EMPIAR-10010 - Full virus map of Brome Mosaic Virus (micrographs and particle coordinates) [multiple data sets in TIFF and MRC formats]

EMPIAR-10010

Full virus map of Brome Mosaic Virus (micrographs and particle coordinates) [multiple data sets in TIFF and MRC formats]

Publication:

An atomic model of brome mosaic virus using direct electron detection and real-space optimization

Wang Z, Hryc CF, Bammes B, Afonine PV, Jakana J, Chen DH, Liu X, Baker ML, Kao C, Ludtke SJ, Schmid MF, Adams PD, Chiu W

Nat Commun 5 (2014) 4808-4808

PMID: 25185801

DOI: doi:10.1038/ncomms5808

Related EMDB entry:

EMD-6000

Deposited:

2014-07-20

Released:

2014-09-07

Last modified:

2014-09-07

Imageset size:

1.72 TB

Imageset DOI:

10.6019/EMPIAR-10010

Experimental metadata:

Download xml json

Version history:

2015-09-25

REL

Added dark and gain correction images:<br>dark_frame.tif<br>gain_frame.tif

2015-11-11

REL

New gain corrected images uploaded.<br>Directory organization changed

Contains:

micrographs - multiframe

Image Sets

1. Brome Mosaic Virus micrographs - non gain corrected

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

424

Image size:

(4096, 3072)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.99, 0.99)

Details:

Each frame is an individual TIFF image. The FinalImage.tif included for each micrograph is a sum image of the frames without drift correction and damage compensation. The .box files (found in the directory data/micrographs/non_gain_corrected/box_files)describe particle locations but are rotated 90 degrees relative to the micrograph frames.
The dark and gain correction images are found in data/micrographs/non_gain_corrected/gain_correction and are called:
dark_frame.tif
gain_frame.tif
Dataset is related to EMPIAR-10011.
This set is a subset of the images in data/micrographs/gain_corrected which were actually used in the final reconstruction.

Files:

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rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

2. Brome Mosaic Virus micrographs - gain corrected

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

647

Image size:

(4096, 3072)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.99, 0.99)

Details:

These images have been gain corrected and are in MRC format. This is the full set of images collected for the project and includes those that were not finally used for image processing. data/micrographs/non_gain_corrected contains only the subset used in the reconstruction.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

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Citations

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He L, Bartesaghi A. (2026)

CryoSIP: unleashing protein high-resolution Cryo-EM via semantic-instance collaborative picking.

Deng Y, Wang S, Xiang M, Li Y, Zhuo L, Cao D, Fu X, Zou Q. (2026)

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Fonseca N, Duraisamy AK, Wang Z, Somasundharam S, Tayebinia M, de Oliveira LC, Ma M, Turner J, Patwardhan A, Kleywegt GJ, Hartley M, Morris KL. (2026)

CryoVirusDB: An Annotated Dataset for AI-Based Virus Particle Identification in Cryo-EM Micrographs.

Gyawali R, Dhakal A, Wang L, Cheng J. (2026)

Dual site targeting of the bacterial 70S ribosome by tetracyclines.

Devarkar SC, Lomakin IB, Wang J, Grada A, Bunick CG. (2026)

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements.

Jones HN, Deshmukh A, Pande K. (2026)

CryoGS: High-Quality Cryo-EM Homogeneous Reconstruction by Gaussian Splatting

Zeng B, Liu S, Cheng S, Xu G, Fan H. (2026)

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Protein Data Bank Japan News

[2026-06-17]

324件のPDBエントリーが新たに公開されました。（2026-06-17付）