Unlike VESPER for MAP-MAP fitting, VESPER(S2M) performs Structure-Map fitting by accurately superimposing Structure and EM Maps using Mean Shift Algorithm and FFT. The given structure model is converted into a density map and then superimposed onto it.

If encounter problems, please contact Daisuke Kihara (dkihara@purdue.edu), Genki Terashi (gterashi@purdue.edu), Han Zhu (zhu773@purdue.edu).

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Example EMD-3238
Reference Map file:emd_3238.map

Target Structure file 5FN3_A.pdb

Contour level: 0.04

Result Example: Result Example
Tutorial

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Reference: https://www.nature.com/articles/s41467-021-22401-y

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Please simply click "Schedule Job" when you filled all input fields.

Reference Map

cryo_em_map :

Author recommend contour level for the reference map

Please make sure your contour level is lower than your focused region. This is absolute density threshold, not standard deviation.

contour_level :

Target Structure (To be superimposed on map1, PDB format)

target_pdb :

Search angle spacing in degrees

angle_spacing :

Search grid spacing in Angstroms

grid_spacing :

Resolution of the reference map

resolution :

The number of conformations to generate

num_conformation :


Job Title (Optional):

Job Note (Optional):
This note will help you distinguish jobs later.