2014-12-17 : 2706 EMDB map entries, 759 PDB coordinate entries PDBe | RCSB    

One-stop shop for 3DEM deposition and retrieval

 

FAQ

EM map deposition questions

EM map-derived coordinate model deposition questions

EM map and model access questions

 

EM map deposition answers

How do I begin a map deposition to EMDB?
Go to http://www.emdatabank.org/deposit.html and select either the UK or US deposition site link.  If this is your first deposition please also look at our deposition guide.

What map formats are accepted by EMDB?
Maps can be deposited in mrc, ccp4, or spider formats; they are converted to standard ccp4 format for redistribution in the EMDB.

My map is bigger than 1.5 GB, what should I do?
The maximum file size that can be handled through our http servers is 1.5 GB. For large files, please notify the processing site annotation staff by email. The staff will send ftp site information where the map can be uploaded.

What is the difference between a deposition session id and an EMDB accession id ?
When you initiate an EMDB deposition, you are assigned a session id (reference code). The session id is a "private" identifier known only to the depositor and the deposition site. When you complete your deposition and submit it to EMDB, you are assigned a public accession code by email. The public accession code is the id you should provide to journals when indicating your EMDB submission; it is also the code by which you can access to your entry in the publicly available EMDB search and atlas pages.

We have two maps for one submitted manuscript, one native, one with cofactor protein. Do we need to complete two separate depositions?
If the maps were generated from different specimen preparations/imaging experiments you will need to make two separate depositions. Time saving tip: complete the submission for the first map (deposition session 1), and then for the second map (deposition session 2) select the option "based on previous submission." You will need to provide the 1st deposition session id and password in order to use this option. 

How can we deposit multiple 3D volumes generated from imaging of a single specimen?
EM reconstruction methods are beginning to yield ensembles of maps representing multiple conformations/enzymatic states within a heterogeneous population of imaged particles.  If you need to deposit multiple maps of this type please see answer above, you may also contact help@emdatabank.org for guidance.

I forgot my deposition session id and/or password, how can I complete my entry?
Send an email message to help@emdatabank.org to let us know. One of our team members will get back to you with the missing information.

Our manuscript has not been officially accepted yet, so please do not release our entry.
The only part of your submission that is released immediately is the experimental information in the header. The header information will only be released after you have had an opportunity to comment on the curated data. The map will not be released until the hold period has elapsed which can be on publication (HPUB), or 1 year from deposition. The map will only be released immediately if you have requested this at the release option stage.

I would like to update my entry with a corrected map, what should I do? 
The corrected map can be emailed to the annotation staff, size permitting. Otherwise, please notify the annotation staff and they will send ftp site information where the map can be uploaded. The old map will be replaced by the new one.

I received an email stating that my map is being released. When will it be available in the EM Data Bank?
EMDB follows a weekly release cycle. Maps queued for release before Thursday at 5pm (UK) will be available from EMDB on the following Wednesday.

My structure has been published, how can I update the citation information for my entry?
Please contact the annotation staff and they will be happy to update the information.

 I resolved an icosahedral virus as an asymmetric particle, or using lower symmetry. Should I classify my map as 'icosahedral virus' or 'single particle'?
Please use the single particle category for your map entry.

The journal I am targetting requires editors and referees access to the structure while my manuscript is under review. Does EMDB provide confidential access to editors or referees if a structure is "on hold"?
We encourage you to deposit your maps and map-derived fitted models starting from the EMDataBank portal (http://emdatabank.org/deposit.html).  Unreleased structural data on hold, both maps and coordinate sets, are kept strictly confidential. After deposition, you will immediately receive EMDB ids for your map entries and PDB ids for your map-derived model entries, which you may include in your manuscript.   In addition, for PDB  model entries you can obtain validation reports that provide assessments of model quality while keeping the coordinate file confidential. We encourage journal editors and referees to request validation reports from depositors as part of the manuscript submission and review process. The reports are date-stamped, and display the wwPDB processing site logo. For more information see http://www.wwpdb.org/validation.html.

