Video Tutorials

X-ray Deposition: file upload, validation, and provide mandatory information

Ligand Deposition: Review and confirm suggested matches to your ligand

Ligand Deposition: How to provide mandatory chemical information

PDBx/mmCIF Data Standard and PDB Data Deposition

Small Molecules in the PDB

OneDep and Small Molecules Tutorial



Tutorial: Using the wwPDB OneDep System

For Coordinate Deposition:

  1. The top-level deposition page at http://deposit.wwpdb.org/deposition/ has two functions: the left panel is used to log into the system using a deposition ID and password, and the main panel on the right can be used to start a new deposition. When starting a new deposition, it is important that the depositor's country of origin be present in order for the best support to be provided. After the form has been filled out and "Start Deposition" has been selected, a Deposition ID and password (depositors have the option to create their own or let the system create one) will be sent to the depositor via e-mail.
  2. The Deposition ID and password can be used to log in to the deposition system using the left-hand panel. The Deposition ID is displayed at the top of the page upon login. Once inside the deposition system, select the "File upload" option from the left-hand navigation panel to upload coordinate and structure factor files (for X-ray structures). Once the files have been uploaded, select the corresponding file types from the drop down menus.
  3. After file upload has been initiated, initial validation calculations begin. The depositor will receive an e-mail notification when validation has completed. Once validation is complete, validation reports are available for review under "Validation Reports" at the bottom of the navigation panel.
  4. It is strongly recommended that you review the "Upload Summary" page carefully as it indicates which data have been uploaded and interpreted correctly.
  5. Use the left-hand navigation panel to move among the different data entry pages.
    1. Yellow icons indicate folders that contain related data entry pages. Clicking on the icon will open and close the folder.
    2. Red exclamation icons represent pages that require the input of mandatory data. These mandatory items will appear in red. It is recommended that you also complete as many non-mandatory fields as possible.
    3. Green check marks indicate that all mandatory data items on a page have been entered.
    4. Data can be reviewed and edited on each individual entry page.
    5. A data field with a red box and warning text must be corrected before submission.
    6. A data field with a yellow box and warning text indicates an unusual value has been entered and should be checked.
  6. As you enter data, the list of minimum mandatory items required for submission is automatically checked by the system. In the left-hand navigation panel, two bars indicate the percentage of completeness of the deposition:
    1. The Submit button is shaded by the percentage of mandatory data items submitted. Clicking on this bar will provide a list of the missing mandatory items. The entry can be submitted when the button is completely green.
    2. The Data Supplied button is shaded by the percentage of all possible data items that have been provided.
  7. To review sequence information, select a molecule page from the "Macromolecules" folder. This page contains summary information about the macromolecule source and reports the results of a sequence consistency check between the author-provided sample sequence and the coordinate sequence. If there is a discrepancy, the depositor must provide either a corrected sample sequence or a new coordinate file that corrects the discrepancy.
  8. To review ligand information, select the "Ligands" page from the left-hand navigation panel. This page reports on the comparison of ligands in the uploaded coordinate file against the Chemical Component Dictionary (CCD). No further action is needed when an exact match is found. If there is a close match, the possible matches found by the system must be reviewed. If there is no match in the CCD, or if there is a chemical difference between the target and the closest match, the depositor is required to either (a) provide the three-letter code of an alternative ligand present in the CCD, (b) provide a SMILES or InChI string for the ligand, or (c) upload a chemical diagram of the ligand. There is an additional option to upload a refinement monomer library file.
  9. Coordinate and experimental data files can be replaced at any time prior to submission using the "Replacement Upload" page available from the navigation panel.
  10. The "Communication" page available from the navigation panel should be used for all correspondence with the wwPDB. This page will store all messages related to the deposition.
  11. Prior to submission, depositors must agree to the Terms and Conditions listed on the "Summary & conditions" page.
  12. Depositors are also asked to review the initial validation report available on the "Validation Reports" page and indicate their acceptance.
  13. Once all mandatory items have been captured (all pages show green check marks on the navigation menu) the "Submit deposition" button in the top left corner will become completely green to indicate that the entry can be submitted.
  14. Processed files and validation reports send by PDB biocuration staff will be available for download and review at the "Communication" page.

