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).
Target Structure file 5FN3_A.pdb
Contour level: 0.04
Result Example: Result ExampleTutorial
Reference: https://www.nature.com/articles/s41467-021-22401-y
Reference Map
Please adjust the contour level for the best fit. Set a contour level that is sufficiently low to cover the entire protein region as a continuous volume. vesper(s2m) does not check map regions below (lower than) the contour level you specified. On the other hand, if you specify the contour level too low, it will take longer time for the program to check every voxels above the contour level.
After adjusting the contour level on the sliding window click "Update Contour Value" to visualize the volume. Note that the map may not be visualized when the map is large and the specified contour level is too low or the specified contour level is too high and the browser runs out of memory.
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.
Target Structure (To be superimposed on map1, PDB format)
Search angle spacing in degrees
Search grid spacing in Angstroms
Resolution of the reference map
The number of conformations to generate
