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Pairwise VESPER Search
VESPER uses a combination of mean shift algorithm and fast Fourier transform (FFT) to identify the best superimposition of two EM maps. Source codes are available here. Alignment using conventional Cross-correlation and the Laplacian filter is available in the provided code.


VESPER has two major steps:
  • Identify the best superimposition between two EM maps with certain voxel spacing and angle spacing.
  • Calculate the normalized z-score for each of top 10 models in VESPER output. Given a query map, normalized z-score is the score we use for ranking all other maps in the database. Empirically, related maps have normalized z-score larger than 10.0.
Search results by VESPER
  • In Step 1, choose the voxel spacing (v, in Å) and angle spacing (A, in degrees). VESPER uses v = 7 Å and A = 30° by default, which takes 1 hour on average. Usage of smaller voxel spacing and angle spacing can improve the accuracy in fitting, but also makes the calculation much slower.
  • In Step 2, provide a reference map ID and a target map ID or upload two EM map files. The reference map is fixed. The target map is superimposed onto the reference map.
  • In Step 3, provide the Email address. After the calculation is done, VESPER sends the calculation results to the provided Email address. To visualize alignment results, follow the instruction included in the zipped files.


Step 1 (Search parameters)

    Voxel Spacing (in Å):
    Angle Spacing (in degrees):


Step 2 (Query maps)

Download Example Input File (Please Unzip First)
    Reference Map EMDB ID:
    Target Map EMDB ID:
    Upload reference map (.map file):
    Recommended contour level for reference map:
    (Use 0.04 for Example Input File provided above)
    Upload target map (.map file):
    Recommended contour level for target map:
    (Use 0.04 for Example Input File provided above)


Step 3 (Email)

    Email address:




Reference: Xusi Han, Genki Terashi, Charles Christoffer, Siyang Chen, & Daisuke Kihara. VESPER: Global and Local Cryo-EM Map Alignment Using Local Density Vectors. Nature Communications. 12.1 (2021):1-12
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