RADDOSE-3D v5

This is the first release RADDOSE-3D version 5. This release includes three major new features.

• RADDOSE-ED to estimate doses for electron diffraction experiments.
• The ability to use intensity decay models to convert the "Diffraction Weighted Dose" output from a "Fluence Weighted Dose" to a "Diffraction-Decay Weighted Dose".
• A new graphical user interface for Linux and Windows.

These features are all described in this publication:
Dickerson J. L., McCubbin P. T. N, Brooks-Bartlett J. C., Garman E. F.. Doses for X-ray and electron diffraction: New features in RADDOSE-3D including intensity decay models. Protein Science. 2024;33(7):e5005. https://doi.org/10.1002/pro.5005

RADDOSE-3D v4.0.1027

Some minor bug fixes to RADDOSE-3D.
The most significant is that for heavy atoms, X-ray energies above the L3 edge but below the L1 edge are now dealt with more accurately.

RADDOSE-3D v4.0.1020

Some minor changes to RADDOSE-3D:

• Inclusion of entry of material from surrounding material for SAXS.
• Bug fixes.

RADDOSE-3D v4.0

This is a major new release of RADDOSE-3D with several new features.
Most notably, the new version includes two new subprograms:

• The first is RADDOSE-XFEL, which can estimate the time-resolved absorbed dose by crystals during XFEL pulses.
• The second is RADDOSE-3D Monte Carlo, which performs Monte Carlo simulations of rotating crystals during synchrotron data collection to provide more accurate doses for microbeams and microcrystals.

(a note that the constants folder must be present in the same directory as the jar file to use these programs)

Other features include:

• The ability to define a pink beam in RADDOSE-3D
• Minor bug fixes

RADDOSE-3D v3.0.814

Minor bug fixes

RADDOSE-3D v3.0.803

This release is based on version 3.0.800.
A minor addition has been made, when defining an oil based surrounding, the user can now define the density and elemental composition instead of the concentration. See user guide for details

RADDOSE-3D v3.0.800

This is a new major release of RADDOSE-3D with many new features.
Most notably, it enables the user to simulate photoelectrons produced from within the crystal and also specify a surrounding material and simulate photoelectrons entering the crystal form the surrounding volume.
Other notable features include:

• The ability to account for the escape of fluorescent photons, significant when heavy elements are present in the crystal
• Compton scattering is now calculated, improving dose accuracy for incident beam energies over 20 keV
• RADDOSE-3D has been adapted so it can be used for small molecule X-ray crystallography
• Define a beam with circular or elliptical collimation
• Quickly specify number of carbohydrate residues for glycosylated proteins
• Minor bug fixes when using FASTA files

RADDOSE-3D v2.1.0

This is an update on the previous version (v2.0.0) of RADDOSE-3D (including SAXS), to include several fixes:

• The ability to read PDB files for crystal composition has been modified to account for the new URL location of such files
• The user can also use a PDB file stored anywhere locally by entering the file path instead of a PDB code
• The ability to retrieve absorption information from online NIST tables has been modified to account for the URL for such information
• Minor bug fixes

RADDOSE-3D includes SAXS

This is a new major release of RADDOSE-3D with many new features. Most notably it enables the user to simulate SAXS experiments.
Other notable improvements

• dedicated cylindrical geometry definition.
• ability to read composition directly from FASTA formatted sequence files
• define a container in which a sample is housed.

RADDOSE-3D v1.2.427

Several improvments to functionality have been incorporated into RADDOSE-3D version 1.2.427 The absorption coefficient calculation is more accurate then in previous versions, particularly for structures containing nucleic acids. The options for the user has increased allowing more flexibility with the dose calculations. The user guide has been updated accordingly and can be found below and in the 'doc' folder of the release.

RADDOSE-3D can be run from the command line using the command:
java -jar raddose3d.jar -?
This will show the command line options available for running RADDOSE-3D. The simplest way to use RADDOSE-3D is to create a single file containing the entire experiment. Then it can be run using the command:
java -jar raddose3d.jar -i Location/Of/ExperimentFile.txt

This release is based on v1.2.415 and includes the updated user guide and a few minor bugfixes.