Raddose - calculate the dose absorbed by a crystal

Job Details

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Crystal

Shape iThe geometric shape used to model the crystal. Cuboid (rectangular block), Spherical (defined by diameter), or Cylinder (circular cross-section with height along the rotation axis).

Dimensions (µm) — X, Y, Z

Z is the beam direction, Y the rotation axis, X completes the right-handed set.

Diameter (µm)

Dimensions (µm) — Diameter, Height

Diameter of the circular cross-section; Height along the rotation axis.

Diameter

Height

Pixels per micron iThis defines the coarseness of the simulation, i.e. how many voxels the crystal is divided into per µm. Preferably set as high as possible, but higher values take longer. Recommended to try increasing between 0.5 and 5 and check that the reported dose converges. As a rule of thumb, the voxel size must be at least 10× smaller than the beam FWHM for a Gaussian beam, e.g. 20 µm FWHM → 2 µm voxels → 0.5 voxels/µm.

Resolution of the dose grid (voxels/µm). Default 0.5.

▾ Crystal orientation…

AngleP (°)

Rotation of crystal around X axis

AngleL (°)

Rotation of crystal around Z axis

Composition

Absorption coefficient method iThe method for calculating absorption and attenuation coefficients. RADDOSE-3D explicitly calculates them from the crystal composition you provide. From PDB entry downloads the structure from the Protein Data Bank and extracts the composition automatically. From amino acid sequence uses the sequence to determine the exact atomic composition. SAXS is for solution scattering experiments (uses protein concentration instead of monomers). Small molecule defines the full unit cell contents explicitly.

Unit cell dimensions (Å) iUnit cell dimensions a, b, c in Ångströms. The unit cell angles α, β, γ default to 90° if not specified (click to expand angles below).

▾ Unit cell angles…

α (°)

β (°)

γ (°)

Monomers in unit cell iNumber of monomers in the entire unit cell (N.B. not the asymmetric unit). For example, if the asymmetric unit contains one monomer and the space group has 4 symmetry operators, enter 4.

Residues per monomer iNumber of amino acid residues in a single monomer chain. Atom counts are estimated assuming an average amino acid composition of 5C + 1.35N + 1.5O + 8H. Sulfur atoms (from Cys/Met) should be added separately via Protein Heavy Atoms below.

RNA nucleotides per monomer iNumber of RNA nucleotides in a single monomer. Atom counts are estimated assuming a mean nucleotide = 11.25H + 9.5C + 3.75N + 7O + 1P. For a more accurate estimate, individual atoms may be entered via Protein Heavy Atoms.

DNA nucleotides per monomer iNumber of DNA deoxynucleotides in a single monomer. Atom counts are estimated assuming a mean deoxynucleotide = 11.75H + 9.75C + 4N + 6O + 1P. For a more accurate estimate, individual atoms may be entered via Protein Heavy Atoms.

Carbohydrate residues per monomer iNumber of carbohydrate (sugar) residues per monomer. Atom counts are estimated assuming an average sugar = 11H + 6C + 5O. For a more accurate estimate, individual atoms may be entered via Protein Heavy Atoms.

Protein heavy atoms (per monomer) iAtoms to add to the protein part of each monomer. Include sulfur from cysteines and methionines, coordinated metals (Zn, Fe, etc.), and selenium from selenomethionine. For example: S 10 would add 10 sulfur atoms; Zn 1 Se 5 would add 1 zinc and 5 selenium atoms per monomer.

Solvent heavy atom concentration (mmol/L) iConcentration of elements (excluding water) in the solvent, in millimoles per litre. For example, Na 1000 Cl 1000 would model 1 M NaCl. Do not declare oxygen or lighter elements. Use this for salts like ammonium sulfate, but not for PEG or other light-element compounds.

Solvent fraction iThe fraction of the unit cell volume occupied by solvent (between 0 and 1). If not given explicitly, this value is estimated assuming densities of 1.35 g/ml for protein and 2.0 g/ml for RNA and DNA.

PDB code

4-character PDB accession code. Composition will be extracted automatically.

Solvent heavy atom concentration (mmol/L, optional)

Unit cell dimensions (Å)

▾ Unit cell angles…

α (°)

β (°)

γ (°)

Amino acid sequence

One-letter amino acid codes (whitespace and numbers are ignored). Paste FASTA content directly.

