VirtualIce v2.0.0

Various bug fixes and version release.

VirtualIce v2.0.0beta

Multiple structures can now be requested (structure sets).

• Use the same --structures flag followed by either a single structure or multiple. Supports any number of structure sets, like this:
  • virtualice.py -s 1TIM [1PMA, 50882] [my_structure1.mrc, 3DRE, 6TIM]
• The above command will make one set of micrographs with only PDB 1TIM, another set with PDB 1PMA and EMD-50882, and another set with a local file (my_structure1.mrc), PDB 3DRE, and PDB 6TIM.
• Preferred orientation, particle distributions, and overlapping & aggregated particles are fully supported.
• Filtering of edge, overlapping, and obscured particles is fully supported.
• Coordinate files are saved independently in .star, .mod, and/or .coord files (one per structure in a structure set).
  This update is significant because it allows for ground-truth datasets of heterogeneous proteins - e.g. continuous or discrete conformations, compositional heterogeneity, or completely different proteins.

VirtualIce v1.0.1

Last release of VirtualIce for single-structure micrographs. Contains minor printout updates compared to v1.0.0.

VirtualIce v1.0.0

First release of VirtualIce. Features:

• Generates half-synthetic cryoEM micrographs and particles from buffer images and PDB IDs, EMDB IDs, or local files.
• Creates coordinate files (.star, .mod, .coord), not including particles obscured by junk/substrate or too close to the edge.
• Adds Poisson noise and dose-dependent damage to simulated frames and Gaussian noise to particles.
• Applies the Contrast Transfer Function (CTF) to simulate microscope optics.
• Control over overlapping particles and particle aggregation.
• Outputs micrographs in MRC, PNG, and JPEG formats, and optionally cropped particles as MRCs.
• Multi-core and GPU processing.
• Extensive customization options including particle distribution, ice thickness, microscope parameters, and downsampling.