Raddose - calculate the dose absorbed by a crystal

Note: This manual interface currently has very limited capabilities. For more extensive functionality, such as:

Extraction of crystal composition from PDB files
The use of irregular polyhedron-shaped crystals
Experimental beam profiles
SAXS or small molecule experiments
The inclusion of 3D photoelectron and fluorescent escape models

please instead refer to either the latest jar file release or the source code on GitHub.

Job title

E-mail address (optional)

Job definition (Input file)

The full RADDOSE-3D syntax is explained in the RADDOSE-3D User Guide (PDF).

##############################################################################
#                                 Crystal Block                              #
##############################################################################

Crystal

Type Cuboid
       # Crystal shape can be Cuboid or Spherical

Dimensions 100 100 100
       # Dimensions of the crystal in X,Y,Z in µm.
       # Z is the beam axis, Y the rotation axis and
       # X completes the right handed set
       #   (vertical if starting face-on).

PixelsPerMicron 0.5
       # This defines the coarseness of the simulation
       # (i.e. how many voxels the crystal is divided into.)
       # Preferably set as high as possible, however for a higher
       # value the simulation will take longer to complete.
       # Recommended to try increasing between 0.5 and 5 and ensure
       # the reported dose value converges as PixelsPerMicron increases.
       # As a rule of thumb, this needs to be at least 10x the beam
       # FWHM for a Gaussian beam.
       # e.g. 20µm FWHM beam -> 2µm voxels -> 0.5 voxels/µm

# NOTE: Use AngleP/AngleL if your crystal is not face-on to the beam.
# See RD3D user guide for more details

# Also need to specify the crystal composition below (Example case for insulin given):
AbsCoefCalc  RD3D
       # Absorption Coefficients calculated
       # using RADDOSE-3D (Zeldin et al. 2013).

UnitCell   78.02  78.02  78.02
       # unit cell size: a, b, c with alpha, beta and gamma angles default to 90°

NumMonomers  24
       # number of monomers in unit cell

NumResidues  51
       # number of residues per monomer

ProteinHeavyAtoms Zn 0.333 S 6
       # heavy atoms added to protein part of the
       # monomer, i.e. S, coordinated metals, Se in Se-Met

SolventHeavyConc P 425
       # concentration of elements in the solvent
       # in mmol/l. Oxygen and lighter elements
       # should not be specified

SolventFraction 0.64
       # fraction of the unit cell occupied by solvent

##############################################################################
#                                  Beam Block                                #
##############################################################################

Beam

Type Gaussian
       # beam profile can be Gaussian or TopHat
Flux 2e12
       # in photons per second (2e12 = 2 * 10^12)
FWHM 20 70
       # in µm, horizontal by vertical for a Gaussian beam
Energy 12.1
       # photon energy in keV

Collimation Rectangular 100 100
       # Horizontal/Vertical collimation of the beam
       # For 'uncollimated' Gaussians, 3xFWHM recommended

##############################################################################
#                                  Wedge Block                               #
##############################################################################

Wedge 0 90
       # Start and End rotational angle of the crystal with Start < End

ExposureTime 50
       # Total time for entire angular range

# AngularResolution 2
       # Only change from the defaults when using very
       # small wedges, e.g 5°.

# NOTE: To define more complex geometries (helical, de-centred, or offset),
# see the StartOffset, TranslatePerDegree, and RotAxBeamOffset keywords
# in the User Guide

RADDOSE-3D

Calculate the dose absorbed by a crystal

Job title

E-mail address (optional)

Job definition (Input file)