 

EM map-derived coordinate model deposition answers

I have fitted coordinates for my map, can I include them with my map entry?
Fitted coordinate models for EM entries need to be deposited to the PDB. Upon completion of map deposition to the EMDB using EMDEP, the user is presented with the option to deposit one or more coordinate models to the PDB using EM-AUTODEP (PDBe) or EM-ADIT (RCSB PDB). Experiment-related metadata entered in EMDEP will be automatically transferred to the PDB coordinate deposition.  Polymer coordinates may be full-residue representations or alpha-carbon or phosphate backbone traces.  Homology models fitted to the map are also accepted.

I obtained coordinates from PDB and used rigid-body fitting to place them into my map. Can I deposit these coordinates to PDB?
You can deposit coordinates derived from any fitting protocol, including rigid-body fitting, flexible fitting, or de novo tracing. The deposited coordinates must be aligned and in frame with the map.

My fitted coordinates correspond to a protein homolog. During the PDB deposition, should I provide the species information/sequence information for the EM sample or for the protein homolog?
The species information should correspond to your EM sample, but the sequence information should correspond to the protein homolog/fitted model.

How are coordinates derived from EM reconstructions validated?
Currently, model fit to an EMDB map is validated through visual inspection of the deposited map + model pair using a 3D graphics program.  Models are also checked for correct stereochemistry and clashes.  We are working with the EM community to develop improved standards for validation of maps and fitted models (see http://vtf.emdatabank.org).

We have a new coordinate model fitted into an EMDB map entry authored by another research group. Can we deposit our coordinates?
Yes, you can deposit your coordinates to one of the wwPDB sites (http://www.wwpdb.org/), selecting experiment type electron microscopy. Include the EMDB map accession id (EMD-XXXX) as the associated EM volume of your coordinate deposition. The PDB policy regarding re-refined entries applies: "A re-refined entry may be deposited prior to publication but will not be processed (will have REFI status) or released until the associated publication has become publicly available." No changes will be made to the EMDB map entry.

 

EM map and model access answers

How can I find/download a map or browse the EMDB database?
Go to http://www.emdatabank.org/search.html and select either the UK or US EMSEARCH query page. You can search by id, author, title, release date, and more.

How can I view EMDB maps?
We provide a java-based viewer on EMDataBank atlas pages, OpenAstexViewer, which allows the user to view the EMDB entry map at different contour levels and to also display any map-derived coordinate model PDB entries. To use the viewer, go to the visualization tab of the atlas page (as in this example) and click the "Launch" button. To view the map on your own computer, you will first need to download the map from the EMDB atlas page ("downloads" tab, see example), and view the map with locally installed software. UCSF Chimera, Pymol, Coot (v. 0.6.2 or later), and other graphics programs can display EMDB maps when loaded as "ccp4" format maps.

How can I download a map that has already been deposited?
Released maps can be downloaded either from the 'DOWNLOAD' tab of the atlas page for the entry or from an ftp site, either ftp://ftp.ebi.ac.uk/pub/databases/emdbftp://ftp.wwpdb.org/pub/emdb or ftp://pdb.protein.osaka-u.ac.jp/pub/emdb

Map download problems: I am unable to download ANY emdep maps.
The problem may be a firewall that restricts large downloads.

Can I use maps and/or map images from EMDB in my thesis/publication?
Data files contained in the EMDB are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of the structural data and the EMDB accession id.  Molecular images created from 3D viewers on EMDataBank atlas pages are available under the same conditions. In that case, EMDataBank.org should also be cited (Lawson et al).  Many of the static EM map images shown on atlas pages have been contributed by the original deposition authors in which case they may also be protected by copyright law, even though EMDataBank.org provides free access to them. The respective copyright holders of author-provided images retain rights for reproduction, redistribution and reuse. Users are responsible for compliance with copyright restrictions and are expected to adhere to the terms and conditions defined by the copyright holder.