The EmDataBank validation reports are prepared according to the recommendations of the EM Validation Task Force (EM VTF; Henderson et al., 2012)

1. Experimental information

This section reports experimental details about the structure determination.

(image of EM experimental details table)

2. Tomogram visualisation

The tomogram visualisation section contains visualisations of the tomogram. These are intended to permit inspection of the internal detail of the tomogram and identification of artifacts. The items in this section are generated using the EMDB Validation-Analysis (To be published) which makes use of TEMPy (Farabella et al., 2015) for analysis.

These artifacts can include but are not limited to

Streaking

May indicate insufficient representation in particular orientations
Mask artifacts

Can indicate whether masks were used and the types of masks applied during processing

2.1. Orthogonal projections

The images show the tomogram projected in three orthogonal directions.

(image of orthongonal projections)

2.2. Central slices

The images show the central slice of the tomogram in three orthogonal projections.

(image of central slices)

2.3. Largest variance slices

The images show the largest variance slices of the tomogram in three orthogonal directions. The index of the slice in the relevant axis is given below the image.

(image of largest variance slices)

2.4. Mask visualisation

This section shows the 3D surface view of the tomogram at 50% transparency in yellow overlaid with the specified mask at 0% transparency in blue. A mask typically either encompasses the whole structure and indicates the removal of noise from the peripheries of the tomogram, or seperates out a domain, a functional unit, a monomer or an area of interest from the larger structure. These images are generated using ChimeraX (Goddard et al., 2018).

(image of mask views)

3. Tomogram analysis

The tomogram analysis section contains statistical analysis of the tomogram. The information is given as a set of graphs.

3.1. Voxel value distribution

The voxel value distribution is plotted in 128 intervals along the x-axis. The y axis is logarithmic.

(image of voxel value distribution graph)

References

  • R. Henderson, A. Sali, M. L. Baker, B. Carragher, B. Devkota, K. H. Downing, E. H. Egelman, Z. Feng, J. Frank, N. Grigorieff, W. Jiang, S. J. Ludtke, O. Medalia, P. A. Penczek, P. B. Rosenthal, M. G. Rossmann, M. F. Schmid, G. F. Schröder, A. C. Steven, D. L. Stokes, J. D. Westbrook, W. Wriggers, H. Yang, J. Young, H. M. Berman, W. Chiu, G. J. Kleywegt, C. L. Lawson, Outcome of the First Electron Microscopy Validation Task Force Meeting, Structure, 20:205–214, 2012. CrossRef

  • Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE. UCSF ChimeraX: Meeting modern challenges in visualization and analysis., Protein Sci., 27(1):14–25, 2018 CrossRef

  • Farabella, I., Vasishtan, D., Joseph, A.P., Pandurangan, A.P., Sahota, H. & Topf, M. TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits. Appl. Cryst. 48:1314–1323, 2015 CrossRef