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Depositor – Deposit data in OneDep

The OpenEM Depositor helps you prepare an electron microscopy dataset in SciCat for deposition in the wwPDB OneDep system. OneDep handles depositions to the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB).

The Depositor reuses scientific metadata stored with the dataset in OSC-EM format, converts it to the mmCIF format accepted by OneDep and combines it with the files you provide. For supported map files, it also attempts to determine the pixel spacing from the file header.

The workflow consists of the following stages:

  1. Open an eligible OpenEM dataset in SciCat.
  2. Choose the electron microscopy method and deposition content.
  3. Provide the depositor information required by OneDep.
  4. Add and review the files required for the selected deposition.
  5. Transfer the prepared files to OneDep or download them for manual upload.
  6. Complete, validate and submit the deposition in OneDep.

Important

The Depositor prepares and transfers files, but it does not replace the OneDep deposition workflow. Review the transferred metadata, complete all remaining mandatory fields and submit the deposition in OneDep.

Before you begin

Make sure that:

  • you can sign in to SciCat;
  • the dataset is registered as an OpenEM dataset and is visible to you;
  • you are authorised to deposit the dataset and its associated files;
  • data acquisition and processing are complete;
  • the scientific metadata in SciCat is accurate and sufficiently complete;
  • you have a valid email address and the ORCID iDs of all users who must have access to the OneDep deposition; and
  • the required maps, model and supporting files are available on your computer.

Check the dataset record before starting. In particular, review the sample, instrument, acquisition, reconstruction and processing metadata. Correct problems at their source where possible; values transferred to OneDep must still be reviewed by the depositor.

Warning

Starting a deposition shares the selected files and metadata with an external repository. Confirm that the data can be shared and that the correct release or embargo policy has been agreed with the principal investigator and all relevant collaborators.

Decide what to deposit

The required files depend on the experimental method and on whether the deposition includes an atomic model. Prepare the files before opening the Depositor.

Deposition content Files to prepare Notes
EM map without an atomic model Primary map and an entry image Creates an EMDB deposition. OneDep may request additional information or method-specific files.
EM map with an atomic model Primary map, atomic coordinates and an entry image Creates a combined PDB/EMDB deposition. Prefer coordinates in mmCIF format.
Electron crystallography Atomic coordinates and either structure-factor data or a density map The exact file set depends on the experiment and must be confirmed in OneDep.
Supporting map data Half maps, masks and additional maps, where applicable Map metadata includes contour level and pixel spacing.
Validation data FSC curve, where applicable Providing an FSC file is strongly recommended for relevant EM methods.

The Depositor backend recognises the following electron microscopy methods:

  • helical reconstruction;
  • single-particle analysis;
  • subtomogram averaging;
  • electron tomography; and
  • electron crystallography.

OneDep determines the definitive mandatory file set from the selected method and whether coordinates are included. Follow any validation messages shown by the Depositor or OneDep.

Supported files and automatic processing

The integration supports the following principal file categories:

File category Typical format Depositor processing
Primary, additional, half or mask map MRC or CCP4; gzip-compressed variants may be accepted Reads the header where possible and transfers pixel spacing, contour level and description to OneDep.
Atomic coordinates mmCIF or PDB; gzip-compressed input may be accepted Converts PDB input to mmCIF when required and merges OSC-EM metadata into the resulting coordinates file.
Metadata only Generated mmCIF Converts the OSC-EM metadata associated with the SciCat dataset into metadata.cif.
Entry image Image accepted by OneDep Transfers the image for public display with the EMDB entry.
FSC curve XML accepted by OneDep Transfers the validation data without map-header processing.

For an MRC or CCP4 map, the Depositor calculates the pixel spacing for each axis from the cell dimensions and sampling information stored in the map header. If the header is incomplete or unsupported, enter and verify the values manually in OneDep.

Note

Automatic conversion reduces duplicate data entry; it does not guarantee that every OneDep metadata field is complete. Information that is not represented in OSC-EM must be entered later in OneDep.

Open the Depositor

  1. Open SciCat and sign in.
  2. Find the dataset you want to deposit and open its details page.
  3. Open the dataset action for depositing data in an external repository.
  4. Select OneDep if the interface asks for a target repository.

Only eligible datasets are offered to the Depositor. If the action is not available, first check that the record belongs to you or one of your groups and that it is marked as an OpenEM dataset.

1. Configure the deposition

Select the method that describes the experiment. Then specify whether the deposition contains atomic coordinates. This selection determines whether the result is intended for EMDB only or for both PDB and EMDB, and which files OneDep requires.

Before continuing, verify that:

  • the selected method matches the dataset;
  • the atomic-model option matches the files you intend to deposit; and
  • the scientific metadata displayed by the Depositor belongs to the selected dataset.

2. Provide depositor information

Enter or review the information used to create the OneDep deposition:

Field What to enter or verify
Email A monitored email address for communication about the deposition.
ORCID iDs The ORCID iDs of users who must be associated with the deposition or have access to it. Use the full 16-digit identifier.
Country The country associated with the deposition, if requested.
OneDep authorisation The credentials or token requested by the deployed integration. Never share these with support staff or include them in screenshots.

