.000 >: 0.5
 Perdeuteration, chain [C] (0 y 1) ...... <        0.000 >: 1.0
 Perdeuteration, chain [D] (0 y 1) ...... <        0.000 >: -1.0
 D2O fraction in solvent (0 y 1) ........ <        1.000 >:
 Fraction of nonexchanged NH peptide .... <       0.1000 >:
 Read atoms and evaluate geometrical center ...
  Number of atoms read .................................. : 17970
  Number of skipped rotamers ............................ : 83
 Percent processed      10  20  30  40  50  60  70  80  90 100
 Processing atoms   :>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 Processing envelope:>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 Coefficients   saved to file Arp23_Active_WC_Actin00.flm
 CRYSON data    saved to file Arp23_Active_WC_Actin00.sav
 --- Structural parameters (sizes in angstroms) ---
 Atomic     Rg   :  46.28       Envelope   Rg      :  48.50
 Shape      Rg   :  49.13       Envelope  volume   : 0.4357E+06
 Shell    volume : 0.7497E+05   Envelope  surface  : 0.2351E+05
 Shell      Rg   :  59.18       Envelope  radius   :  91.83
 Shell    width  :  3.000       Envelope  diameter :  169.9
 Solvent density [10**10 cm**-2] ........ <        6.404 >:
                                                             
 Molecular weight: 0.2569E+06   Dry volume         : 0.3114E+06 
 Displaced volume: 0.3210E+06   Average atomic rad.:  1.622
 Solvent density :  6.404       Particle contrast  : -2.328
 Number of residuals :            2263
 Fit the experimental curve [ Y / N ] .. <          Yes >: n
 Contrast of the solvation shell ........ <       0.6404 >:
 Average atomic radius .................. <        1.622 >:
 Excluded Volume ........................ <  3.2101E+005 >:
 Average atomic volume .................................. : 17.86
 Radius of gyration from atomic structure                                                                                
 Rg ( Atoms - Excluded Volume + Shell ) ................. : 53.34
 Rg from the slope of net intensity ..................... : 51.02
 Intensities    saved to file Arp23_Active_WC_Actin00.int
 Net amplitudes saved to file Arp23_Active_WC_Actin00.alm

CRYSON manual

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