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@jdickerson95 jdickerson95 released this Sep 20, 2019 · 6 commits to master since this release

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
Assets 5

@jdickerson95 jdickerson95 released this Dec 15, 2018 · 195 commits to master since this release

Minor bug fixes

Assets 4

@jdickerson95 jdickerson95 released this Aug 22, 2018 · 206 commits to master since this release

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

Assets 4

@jdickerson95 jdickerson95 released this Aug 14, 2018 · 209 commits to master since this release

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
Assets 4
Aug 10, 2018
Made ciruclar colliamtion clearer in user guide

@charliebury charliebury released this Jan 16, 2018 · 291 commits to master since this release

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
Assets 4

@JonnyCBB JonnyCBB released this Jan 2, 2017 · 451 commits to master since this release

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.
Assets 3

@Anthchirp Anthchirp released this Dec 18, 2014 · 582 commits to master since this release

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.

Assets 4

@Anthchirp Anthchirp released this Dec 9, 2014 · 594 commits to master since this release

Several improvments to functionality have been incorporated into RADDOSE-3D version 1.2.415. 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 which can be accessed from here: http://www.raddo.se/rd3d/RD3D-User-Guide.pdf.

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

Assets 3
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