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File upload

Choose files to be uploaded. Continue this process untill all necessary files have been added to the deposition. File uploads are confirmed in pop-up windows, please make sure that your browser allows them.


Selection of files

Select the relevant file option and click on "Select" button.

  • Uploaded map and masks will be converted to the EMDataBank map format. For large maps the conversion maybe slow - we appreciate your patience.
  • Map must have positive densities (contrast), irrespective to the type of electron microscope images (negative stain, or frozen-hydrated). If the contrast density for the map is found to be negative, a scale factor of (-1) will be applied to make the density positive, following the convention recommended by Heymann et al. J. Struct. Biol. 2005 (2):196-207
  • If you wish to upload map files larger than 1.5Gb please contact us directly to obtain alternate upload mechanisms before proceeding.
  • It is highly recommended that you upload a Fourier Shell Correlation (FSC) curve. You can generate a FSC XML file using PDBe FSC server (beta).
  • You may optionally upload files in the following compressed formats: '.zip', '.gzip' or '.bz2'.
  • Please, upload an image of your map (500x500 pixel, white background preferred) free from copyright restrictions to display on the atlas pages for your entry when the map is released.
Choose type of file you want to upload:    

List of uploaded files

File typeOriginal file nameInterpreted file(s)File size (kb)
Volume (map) filemy.mapmy.map, EMD-sample.map7814, 7814
Mask file(s)mask.mapmask.map, EMD-sample.msk7814, 7814
Image file(s)my.gifEMD-sample.gif84
FSC xmlfsc.xmlEMD-sample_fsc.xml7

Overwrite map

If you choose "Yes", when you press save you will overwrite the existing map file. Choose "No" to cancel the operation and keep the existing map.

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Overwrite structure factor file

If you choose "Yes", when you press save you will overwrite the existing structure factor file. Choose "No" to cancel the operation and keep the existing structure factors.

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Type of uploaded files

It is MANDATORY to upload ONE map (volume) file to continue submission. Other (optional) files that you may wish to upload include:
Files may be COMPRESSED before uploading as '.tar', '.zip', '.gzip' or '.bz2' archives.

Note about structure factors:
Please note that strictly speaking, 2D crystals also give lattice lines in the Z direction with continuous data along them which are equivalent to the helical layer-lines. However, it is normal to sample the lattice lines at an interval larger than the crystal thickness so as to generate h,k,l structure factors equivalent to X-ray structure factors. The unit cell can then be reconstructed using an X-ray 3D fourier transform program.

Note about layer-lines:
In the case of helices, the layer-lines are kept as continuous data (i.e. they are sampled at the radial points on the fourier transform) and the helix reconstructed using a Fourier-Bessel tranform.

Note about images:
Image files with extensions '.tif', '.png', '.gif', '.jpg' can be uploaded.

Note about FSC XML file:
Fourier Shell Correlation (FSC) data, in the form of an X-Y plot of correlation coefficient against spatial frequency (1/angstrom), can be uploaded as an XML file. The uploaded FSC data xml file must conform to the FSC schema. Schema and documentation, including visual representation, can be downloaded from EMDataBank FTP servers at RCSB or EBI.

Example: em_image_1.tif
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Map (volume) format

The uploaded map must be in the following supported formats:

Example: SPIDER
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Pixel spacing (size)

The pixel spacing, in angstroms, is determined from the magnification of the digitised micrograph and the sampling interval of the densitometer, scanner or CCD camera. For example, if micrograph magnification is 50,000 times and sampling step size of densitometer is 5.00 microns then: pixel spacing = step size / magnification = 5.0 e-4 / 5.0 e-4 = 1.00 angstrom.

It is usual to coarsen the images by some factor. For example, if the images are coarsened by a factor of 2, then the pixel spacing would 2.00 for the previous example.

Example: 2.00
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Pixel spacing (size)

The pixel spacing, in angstroms, is determined from the magnification of the digitised micrograph and the sampling interval of the densitometer, scanner or CCD camera. For example, if micrograph magnification is 50,000 times and sampling step size of densitometer is 5.00 microns then: pixel spacing = step size / magnification = 5.0 e-4 / 5.0 e-4 = 1.00 angstrom.

It is usual to coarsen the images by some factor. For example, if the images are coarsened by a factor of 2, then the pixel spacing would 2.00 for the previous example.

Example: 2.00
close

Pixel spacing (size)

The pixel spacing, in angstroms, is determined from the magnification of the digitised micrograph and the sampling interval of the densitometer, scanner or CCD camera. For example, if micrograph magnification is 50,000 times and sampling step size of densitometer is 5.00 microns then: pixel spacing = step size / magnification = 5.0 e-4 / 5.0 e-4 = 1.00 angstrom.

It is usual to coarsen the images by some factor. For example, if the images are coarsened by a factor of 2, then the pixel spacing would 2.00 for the previous example.

Example: 2.00
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Recommended contour level

The recommended contour level is the density value that yields the optimal representation of the molecular envelope when the volume is displayed in an isosurface representation.
The supplied number must be a raw density value between the minimum and maximum density recorded in the map file.

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Annotation details

Please supply any annotation details for the uploaded files.
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Mask (volume) format

The uploaded mask must be in the following supported formats:

Example: SPIDER
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Pixel spacing (size)

The pixel spacing, in angstroms, is determined from the magnification of the digitised micrograph and the sampling interval of the densitometer, scanner or CCD camera. For example, if micrograph magnification is 50,000 times and sampling step size of densitometer is 5.00 microns then: pixel spacing = step size / magnification = 5.0 e-4 / 5.0 e-4 = 1.00 angstrom.

It is usual to coarsen the images by some factor. For example, if the images are coarsened by a factor of 2, then the pixel spacing would 2.00 for the previous example.

Example: 2.00
close

Pixel spacing (size)

The pixel spacing, in angstroms, is determined from the magnification of the digitised micrograph and the sampling interval of the densitometer, scanner or CCD camera. For example, if micrograph magnification is 50,000 times and sampling step size of densitometer is 5.00 microns then: pixel spacing = step size / magnification = 5.0 e-4 / 5.0 e-4 = 1.00 angstrom.

It is usual to coarsen the images by some factor. For example, if the images are coarsened by a factor of 2, then the pixel spacing would 2.00 for the previous example.

Example: 2.00
close

Pixel spacing (size)

The pixel spacing, in angstroms, is determined from the magnification of the digitised micrograph and the sampling interval of the densitometer, scanner or CCD camera. For example, if micrograph magnification is 50,000 times and sampling step size of densitometer is 5.00 microns then: pixel spacing = step size / magnification = 5.0 e-4 / 5.0 e-4 = 1.00 angstrom.

It is usual to coarsen the images by some factor. For example, if the images are coarsened by a factor of 2, then the pixel spacing would 2.00 for the previous example.

Example: 2.00
close

Recommended contour level

The recommended contour level is the density value that yields the optimal representation of the molecular envelope when the volume is displayed in an isosurface representation.
The supplied number must be a raw density value between the minimum and maximum density recorded in the map file.

close

Annotation Details

Please supply any annotation details for the uploaded files.
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File type

The file type which was selected from the above dropdown list.

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Original file name(s)

File names may vary slightly to that what was uploaded originally.

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Interpreted file(s)

The file(s) processed by the EmDep system, these names are for internal use and do not correspond to the actual file uploaded.

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File size(s) (kb)

The size of the file based to the in interpreted file.

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