We welcome your feedback on the OneDep Deposition system and on this tutorial. Please let us know if the instructions need clarification or if you have encountered a problem during deposition at firstname.lastname@example.org.
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:
Depositors are encouraged to also upload the following files:
File upload checks for NMR depositions
During file upload, the following checks are performed:
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.
Upload of the following files is mandatory:
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:
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.).
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.