Contents

VESPER(S2M) Tutorial

Overview

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 with resolution up to 0-20 Å. The given structure model is converted into a density map and then superimposed onto it.

Overall Pipeline

flowchart

  1. To identify the best superimposition of two EM maps, each map is firstly converted to a set of unit vectors using the mean shift algorithm.
  2. The best superimposition of two maps is identified using the fast Fourier transform (FFT). For each rotation sampled, a translation scan is performed using FFT to optimize the summation of dot products of matched vectors (DOT score).
  3. For each of the top 10 models from FFT search, VESPER performs 5° local refinement along each axis and then write top 10 models after the refinement into the output file.

Input Files

3D cryo-EM maps in .mrc format

Protein Structure in .pdb format

Output Files

Superimposed structure (.pdb) and EM map

Job Submission

  1. Prepare Input Map

    2. Collect 3D cryo-EM map from microscope in .mrc and .map format.
    Example map
    You can also find many maps in EMDataResource as testing examples.

  2. Prepare Protein Structure

    3. Upload your structure model in pdb format

    Example pdb

  3. Decide the contour level

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

  4. Decide the angle spacing

    5. Search angle spacing in degrees.

  5. Decide the grid spacing

    6. Search grid spacing in Angstroms.

  6. Decide the resolution

    7. Resolution of the reference map.

  7. Decide the number of conformation

    8. The number of conformations to generate.

  8. Submit your job

    9. Once you collected the input files, please submit your job here. For each input field, please input the files/info collected before.

    Step 3 Screenshot

    Once you finished input, simply click the upload button to submit jobs. After submission, you will be redirected to the “view job“ page. If you are not registered, please bookmark the link. Once the job is done, you can view jobs from this link. If you are registered, you will receive email notifications once job is done and you can also check job status from my jobs list under job manager.

  9. View your job results

    10. Once job is done, you can check the modeled structure from the link bookmarked before. Here you can also download the modeled structure in .pdb format by clicking the “Download Outputs” button. You can also visualize the 3D cryo-EM map online to check its consistency with the modeled structure. For more detailed instructions, please see the “Instructions” in the same page.

    results

  10. Submit for backend review (optional)

    11. If you noticed any strange outputs or job failure on your side, please submit a backend review by using the field in the bottom of the “View Job” page. We will get back to you as soon as possible.

    review

Availability (Other)

  1. GitHub

    Full code is available here.

Reference

Han, X., Terashi, G., Christoffer, C., Chen, S., & Kihara, D. (2021). VESPER: global and local cryo-EM map alignment using local density vectors. Nature Communications, 12(1), 2090. https://www.nature.com/articles/s41467-021-22401-y