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J Struct Biol. 2016 May;194(2):164-70. doi: 10.1016/j.jsb.2016.02.012. Epub 2016 Feb 10.

Web-based volume slicer for 3D electron-microscopy data from EMDB.

Author information

1
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom; Present address: Universitat Politècnica de València, DISCA, Edificio 1G - Lab 3S-15, Camino de Vera S/N, 46022 València, Spain. Electronic address: josator@gap.upv.es.
2
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom. Electronic address: andrii@ebi.ac.uk.
3
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom. Electronic address: ingvar@ebi.ac.uk.
4
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom. Electronic address: eduardo@ebi.ac.uk.
5
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom. Electronic address: gerard@ebi.ac.uk.
6
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom. Electronic address: ardan@ebi.ac.uk.

Abstract

We describe the functionality and design of the Volume slicer - a web-based slice viewer for EMDB entries. This tool uniquely provides the facility to view slices from 3D EM reconstructions along the three orthogonal axes and to rapidly switch between them and navigate through the volume. We have employed multiple rounds of user-experience testing with members of the EM community to ensure that the interface is easy and intuitive to use and the information provided is relevant. The impetus to develop the Volume slicer has been calls from the EM community to provide web-based interactive visualisation of 2D slice data. This would be useful for quick initial checks of the quality of a reconstruction. Again in response to calls from the community, we plan to further develop the Volume slicer into a fully-fledged Volume browser that provides integrated visualisation of EMDB and PDB entries from the molecular to the cellular scale.

KEYWORDS:

Electron Microscopy; Visualisation; Web components

PMID:
26876163
PMCID:
PMC4819904
DOI:
10.1016/j.jsb.2016.02.012
[Indexed for MEDLINE]
Free PMC Article

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