Protein heavy atoms (per monomer, optional)

Solvent heavy atom concentration (mmol/L, optional)

Solvent fraction (optional)

Unit cell dimensions (Å)

Protein concentration (g/L) iThe protein concentration used in the SAXS experiment, in grams per litre. This replaces the NumMonomers keyword used in standard MX experiments.

Residues per monomer

RNA nucleotides per monomer

DNA nucleotides per monomer

Protein heavy atoms (per monomer)

Solvent heavy atom concentration (mmol/L)

Solvent fraction (optional)

Unit cell dimensions (Å)

▾ Unit cell angles…

α (°)

β (°)

γ (°)

Monomers in unit cell iNumber of formula units (monomers) in the unit cell. If omitted, 1 is assumed.

Small molecule atoms (per monomer in unit cell) iExplicitly define the full atomic contents of the unit cell per monomer, including all atoms (C, H, N, O, metals, etc.). This replaces NumResidues and ProteinHeavyAtoms. For example: C 18 H 15 Bi 8.

▾ Advanced crystal options…

Container material iIf the sample is inside a container (e.g. a capillary for SAXS), specify the material here. The beam is attenuated by the container before reaching the sample.

Container type

Material name iThe NIST material name, e.g. “pyrex” for borosilicate glass, “silicon”, “kapton”. See the NIST X-ray mass attenuation coefficient tables for valid names. Requires internet.

Material elements (formula ratio) iSpecify the elemental composition of the container material as element/count pairs. For example, quartz (SiO₂) would be: Si 1 O 2. Requires internet for mass attenuation data.

Thickness (µm)

Density (g/cm³)

Photoelectron & fluorescent escape iEnable explicit 3D models for photoelectron and/or fluorescent X-ray escape from the crystal volume. These are more physically accurate but slower. Recommended for small crystals or when heavy atoms are present.

Photoelectron escape Fluorescent escape

Include surrounding material entry

Surrounding heavy atom concentration (mmol/L)

Density-based surrounding

Surrounding elements (formula ratio)

Surrounding density (g/mL)

Dose decay model iModel for how diffraction intensity decays with absorbed dose. By default, no decay is modelled. The Leal model requires three parameters (γ, B₀, β).

Model

Decay parameters iThe three parameters for the Leal dose decay model: γ, B₀, and β.

B₀

Subprogram iSelect a specialised simulation mode. XFEL calculates time-resolved dose for free-electron laser experiments. Monte Carlo uses MC simulations for photoelectron/Compton tracking. Electron diffraction (MicroED) calculates doses for electron diffraction experiments.

Mode

Number of runs iNumber of times the simulation is repeated. More runs give better statistics.

Simulated photons iNumber of photons to simulate. More photons give better statistics but take longer.

Surrounding thickness (µm) — X, Y, Z iThickness of the surrounding material for Monte Carlo simulations, in µm along X, Y, Z.

Number of runs

Simulated photons

Goniometer & polarisation

Goniometer axis iOrientation of the goniometer: 0 = horizontal (default), 90 = vertical.

Polarisation direction iDirection of beam polarisation: 0 = horizontal (default), 90 = vertical.

Beams & Wedges

Each beam is followed by one or more wedges that use it. Most experiments need a single beam and wedge.

▾ Preview generated input file

RADDOSE-3D

Calculate the dose absorbed by a crystal

Job Details

Crystal

Composition

Container material iIf the sample is inside a container (e.g. a capillary for SAXS), specify the material here. The beam is attenuated by the container before reaching the sample.

Photoelectron & fluorescent escape iEnable explicit 3D models for photoelectron and/or fluorescent X-ray escape from the crystal volume. These are more physically accurate but slower. Recommended for small crystals or when heavy atoms are present.

Dose decay model iModel for how diffraction intensity decays with absorbed dose. By default, no decay is modelled. The Leal model requires three parameters (γ, B₀, β).

Subprogram iSelect a specialised simulation mode. XFEL calculates time-resolved dose for free-electron laser experiments. Monte Carlo uses MC simulations for photoelectron/Compton tracking. Electron diffraction (MicroED) calculates doses for electron diffraction experiments.

Goniometer & polarisation

Beams & Wedges