The VESPER program is available on Github Page.

• Benchmark dataset of Joseph, Agnel Praveen, et al. "Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy." Journal of Structural Biology 199.1 (2017): 12-26. (20 maps).
  • Rotation, Translation, and RMSD tables (100 superimpositions per target.)
    • 1-9th columns: Rotation Matrix (3*3)
    • 10-12th columns: Translation Vector (3)
    • 13th column: log(ALCPS)
    • 14th column: Angle difference between the reference and current fit (theta)
    • 15th column: Distance of Translation between the reference and current fit (r)
    • 16th column: RMSD
  • Reference PDB model (Superimposed)
  • 18 metrics and DOT score tables
    Filename is formatted as [emid1]_[emid2]_[Score Type].dat
    The first row shows emid1 and emid2. From the second row, 1st column is the score. 2nd column is the model ID.

    • Score types	Description
      CCC	Global Cross-Correlation
      SCCC	Local Cross-Correlation
      SMOC	Segment based Mander' Overlap Coefficient
      LMI	Local Mutual Information
      NMI	Normalized Mutual Information
      CDT	Chamfer Distance of surface based on a density Threshold
      CDA	Chamfer Distance of surface based on All points on the contour surface
      CDM	Chamfer Distance of surface based on Mean filter
      CDT_GDT	Weighted CDT
      CDA_GDT	Weighted CDA
      CDM_GDT	Weighted CDM
      NVT	Normal Vector score at surface points at a density Threshold
      NVA	Normal Vector score at surface points at the contour surface
      NVM	Normal Vector score at surface points at Mean filter
      OVR	Overlap score
      SCCC_OV	Combined score of SCCC and OV
      SMOV_OV	Combined score of SMOV and OV
      LMI_OV	Combined score of LMI and OV
      DOT	Unit-vector based score in VESPER

• Benchmark dataset of Partial map alignment (57 targets)
  • PDB files: Reference PDB
  • MRC files: Simulated EM maps at the resolution of the original map. Simulated maps were generated by "molmap" command in UCSF Chimera.
  • Reference PDB files and simulated maps.