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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.


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.


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, Siyang Chen, & Daisuke Kihara. VESPER: Global and Local Cryo-EM Map Alignment Using Local Density Vectors. Manuscript in preparation. (2019)
Copyright © 2020 KIHARA Bioinformatics LABORATORY , PURDUE University