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A brief description of the job
Cuboid or Spherical
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
Pixels per Micron
The resolution of the grid used to calculate dose in voxels/µm. Defaults to 0.5.
The method for calculating the absorption and attenuation coefficients. Average uses average atomic crystal compositions
based on a PDB survey. RADDOSE explicitly calculates the coefficients using the crystal parameters.
Unit cell dimensions a, b, c in Å. The unit cell angles alpha, beta, gamma in degrees. Default 90 degrees.
Number of Monomers
Number of monomers, n, in the unit cell. (N.B. NOT the asymmetric unit).
Number of Residues
Number of amino acid residues in a single chain. The number and types of atoms are calculated assuming an average amino acid content defined as amino acid = 5 C + 1.35 N + 1.5 O + 8H. Sulfur atoms should be added explicity using Protein Heavy Atoms.
Number of RNA
Number of RNA nucleotides in a monomer. The number and types of atoms are calculated assuming an average nucleotide content defined as mean nucleotide = 11.25H + 9.5C + 3.75N + 7O + 1P. If a more accurate estimate is required individual atoms may be entered explicitly using Protein Heavy Atoms.
Number of DNA
Number of DNA deoxynucleotides in a monomer. The number and types of atoms are calculated assuming an average deoxynucleotide content defined as mean Nucleotide = 11.75H + 9.75C + 4N + 6O + 1P. If a more accurate estimate is required individual atoms may be entered explicitly using Protein Heavy Atoms.
Protein Heavy Atoms
Define atoms to add to the protein part of the scattering. 'S 10 Se 2' would add ten sulfur and 2 selenium atoms per monomer.
Solvent Heavy Atom Concentration
Define the concentration of elements (not including water) in the solvent in millimoles per litre. 'Na 1000 Cl 1000' would add 1 M sodium chloride. Do not use this to define oxygen and lighter elements (i.e. do not declare PEG, but ammonium sulfate).
The fraction of the unit cell that is occupied by solvent. If not given explicity, this value is estimated using 1.35 g/ml for protein, 2.0 g/ml for RNA and DNA.
Either Gaussian or TopHat. If it is Gaussian, you must specify FWHM for the beam.
Full Width at Half Maximum*
The vertical and horizontal FWHM of the beam in µm.
Total beam flux in photons/sec of the collimated beam. Scientific (e.g 1e12) notation is acceptable.
Energy of the beam in keV.
The vertical and horizontal size of the collimated beam in µm as defined by the slits. For an uncollimated Gaussian beam this should be set to ~3xFWHM. Required for TopHat beam type.
Angular range of wedge (in degrees), relative to the starting position of crystal.
Total exposure time for the wedge in seconds.
Size of the angular steps (in degrees) to be taken during simulation. Default 2 degrees.
Offset of centre of crystal from the start position in µm. This is the translation vector applied to the crystal, not to the beam.
Translation of the crystal during data collection in µm/degree.
Rotation Axis Offset
Any offset in x (normally vertical) between the rotation axis of the crystal and the beam axis in µm.
Developed by the Garman Lab, University of Oxford.
RADDOSE-3D: time- and space-resolved modelling of dose in macromolecular crystallographyZeldin, Gerstel, Garman. (2013). J. Appl. Cryst. 46, 1225–1230
We also support the old RADDOSE version 2 online interface
Contact us on elspeth.garman AT bioch.ox.ac.uk