EMPIAR-10005 - TRPV1 dataset taken on a K2 direct electron detector [multiple data sets in MRC format]

EMPIAR-10005

TRPV1 dataset taken on a K2 direct electron detector [multiple data sets in MRC format]

Publication:

Structure of the TRPV1 ion channel determined by electron cryo-microscopy

Liao M, Cao E, Julius D, Cheng Y

Nature 504 (2013) 107-112

PMID: 24305160

DOI: doi:10.1038/nature12822

Related EMDB entry:

EMD-5778

Deposited:

2013-10-25

Released:

2013-12-04

Last modified:

2016-01-19

Imageset size:

6.32 TB

Imageset DOI:

10.6019/EMPIAR-10005

Experimental metadata:

Download xml json

Version history:

2015-07-13

REL

Added two datasets - raw multi-frame micrographs and summed-frame micrographs

2015-12-04

REL

Corrected the resolution of "TRPV1 raw multi-frame micrographs" image set to be 0.6078 ‎Å instead of 1.2156 ‎Å

2016-01-18

REL

Added picked_coordinates directory to micrographs

2016-01-19

REL

Moved picked_coordinates directory so that it is under micrographs/summed_frames and updated annotation for picked coordinates

Contains:

tilt series
micrographs - multiframe
micrographs - single frame

Image Sets

1. TRPV1 picked particles

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

35645

Image size:

(256, 256)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.2156, 1.2156)

Details:

(1)
"tv1_f01-30.mrc" contains the particles from summing frame 1 to 30.
"tv1_f03-16.mrc" contains the particles from summing frame 3 to 16.
All particles are boxed after motion correction. The particles are normalized (mean=0, standard deviation=1), and also contrast-inverted (white particles with black ground).
"tv1_relion_data.star" is the final output of RELION auto-refine, containing all particle information.

(2)
30 particle stacks in MRC format, named as "f01.mrc", "f02.mrc", etc., store all frames of all particles. For example, "f01.mrc" contains the 1st frame of each particle, and "f02.mrc" contains the 2nd frame of each particle. These particles are boxed after motion-correction, and a direct sum should generate particles as those in "tv1_f01-30.mrc", except that the particles in "f??.mrc" are not normalized and are in original contrast (black particle with white background).

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. TRPV1 raw multi-frame micrographs

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

966

Image size:

(3710, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.6078, 0.6078)

Details:

These files are named stack_0001.mrc -> stack_0966.mrc

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. TRPV1 summed frame micrographs

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

966

Image size:

(3710, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.2156, 1.2156)

Details:

These files are named stack_0001_2x_SumCorr.mrc -> stack_0966_2x_SumCorr.mrc
The picked particle coordinates can be found in:
micrographs/summed_frames/picked_coordinates
They correspond to 3x binned images, so the values need to be multiplied by 3 to correspond to the unbinned image.
The TRPV1_coords_88915 folder reflects the initial particles that were selected for further processing. The TRPV1_coords_35645 one relates to the final particles used to obtain the high-resolution map (meaning: we initially extracted 88915 particles, then post 2d and 3d classification we proceeded to minimize the stack by subselecting the final group of particles from “star” files -> the 35645 particles).

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)

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