The EmDataBank validation reports are prepared according to the recommendations of
the EM Validation Task Force (EM VTF;
Henderson et al., 2012)
This section reports experimental details about the structure determination.
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
May indicate insufficient representation in particular orientations
Can indicate whether masks were used and the types of masks applied during processing
The images show the tomogram projected in three orthogonal directions.
The images show the central slice of the tomogram in three orthogonal projections.
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.
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).
The tomogram analysis section contains statistical analysis of the tomogram.
The information is given as a set of graphs.
The voxel value distribution is plotted in 128 intervals along the x-axis.
The y axis is logarithmic.
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,
Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE.
UCSF ChimeraX: Meeting modern challenges in visualization and analysis.,
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.