Composite Map Deposition Guide

Introduction

The deposition of a composite map entry set follows the recommendations laid out by the community in 2020 (https://doi.org/10.48550/arXiv.2311.17640). In accordance with these recommendations we require the composite map, all constituent maps (henceforth referred to as focused refinements), and the un-focused full structure (henceforth known as a consensus map) to be deposited as their own entries so that validation can be carried out for each of the deposited maps. In addition, the composite map entry must appropriately reference the focused refinements and consensus map. In this tutorial we will summarise the workflow to deposit a composite map set of entries in the most efficient manner possible.

In this tutorial we will use publicly available data EMDB: EMD-43299 and PDB: 8VK3.

Graphical Overview

To complete a deposition of a composite map set you will need several maps. These maps are described graphically below and EMD-IDs are included for an example composite map deposition set that can be found on the EMDB website. 

 

 

 

Summary

Reminder: A composite map deposition must consist of separate depositions describing the composite map, consensus map, and focused map(s).

  1. Create a composite map deposition (Do not submit).
  2. Create focused refinement and consensus depositions (after completing composite map deposition). Pull the metadata from the composite map deposition. 
  3. Associate the focused refinement and consensus depositions to the composite map deposition by filling the IDs in the “related entries” and submit.

Deposition Table

  Composite Map Consensus Map Focused Map(s)
Primary Map

Required

Required

Required
Half-maps

Optional (If provided they must be composite half-maps)*

Required

Required
Entry Image

Required

Required

Required
mmCIF file

Optional (unless also depositing a model)

Optional (unless also depositing a model)

Optional (unless also depositing a model)
FSC Curve file

Optional (If provided it should be calculated from the composite half-maps and described appropriately)**

Optional

Optional
Mask(s)

Optional

Optional

Optional
Additional Map(s)

Optional

Optional

Optional
Layer line file

Not expected

Not expected

Not expected

*If depositing half-maps as part of a composite-map deposition, only composite half-maps should be provided. Consensus and focused half-maps should be provided with the relevant, separate, depositions.

**EMDB recommends using the mean resolution of the focused maps as the resolution of the composite map

Step by Step

  1. Start the composite map deposition

We recommend you start by creating the composite map deposition. This entry should contain all the metadata relevant to the other entries and we will be able to copy this across to those entries later. The deposition setup for this can be seen in Figure 1. Don’t forget to sign in with ORCID to enable easy access to all your depositions later on. In this example the model has been built into the composite map, therefore the composite map and model will be deposited together so that map-model validation can be carried out in this entry.

Figure 1: Setting up a composite map deposition.

Once the setup is complete and you have clicked ‘start deposition’ you should receive the details to login to the deposition via email and find it in your ORCID list of depositions if you were signed in with ORCID. The first step is to upload your files, an example of which can be seen in Figure 2, since this is a composite map deposition no half-maps are expected. Don’t forget that the mmCIF file format is also a metadata file format. All metadata provided in the uploaded mmCIF will automatically be used to fill the deposition interface. For users who wish to learn more about mmCIF files the mmCIF dictionary is available online (https://mmcif.wwpdb.org/) and example mmCIF files with EM metadata are available from the EMDB (e.g. https://www.ebi.ac.uk/emdb/EMD-43299?tab=links) under the Metadata section as a cif.gz download.

 

Figure 2: File upload page for a composite map entry.

After completing this section, the deposition interface will allow all metadata to be entered. Anything that was in the mmCIF file should already be in the deposition interface. Once all metadata sections are filled the entry should look similar to Figure 3. 

DO NOT SUBMIT THE DEPOSITION YET!

Figure 3: a completed composite map deposition user-interface

We can now log out of this entry and start the deposition of the other entries.

2. Focused/Consensus map deposition

Now we are going to deposit the focused map(s) and consensus map. There should be one or more  focused refinements and one consensus map deposited for every composite map deposited. In this example we will show you the deposition of a single focused refinement map, the method for depositing the others should be identical. 


Once again we start by setting up the deposition (Figure 4). This time we will approach it as a regular map deposition (not composite). We have also already deposited coordinates with the composite map, as a result we will deposit the focused refinement(s) and consensus map without a coordinate model. If you have good reason to deposit portions of the model with the focused refinement(s) you are free to do so but where efficiency of deposition is concerned depositing the maps alone will be quicker.

Figure 4: Setting up a deposition for a focused/consensus map


As before, once the deposition is started you will get to the file upload screen. This time you can use the ‘based on a previous wwPDB deposition’ (Figure 5) option during the file upload process. This allows you to copy across various metadata from a previous deposition. Once the file upload is complete you should now see that, where possible, metadata has been transferred to the new deposition (Figure 6). This deposition can now be completed and submitted. Once submitted you will receive an EMD accession code which is needed for the next step.

Figure 5: Copying metadata from the composite map deposition

Figure 6: Metadata pulled from a previous deposition automatically fills relevant pages, in some cases already providing all required information (green tick).

3. Complete the composite map deposition

Now that you have completed all your focused refinement and consensus map depositions we can return to the composite map deposition and associate the new depositions to them. To do this we are going to go to the ‘Related entries’ page and fill the table out. The ‘content type’ drop-down menu will allow you to define the maps as focused or consensus. An example of this can be seen, including how it will be displayed on the EMDB website, in Figure 7. Once this is complete you are ready to submit the composite map deposition. If the composite map is accidentally submitted prematurely, or more entries are generated that you wish to be associated with the composite map after its submission, this can be corrected by contacting a wwPDB biocurator through the communication tab in OneDep. 

Figure 7: Filling in the related entries for the composite map deposition.

Recommendation from EMDB: It is advised to use correlated yet distinct titles for entries related to a composite map.