EMPIAR-12287 - CryoEM ice images and labels used for VirtualIce [multiple data sets in MRC, MRCS and JPEG formats]

EMPIAR-12287

CryoEM ice images and labels used for VirtualIce [multiple data sets in MRC, MRCS and JPEG formats]

Publication:

VirtualIce: Half-synthetic CryoEM Micrograph Generator

Noble AJ

bioRxiv (2024)

DOI: 10.1101/2024.09.28.615520

Related EMDB entry:

Deposited:

2024-09-05

Released:

2024-10-11

Last modified:

2024-10-11

Imageset size:

308.55 GB

Imageset DOI:

10.6019/EMPIAR-12287

Experimental metadata:

Download xml json

Contains:

micrographs - single frame
micrographs - multiframe

Image Sets

1. Micrographs of vitrified buffer with labels of objects that can obscure particles

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

678

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.096, 1.096)

Details:

Frame-aligned micrographs of vitrified buffer with associated labels (.json files in AnyLabeling v0.3.3 format) of objects that can obscure particles.
This directory must either go in your VirtualIce installation directory for it to work automatically or in a different directory and pointed to with VirtualIce.

Files:

Archives and downloads the selected files into an uncompressed zip file.

Depending on the number and size of files to be downloaded, this can take an enormous amount of time. Also, this feature is unstable and may not work properly, and checksums of downloaded files are not verified.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

2. Frame stacks of vitrified buffer

Category:

micrographs - multiframe

Image format:

MRCS

No. of images or tilt series:

900

Image size:

(3838, 3710)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(1.096, 1.096)

Details:

Bzip2 compressed frame stacks of vitrified buffer. Collected on a Krios, Cs corrector, BioQuantum-K2 (15eV slit width), 50.81 e-/Å2 total dose, nominal defocus range randomly chosen between 1 and 3 µm. References included.

Files:

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

3. Micrographs of vitrified buffer

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

897

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.096, 1.096)

Details:

Frame-aligned micrographs of vitrified buffer.

Files:

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

4. Downsampled micrographs of vitrified buffer tinted green with labels of objects that can obscure particles

Category:

micrographs - single frame

Image format:

JPEG

No. of images or tilt series:

900

Image size:

(960, 928)

Pixel type:

16 BIT FLOAT

Pixel spacing:

(4.384, 4.384)

Details:

Frame-aligned, downsampled by 4 micrographs of vitrified buffer converted to JPEG and tinted green to expedite the visualization process. Associated labels (.json files in AnyLabeling v0.3.3 format) of objects that can obscure particles are included.

Files:

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

Browse All Files

Quick Links

Talks and Tutorials

EMPIAR Quick tour

Statistics

Publications

Re-use case study

EMPIAR in the news

Claim entries to your ORCiD

COVID-19 Data Portal

EMDB

PDBe

BioImage Archive

EMNavigator@PDBj

PDBj

RCSB@PDBj

EMDataResoruce@RCSB,EMDB,NCMI

Citations

Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing.

Abe KM, Li G, He Q, Grant T, Lim CJ. (2024)

Outer membrane protein assembly mediated by BAM-SurA complexes.

Fenn KL, Horne JE, Crossley JA, Böhringer N, Horne RJ, Schäberle TF, Calabrese AN, Radford SE, Ranson NA. (2024)

Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.

Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C. (2024)

Molecular recognition of an odorant by the murine trace amine-associated receptor TAAR7f.

Gusach A, Lee Y, Khoshgrudi AN, Mukhaleva E, Ma N, Koers EJ, Chen Q, Edwards PC, Huang F, Kim J, Mancia F, Veprintsev DB, Vaidehi N, Weyand SN, Tate CG. (2024)

The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation.

Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau VV, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. (2024)

See all citations

Protein Data Bank Japan News

[2024-11-20]

224 new PDB entries have been released on 2024-11-20.

[2024-11-01]

A new portal integrating genome variants and protein structures has released

[2024-10-30]

[wwPDB] Deprecation of FTP File Download Protocol on November 1, 2024

[2024-10-25]

PDBj luncheon seminar at APBJC 2024

[2024-10-17]

[wwPDB] The Nobel Prize in Chemistry 2024