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Crystal

Crystal Type

Cuboid or Spherical

Crystal Dimensions*

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.

Absorption Coefficient

The method for calculating the absorption and attenuation coefficients.RADDOSE explicitly calculates the coefficients using the crystal parameters. PDB Downloads the PDB file from the Protein Data Bank

Unit Cell

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).

Solvent Fraction

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.

Beam

Beam Type*

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.

Flux*

Total beam flux in photons/sec of the collimated beam. Scientific (e.g 1e12) notation is acceptable.

Energy*

Energy of the beam in keV.

Rectangular Collimation

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.

Wedge

Wedge*

Angular range of wedge (in degrees), relative to the starting position of crystal.

Exposure Time*

Total exposure time for the wedge in seconds.

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