deposition . biochemical sample specimen preparationimaging image processing reconstruction...
TRANSCRIPT
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Deposition
http://www.ebi.ac.uk/msd-srv/emdep
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BIOCHEMICALSAMPLE
SPECIMENPREPARATION IMAGING
IMAGEPROCESSINGRECONSTRUCTION
MAP-FITTING
ELECTRONICNOTEBOOK
MICROSCOPEFILM/CCD
ELECTRONICNOTEBOOK
SCANSPARTICLE –
PICKING
3D RECON-STRUCTIONSOFTWARE
MAP FITTINGSOFTWARE
3DEM WORKFLOW PIPELINE
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EM Data Collection
Structure AnalysisImage Processing
EM SpecimenPreparation
Biochemical Preparation
EM
em_assembly
_em_assembly.id
_em_assembly.entry_id
_em_assembly.name
_em_assembly.aggregation_state
_em_assembly.composition
_em_assembly.num_components
_em_assembly.mol_wt_exp
_em_assembly.mol_wt_theo
_em_assembly.mol_wt_method
_em_assembly.details
Biological Sample
Biological Sample
em_assembly
em_entity_assembly
em_entity_assembly_list
em_icos_virus_shells
em_virus_entity
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Growth of EM Entries
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Data filesData files
3D-EM map3D-EM map
MetadescriptorsMetadescriptors
Release: immediateTitle: “The Structure of the Semliki Forest Virus at 9 Å resolution”Authors: E. Mancini M. Clarke B. E. Gowen T. Rutten S. D. FullerReference paper: Mol Cell (2000) 5, 255Complex
Name: Semliki Forest Virus SFVAggregation: icosahedralDescribe composition: partial
ComponentsName:
spike glycoprotein E1spike glycoprotein E2spike glycoprotein E3coat protein C
Type: proteinSource: naturalSource organism: Semliki Forest Virus
ExperimentMicroscope: TEMTemperature range: liquid nitrogenReconstruction method: fourier-bessel
Mandatory
Optional
Database content
Figures
Slices
Masks
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3D-EM Deposited Data
MANDATORY: 3D- EM MAPS
TEXTUAL DESCRIPTORS
OPTIONAL ADDITIONAL DATA FILES:
MASKS
SUPPLEMENTARY FIGURES
ORTHOGONAL MAP SLICES
STRUCTURE FACTORS
FSC .xml FILE
LAYER-LINE DATA
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Biological Sample
Biochemical Preparation
EM Specimen Preparation
EM Data Collection
Image Processing
Structure Analysis
Textual Descriptors
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EM Deposition
INTERACTIVE DEPOSITION SYSTEM:
13 DEPOSITION PAGES
120 DATA ITEMS
INFORMATION AND HELP ON PAGE
UPLOADED FILES
'BASED ON' FACILITY
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Sample Details Page
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XML data automatically
Filled in by software
Reading map headers
MAPS em2em – CCP4
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EM Deposition Data
SINGLE PARTICLES ICOSAHEDRAL VIRUSES TOMOGRAPHY HELICAL ASSEMBLIES 2D-CRYSTALS
EM DATA FROM METHODOLOGIES INCLUDING:
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Demonstration
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Worldwide Protein Data Bankwww.wwpdb.org
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Proposed Method for Depositing and Retrieving EM Data
IntegratedRCSB deposition
system
IntegratedMSD deposition
system
EB
IR
CS
B
map and fitted coordinateFTP repository
EM map/model assessment, visualization
and analysis tools
MSDDatabase
RCSBDatabase
Electron Microscopy Access Portal
Combined Dictionary for Map and Coordinate Data
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Next slides only to be used if demo fails
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Title author
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Sample components
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Sample components
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Single Particle
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Individual Structure (Tomogram)
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2d/3d crystal
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icosahedral
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helical
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TO FINALLY DEPOSIT THE ENTRY:
click on ‘GET ACCESSION NUMBER’ button (upper left).
You will receive by email an ‘ACCESSION’ number for your entry (eg EMD-1234) which can be used in EMsearch to link to the atlas pages for your entry.