For NMR-specific Depositions:


Deposition start page

At the start of deposition, the depositor will be asked to provide information about the experimental methods employed to determine the structure.

For an NMR deposition that includes a coordinate file, select "Solution NMR" or "Solid-state NMR" as the Experimental Method. Once "Solution NMR" or "Solid-state NMR" has been selected as the Experimental Method, you will see questions about whether you are depositing coordinates and/or experimental data. After you answer the questions, the PDB and BMRB check boxes will automatically be checked for the appropriate accession codes. Press the "Start deposition" button to initiate a deposition session.

For an NMR deposition that does not include a coordinate file, select "Solution NMR" or "Solid-state NMR" as the Experimental Method and you will then be asked "Are you depositing coordinates with this submission?". Select "No, experimental data only", and you will see that BMRB is the only requested accession code, and a "Deposit NMR data at BMRB" button will appear at the bottom of the screen. Once you click the button, you will then be re-directed to the BMRB deposition start page. Please note that if you make a BMRB-only deposition, later deposition of associated coordinates will require that an additional, new PDB-only deposition be made.


File upload requirements

Upload of these files is mandatory:

  • Coordinates
  • Restraints
  • Chemical shifts

Depositors are encouraged to also upload the following files:

  • Peak lists


File upload checks for NMR depositions

During file upload, the following checks are performed:

  1. Consistency checks are performed on the coordinate file to make sure each model has the same chemistry (identical atoms).
  2. Chemical shift value checks are performed on the chemical shift file.
  3. Atom nomenclature checks are performed on the chemical shift and coordinate files.

If there are any warnings or errors generated by these checks, they will be reported as follows:

Warning messages: Warning encountered upon file upload will be presented in the "File format validation for model coordinates and data files" window. For NMR entries, warning messages provide information about chemical shift values outside of acceptable ranges. Warning messages are provided for depositors to review and either verify or correct as appropriate.

Error messages: Errors encountered upon file upload will be presented in two places: (1) on the diagnostic screen (headed by a graphic of red gears) that appears after the "Populate" or "Repopulate" button on the "File upload" page has been pressed, and (2) on the "Upload Summary" page of the deposition interface. For NMR entries, error messages highlight atom nomenclature issues that must be corrected. If an error is present, new coordinate and/or chemical shift files must be uploaded before the deposition can be completed.

Entering NMR Data into the deposition interface

For NMR depositions, it is best to enter information starting from the top of the left-hand navigation panel and working downward sequentially, page by page, as some values on later pages (lower on the navigation panel) are dependent upon information entered on earlier pages (higher on the navigation panel).

In particular, the chemical shift connection page cannot be completed until after mandatory data items in the NMR experimental section and NMR software section have been completed. The chemical shift connection page links data used to assign the chemical shifts with information contained in other NMR sections, i.e., chemical shift files names, chemical shift references, NMR samples, sample conditions, NMR experiments, and software.

In addition, the spectral peak list section becomes mandatory when NMR peak list files are uploaded.

For Electron Microscopy Volume Map Depositions:

File upload requirements

Upload of the following files is mandatory:

  1. Primary map (.mrc or .ccp4 format, may use gzip or bzip2 compression) along with voxel size and recommended contour level
  2. Half maps (as used for FSC calculation; two maps must be uploaded). Half-maps must be uploaded for SPA, STA, and Helical 3DEM depositions. These half-maps should remain unmodified from their original output in the 3D refinement protocol used.
  3. Image of the map (500 x 500 pixels in .jpg, .png, etc. format)
Upload of these additional files is encouraged by EMDB:
  1. Additional maps
  2. FSC curves
  3. Layer line data
  4. Structure factor data
All of these files are made publicly available upon release of the EMDB entry.

Macromolecules page for EMDB map-only deposition

Depositors may provide sample sequence information along with appropriate UniProt and/or GenBank references. For a map-only deposition (no coordinates provided), sequence information is optional.

