Below you will find short instructions how to use CRYSON by Dmitri Svergun. Instructions for CRYSOL are here. The information below corresponds to the file /hosts/lass2/d1/lss/svergun/Crysol/cryson.ins.

At the ILL, use the command cryson.

               C R Y S O N

This is a short information on how to use beta-release of Cryson,
which is a version of CRYSOL for neutron scattering.


IBM-PC version:

Hardware requirements: IBM-PC compatible (486 and higher)
with 2 Mb RAM and VGA or SVGA graphic card.

Operating systems:  DOS/Win3.1/Win95/WinNT.
                    The program works in a full-screen DOS window.
                    Under Win3.1 one should call a full-screen DOS prompt.
                    Under Win95, one should invoke a Real DOS mode.
                    Under WinNT, one should reboot in DOS mode or
                                 switch off the EMS usage in the properties
                                 of the DOS window.

The programs CRYSON.EXE requires the same DOS-extender
as Crysol, namely, DOSXMSF.EXE (Phar Lap), and also
the font file COURB.FON to be in the current directory
or in the root directory C:\.

SGI version was compiled under IRIX 6.4, Fortran compiler 7.4



For the general information see file  Crysol.ins in the Crysol
distribution file. The differences between Crysol and Cryson are:

(i) instead of the solvent density in e/A**3 required by
    Crysol, Cryson prompts for the D2O content in the solvent.
    The solvent density SD is then evaluated as

   SD =  ROH2O*(1.- Y) + ROD2O*Y

   where Y is the D2O concentration (ranges from 0 to 1)
   ROH2O = 0.562 is the H2O scattering length density (10**10 cm**-2)
   ROD2O = 6.404 is the D2O scattering length density (10**10 cm**-2)


   The user may change the solvent density value manually.

(ii) if Y 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 in proportion Y, except for the main-chain NH
   groups, for which the probability is Y*(1-DNEXCH). Default value
   DNEXCH = 0.1 is generally accepted. The scattering length density B of
   any atom/atomic group at the D2O concentration Y is evaluated as

      B(Y) = B(0) + EXCH * Y * ( BD - BH ) * Afac

      where B(0) is the scattering length in H2O,
      BH   = -0.3742  is the scattering length of hydroden  (10-12 cm),
      BD   =  0.6671  is the scattering length of deuterium (10-12 cm),
      EXCH is the number of exchangeable hydrogens in the group,
      Afac = 1-DNEXCH for the main chain NH groups, otherwise 1.

The scattering lengths and the number of exchangeable hydrogens are taken
as below:

   Scattering lengths at 0%D2O (in 10-12 cm)

      C     CH     CH2   CH3    N    NH    NH2   NH3
     .6651,.2909,-.083,-.458, .940,.5658,.1916,-.1826,
      O      OH    S     SH     P     FE   CU    CA    MG   MN    ZN
     .5804,.2062,.2847,-.090,.5170, .95 , .76 , .47 , .52,-.39 , .57,
      N(Histidine)
      .7529

  Number of exchangeable protons

      C   CH  CH2  CH3  N   NH  NH2  NH3  O  OH
      0.,  0., 0.,  0., 0.,  1., 2.,  3., 0., 1.,
      S    SH   P    FE   CU   CA   MG   MN   ZN N(Histidine)
      0.,   1., 0.,   0.,  0.,  0.,  0.,  0.,  0., 0.5



- by default, Cryson searches for the contrast in the hydration shell
in the range 0 < DroShell < 0.2*ABS(SD) [10**10 cm**-2]. For proteins in
H2O and D2O, positive DroShell means more dense solvent in the shell,
as seen from the figure below. One can, however, also imagine the
situation when the positive DroShell would mean less dense solvent
in the shell. The user can perform the search both in positive and
negative ranges of DroShell, if necessary.


                                      ---   Hydration shell ----
                                                               |
        IN WATER                      --- Solvent (D2O)  ----  |
                                                     |         |
                                                    Dro       DroShell
                                                     |         |
                                                     |         |
--------  Protein --------            --------  Protein --------
               |         |
              Dro        |
               |        DroShell              IN HEAVY WATER
--- Solvent (H2O)  ----  |
                         |
---   Hydration shell ----



The units for the contrasts and the scattering length densities are
always 10**10 cm-2, the intensities in the *.int file are in cm**2.


(iii)  CRYSON also fits a flat background. The value to be
subtracted/added is searched for in units of an average of the ten
last experimental points.

(iv) CRYSON smears the theoretical curves using the resolution function
introduced by J.Skov Pedersen et al. (1990), J.Appl. Cryst., 23, 321
Several subroutines for data smearing are provided by J.Skov Pedersen
and modifies for the use in CRYSON. The program prompts for a resolution
file which should have the following format (the numbers describe a setting
at RISOE SANS instrument):

   0.8  , Effective collimation slit diameter in cm
   0.35 , Effective sample diameter in cm
  300.  , Collimation distance in cm
  105.  , Sample-detector distance in cm
   3.   , Lambda in Angstroems
  0.18  , Delta(Lambda)/Lambda
  1.1   , Pixel size in cm
 0.0000 , Averaging error (accounted for in Pixel size)


If the file is corrupted or does not exist, no smearing is performed.
An example of the resolution file is provided (file ill.res).