The current Depositor backend expects a OneDep authorisation token. The latest backend release reviewed for this guide did not yet support automatic ORCID-based authorisation.

3. Add the deposition files

Add each required file and assign the correct OneDep file category. Do not infer the category from the filename alone.

  1. Add the primary map and classify it as the primary volume map.
  2. If the deposition contains an atomic model, add the coordinate file.
  3. Add the entry image required for the EMDB record.
  4. Add applicable half maps, masks, additional maps and the FSC curve.
  5. For each map, enter or review the contour level and description.
  6. Wait for each upload to finish and review all warnings and errors.

For map files, compare the automatically detected pixel spacing with the value used during reconstruction. A successful upload does not by itself prove that the value is scientifically correct.

Warning

Assigning the wrong file category can create misleading metadata or cause OneDep validation to fail. If you are unsure whether a map is a primary map, half map, mask or additional map, check the processing records or ask the person who produced it.

4. Review the generated metadata

The Depositor converts the dataset's OSC-EM metadata to mmCIF. When coordinates are supplied, it creates a coordinates file containing both the model and the converted metadata. For a map-only deposition, it creates a separate metadata.cif file.

Review at least:

  • dataset and experiment identity;
  • sample and specimen information;
  • microscope, detector and acquisition parameters;
  • reconstruction and processing parameters;
  • pixel spacing and contour levels; and
  • filenames and OneDep file categories.

Return to SciCat or the relevant source system if a transferred value is wrong. Record any manual corrections made later in OneDep so that the catalogue record can also be improved.

5. Transfer to OneDep

When all required files and metadata have been reviewed, start the transfer to OneDep. Do this once and wait for the response. OneDep checks whether the file set is complete and reports format or consistency problems.

If direct transfer is unavailable, use the Depositor's download option to create the prepared mmCIF file, then upload the generated file and the remaining deposition files manually through the OneDep website.

Keep the OneDep deposition identifier shown after creation. You need it to find the deposition again and to request support.

6. Complete the deposition in OneDep

Continue in OneDep after the files have been processed:

  1. Open the deposition using the link or identifier supplied by the Depositor.
  2. Review the processed files and resolve all errors.
  3. Complete the mandatory administrative, author, citation, sample and release information not supplied by OpenEM.
  4. Review the OneDep validation report.
  5. Select the appropriate release or hold option.
  6. Submit the completed deposition for biocuration.

After hand-off, make requested corrections in OneDep unless your local support team explicitly instructs otherwise. Preserve the PDB and/or EMDB accession codes and add them to the relevant SciCat record or project documentation when they become available.

Troubleshooting

The Depositor action is not shown

  • Confirm that you are signed in and have access to the dataset.
  • Check that the dataset contains the OpenEM keyword.
  • Reload the dataset details page after correcting the record.
  • Contact Support if another eligible dataset shows the same problem.

OneDep authorisation fails

  • Check that the token or session has not expired.
  • Sign in to the correct OneDep environment and create a new token if required.
  • Do not repeatedly submit the form; first confirm whether a deposition was already created.
  • Never send a token, password or session cookie to support staff.

A file cannot be uploaded or processed

  • Check that the file is complete, readable and in a supported format.
  • Verify that the selected OneDep file category matches the file.
  • For compressed input, confirm that the gzip archive is valid.
  • Record the filename, file category and complete error message before retrying.
  • Replace the file only after correcting the reported problem.

Pixel spacing is missing or implausible

  • Confirm that the map is an MRC or CCP4 file with a valid header.
  • Compare the detected values with the reconstruction settings.
  • Enter the correct spacing manually in OneDep when automatic extraction fails.
  • Report systematic header-reading problems to support without attaching confidential research data unless requested through an approved channel.

OneDep reports missing files

  • Recheck the selected experimental method and atomic-model option.
  • Add every file marked as mandatory by OneDep.
  • For a model deposition, confirm that both coordinates and the primary map were supplied.
  • For an EMDB deposition, confirm that an entry image was supplied.

The transfer stops or returns an unclear error

  • Keep the SciCat dataset identifier and, if one was created, the OneDep deposition identifier.
  • Note the time, selected method, failed step and complete error message.
  • Check whether the deposition already exists in OneDep before starting again.
  • Contact Support with this information, but do not include credentials or tokens.

Documentation TODOs

Before this chapter is considered complete:

  • [ ] Verify the available target repositories and production status of the OneDep integration.
  • [ ] Walk through a map-only and a map-plus-model deposition in the deployed SciCat environment.
  • [ ] Replace generic UI wording with the exact field and button labels.
  • [ ] Add screenshots for opening the Depositor, choosing a method, adding files, reviewing metadata and completing the hand-off.
  • [ ] Confirm authentication, token handling and ORCID requirements.
  • [ ] Confirm supported formats, compression types and effective upload limits.
  • [ ] Add the authoritative method-specific list of mandatory and optional OneDep files.
  • [ ] Document the manual-download fallback and generated filenames.
  • [ ] Document how PDB and EMDB accession codes are recorded back in SciCat.
  • [ ] Test every troubleshooting instruction against the production deployment.