FAQ

EM map volume deposition questions

EM fitted coordinate model deposition questions

Map access questions

 

EM map volume 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.

What map formats are accepted by EmDep?
Maps can be deposited in a number of different formats, including mrc, spider, amira, and ccp4; they are converted by em2em to ccp4 format for redistribution in the EMDB. please see: http://www.ebi.ac.uk/pdbe/docs/iims/3D_EM.html

I am having trouble uploading an EMAN MRC map to EMDep.
Select format "OLD MRC" for EMAN MRC maps.

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 submit two separate depositions or can they be combined into one?
EMDB accepts only one map per deposition so you will need two separate EMDEP deposition sessions in this case. 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.

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 to go live 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), 1 year or 2 years from deposition. The map will only be released immediately if you have requested this at the release option stage.

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.

 

EM fitted 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.

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.

 

Map 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?
The simplest way to view an EMDB map is to use EMViewer, a java-based viewer that provides a simple, single isosurface representation. To use the viewer, go to the visualization tab of the EMDB atlas page (as in this example) and click on the "Launch EMViewer" button. To view the map on your own computer, you will 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, 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/emdb or ftp://emdb.rutgers.edu.

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