cryson
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.
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, D ~2~ O 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 D~2~O 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 thePDB file. For each chain found, it is possible to provide fraction of perdeuteration. |
| D2O fraction in solvent? | 1.0 | D~2~O content in the solution (ranges from 0 to 1). It is used to evaluate solvent density SD:SD = ROH ~2~ O(1.-Y) + ROD ~2~ OY where Y is D ~2~ O content ROH ~2~ O = -0.562 is the H ~2~ O scattering length density (10 ^10^ cm ^-2^ ) ROD ~2~ O = 6.404 is the D ~2~ O scattering length density (10 ^10^ cm ^-2^ ) |
| Fraction of nonexchanged NH peptide? | 0.1 | If D~2~O 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, NH~2~, NH~3~, OH and SH groups) are replaced by deuteriums proportional to D~2~O content, except for the main-chain NH groups, for which the probability is D~2~O*(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 | \lambdainÅ |
| 6 | 0.18 | \delta(\lambda)/\lambda |
| 7 | 1.1 | Pixel size in cm. |
| 8 | 0.0000 | Averaging error (accounted for in Pixel size). |
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 D ~2~ O 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