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EmDep notes for first time users

This is a description of how to submit data via EmDep to the EM Data Bank. 1 EmDep guides you through the process of completing your submission. Please also see our guide for map + model deposition.

How to begin your submission

  • The deposition can be based on a previous, fully or partly-completed, deposition
  • A new deposition can also be started from scratch

If the new deposition is based on a previous deposition, EmDep merges the relevant data, and this information is displayed in the relevant sections in EmDep. Please make sure that you delete the information that is not applicable to your entry.

Every data item is partially verified as you add new information.

The whole entry is checked by EmDep processing programs and the EM Data Bank processing site returns this report via EmDep for your information.


Overview of the process

Security and confidentiality: We provide you with a deposition session id consisting of three letters, a dash, and a number, and ask you to provide a password. Anyone who knows both the deposition session id and the password has access to your submission. This allows you to make future submissions based on earlier ones. If you prefer us to block all access after completion of the deposition process, please instruct us accordingly.

You may change your password at any time by choosing Change password in the Control panel.

The first 6 sections are mandatory and have to be completed and a map file has to be uploaded in order to proceed with the deposition. The mandatory sections consist of:

  • Author contact
  • Deposition instructions
  • Title, author & keywords
  • Citation
  • File deposition
  • Map parameters

Author contact:

The first requires information about contact author. The contact author has authority to grant approval for release of the completed entry. The review copy of the entry, validation diagnostics, and approval request will be sent to the contact author. The contact author should be able to help in preparing the entry if questions arise or clarification is needed.

Deposition instructions:

Once you complete the Author contact section you are asked about specific processing details, data release or hold requests, and whether this data set replaces an existing released entry.

The EM Data Bank does not allow you to request a specific ID code.

Title, author & keywords:

Once you complete the Deposition instructions section you are asked about the title, authors and keywords for this entry. The title is free text and describes the contents of the entry and procedures or conditions that set this entry apart from others. The title presents an opportunity for the depositor to emphasize the underlying purpose of this particular experiment. Keywords relevant to the structural entry are also requested.

Citation:

Once you complete the Title, author & keywords section you are asked to cite both the primary reference that identifies the deposited set of coordinates as well as other important references. If you have chosen to release your data upon publication, you must notify the EM Data Bank as soon as your paper is published.

File deposition:

You will need to upload your map file which must be in MRC, CCP4, or Spider format.

Other files that you may upload: structure factors, layer-line data, images, and masks.

We encourage you to send your structure factors in ASCII format.

In order to upload files first select the description that best describes the files you want to upload and click 'select'. Enter its complete path and filename by typing it in the field or by using the Browse button, and click on the Upload button. Repeat these steps for every file being uploaded.

Provide information as needed on files being sent, being sure to click on the Save button to store the information.

Remaining sections:

Continue your EmDep session by selecting the next section from the control panel. From this point on, EmDep will jump automatically to the next unfinished section each time you successfully complete a section.

Complete the remaining sections, taking time to make the best submission possible.

After writing your values into the fields on a page, you must click on the Save button found at the bottom of every section in order to write the data to your EmDep session. If you do not do this before moving on to the next section, this information will be lost.

The n/a button to the right of every non-mandatory field places the value n/a, for not applicable, into that field. Mandatory fields expect the answer n/a, none or null to be acceptable. The example given at the right of the answer field shows the type of answer that is acceptable.