Sample information for an Electron Microscopy experiment

Information about the sample used in an electron microscopy experiment and about its source(s) is collected in a hierarchical fashion. An example is provided below:

  1. Overall sample description: ribosome
    1. subcomponent: 50S large ribosomal subunit
      1. subcomponent: 5S rRNA
      2. subcomponent: 23S rRNA
      3. subcomponent: SeC6
      4. subcomponent: 50S ribosomal protein L4
    2. subcomponent: 30S small ribosomal subunit
      1. subcomponent: 16S rRNA
      2. subcomponent: eIF2
      3. subcomponent: 30S ribosomal protein S1
      4. subcomponent: 30S ribosomal protein S2

NOTE: Subcomponents can be added and/or deleted as necessary, but deletion of a subcomponent will result in deletion of all child subcomponents (e.g., deletion of b. from the example above will also delete i., ii., iii., and iv.).

Experimental information

There are five sections in the "EM experiment" folder in the deposition interface. Within each of these sections are data items that link to other experimental sections as well as to back to the overall sample description and its subcomponents (see previous section). As such, it is recommended that the overall sample description and any necessary subcomponents be completed prior to the entry of experimental information into the "EM experiment" section. In addition, it is also recommended that the experimental sections be completed sequentially from the top down.

Details regarding each subsection follow. Please note that there are mandatory items in most of the experimental sections that must be filled in before the deposition can be finalized and submitted.

  1. Specimen preparation. This section comprises information regarding sample vitrification, staining, embedding, and shadowing, as well as details about the sample grid and its pretreatment, film support, and crystal formation (where applicable).
  2. Microscopy. This section comprises comprehensive information regarding the microscope(s) used for data collection, including electron source, specimen holder, energy filters, etc., as well as the microscope settings and other parameters used for each imaging session (magnification, defocus, alignment procedure, etc.). Multiple imaging sessions can be included within the deposition interface by clicking the "+" button at the bottom of the "Microscopy" page.
  3. Image recording. This section comprises information about the detector(s) or other device(s) used for image recording, including the both the physical properties of the detector and the manner in which the images were collected, e.g., data handling during and directly after capture, number of images, rate of movie frame collection, etc. As in the "Microscopy" section, the "+" can be used if multiple detectors were used for image recording.
  4. Reconstruction. This section comprises the details of the method or methods used to generate three-dimensional map(s) from two dimensional images, including particle selection, classification, alignment, angular assignment, and reconstruction. Information about multiple reconstructions can be included.
  5. Fitting interpretation. This section is for information about the fitting of pre-existing atomic coordinates and/or ab initio models to the map, if applicable. Multiple fitting instances can be added (by clicking the "+" button at the bottom of the page) and each instance can accommodate multiple starting models if necessary. Additional details that can be provided include software and settings for any model building, fitting, and/or refinement that was used to generate the final model.

Importing data in repeated depositions

When depositing a related structure, the OneDep File upload page offers Based on a previous wwPDB deposition. This lets you copy selected metadata from a previous wwPDB entry into your new deposition.

How to use it

  1. Open File upload in your deposition session at deposit.wwpdb.org.
  2. Under Based on a previous wwPDB deposition, select Yes.
  3. Enter the previous deposition ID (D_xxxxxxxxxx) and authenticate with the related entry's password, or sign in with ORCID if the entry is yours. The previous entry must be deposited at the same wwPDB site as the current entry.
  4. Select the metadata categories to import (for example authors, citation, funding, keywords, macromolecules, or method-specific experimental information).
  5. Upload your new coordinate, map, and/or data files, then process them as usual.

After processing, the Summary page shows which categories were imported, skipped, or blocked, with a detailed import log.

What can be imported

Typical categories include authors and contact information, entry keywords, citation information, funding information, macromolecules, and X-ray, NMR, or EM experimental information. Method-specific options appear only when the previous and current depositions use compatible experimental methods. For EM, the reconstruction sub-method must also match to import EM experimental information.

Coordinates, maps, and structure factors are not copied from the previous entry: you always upload new data files for the current deposition.