Map deposition has been integrat-ed with fitted coordinate modeldeposition to the PDB. Upon com-pletion of an EMDEP3 map depo-sition session, the user is presentedwith the option to deposit one ormore coordinate models to thePDB using AUTODEP (PDBe) orADIT (RCSB PDB). Experiment-related metadata is automatically
transferred to the PDB coordinate deposition session.USA: http://emdep.rutgers.eduUK: http://www.ebi.ac.uk/pdbe-emdep/emdep
EMDEP3–a web-based tool for the deposition and validation ofelectron microscopy derived macromolecular information.Features:• password protected• may be interrupted and resumed• forms can be completed in any order• PDB deposition
Christoph Best1, Catherine Lawson2, Richard Newman1, Batsal Devkota2, Glen van Ginkel1, Raul Sala2, Chunxiao Bi2, John Westbrook2,Sameer Velankar1, Joe Warren3, Lavu Sridhar3, Powei Feng3, Matthew Baker4, Steven Ludtke4, Ian Rees4, Kim Henrick1, Helen M. Berman2, Wah Chiu4
• A single dictionary for maps andmodels has been created, incorporatingEM-community recommendations(see table above)
• Community recommendations willcontinue to be welcomed
A Unified Data Resource for CryoEM4National Center for Macromolecular Imaging, Vernaand Marrs McLean Department of Biochemistry andMolecular Biology,Baylor College of Medicine, Houston, TX 77030, USA
3Department ofComputer Science,Rice University,Houston, Texas, USA
2RCSB Protein Data Bank,Department of Chemistry andChemical Biology, Rutgers, The StateUniversity of New Jersey,Piscataway, NJ 08854-8087, USA
1Protein Data Bank Europe,European Bioinformatics Institute, EMBLOutstation-Hinxton,Cambridge CB10 1SD, UK
JOINT MAP AND MODEL DEPOSITION
EBI is collaborating with the OpenMicroscopy Environment (OME,www.openmicroscopy.org), one of theleading bioimage informatics tools forlight microscopy, under a BBSRC grantrecently awarded jointly to G. Kleywegtand C. Best at EBI and J. Swedlow at theUniversity of Dundee.The grant focuses on improving theusability of EMDB by harnessing visual-ization and analysis technology fromOME, and on integrating electronmicroscopy into OME.
The project will focus on the following topics:• Enhancement of data formats for single-particle analysis and for tomography in OME• Improved tools for web-based submission, upload, metadata harvesting,and data management• Visualization tools for large data sets, including single-particle stacks and large tomograms• Tools for handling complex data sets containing several maps, masks, coordinate files,and other information sets in EMDB entries• Grid/cloud-enabled data storage and processing• Quality assessment tools and algorithms for single-particle and tomography data sets
SUMMARYOur goal is to create a robust sys-tem for the collection, validation,annotation, distribution andvisualization of data derivedfrom cryoEM experiments andanalyses. We will provideresearchers with an integrated"one-stop shop" for depositingand assessing related meta-data,maps, and models.
This site will also offer a compre-hensive and quantitative descrip-tion of the deposited data andlink to relevant databases. To dothis, we will enhance the existingsystems for the deposition and
distribution of 3D atomic models and distribution of electron microscopy-based reconstructionmaps. The result will be the full integration of cryoEM experimental data into the PDB archive.
3DEMDepositor
EMDEP2@EBI-PDBe
EMDEP2@RCSB PDBEMDB(maps)
AUTODEP@EBI-PDBe
ADIT@RCSB PDBPDB(coordinates)
3DEMUser
EMDB XML Schema (maps, metadata)
PDB Exchange Dictionary (PDBx) (coordinates, metadata)
MSD-EBI
RCSB PDB
ANNOTATE ARCHIVEHARVEST
PDB Exchange Dictionary (maps, coordinates, metadata)
PDBmaps +coordinates
VisualizationValidationSegmentation
ACCESS
3DEMDepositor
3DEMUser
Deposition and Retrieval, 2008
Deposition and Retrieval, 2012
ARCHIVEANNOTATE
3DEM Software
DICTIONARYTwo dictionaries for archiving EM data arein current use:• EMDB dictionary for EM maps• PDBx dictionary for fitted coordinates
SEARCH
EmSearch–a simple, fast, easy to useform-based query system to search theEM database.http://www.ebi.ac.uk/pdbe-srv/emsearchhttp://emsearch.rutgers.edu
VISUALIZATION
Two viewers are availablewithin the atlas pages:
EMViewer is a Java appletdesigned to produce a sim-ple 3D rendering of EM vol-ume data. It will be a fea-ture of the unified cryoEMresource. A back-end systemgenerates simplified 3Dpolygonal meshes for eachdeposited EM and for eachspecified isovalue. EMViewer will parse the cached polygonal data and render the polygonal mesh. Moreover, thisviewer has the ability to show individual masked regions or a combination of masked regions provided that thedepositor has submitted masks. The viewer supports common 3Dviewing operations such as pan, zoom, androtate. The viewer also supports wire-frame and silhouette rendering. Possible future additions include clipplanes and custom lighting.
AstexViewer, also a Java applet, is designed to visualize both map and coordinates together.
EMViewer AstexViewer SEGMENTATION
Volviz is a cross-platform program that focuses onediting and visualizing molecular volume data.Much like using a "paintbrush" to edit a picture intraditional 2D image manipulation, Volviz pro-vides the ability to edit 3D volumes by painting in3D. By first selecting a range of isovalues, the usercan choose from a variety of paintbrushes to paintover the volume. While painting, Volviz associatesthe paintbrush with a color, and each color repre-sents a different mask over the volume. The result-ing output is a volume that associates each voxel inthe original data with a mask value. Volviz wasbuilt to accelerate volume segmentation/ classifica-tion, and it can be extended to annotation of thefeatures of a molecular structure. Additionally, itsupports iso-surface rendering using polygonalmeshes and mesh simplification for output.
FUNDINGThe Electron Microscopy Data Bank(EMDB) is currently funded by theNIH award GM079429 to BaylorCollege of Medicine, RutgersUniversity, and the EuropeanBioinformatics Institute (EBI).Additional support comes from a col-laboration between the EBI and theUniversity of Dundee with the BBSRCgrant BB/G0225771/1. Previous sup-port has come from an EU SixthFramework Programme, the 3D-EMNetwork of Excellence contract LSHG-CT-2004-502828 to the EBI.
QUESTIONS/COMMENTS
http://[email protected]@rcsb.rutgers.edu
http://emdatabank.org
OPEN MICROSCOPY ENVIRONMENTCONVENTIONS
Heymann et al.1 proposed common con-ventions for exchanging and archiving3DEM data. We are participating in aninternational collaboration with severalresearch groups to create the 3DEMConventionsWeb Site, a repository of geom-etry specifications for current software
(http://conventions.cnb.uam.es).
1JB Heymann, M Chagoyen, DM Belnap (2005) J Struct Biol.151(2):196-207.
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