NMR data deposition

pdbe.org/nmr

ECI: preparation of CCPN projects for deposition

Getting started ECI Menus ECI Tabs What's next?
Tabs:

ECI Tabs

ECI is tab-based, and above is a list of the tabs together with a link to a separate page about each tab and example screenshots.

Main

At the bottom of the Main tab in CcpNmr ECI, it is possible to add an "Entry" object. If your project contains multiple datasets that you wish to publish separately, you can add multiple "Entry" objects, which can be switched between by using the "Deposition Entry" pulldown menu at the top of the top frame.

On the top frame of this tab, it is possible to fill in basic information about your deposition such as a title to be used in the PDB file. You will also need to select the molecular system (a "MolSystem" object in CCPN terminology) that was used to collect your NMR data. If your project includes multiple "MolSystems", please select the correct one. Once a "MolSystem" has been selected, it is possible to view and check the chain, molecule and unusual chemical components in the Molecules tab.

Other fields on the Main tab include boxes to add study keywords, text for a detailed description of the study (like a mini abstract), additional instructions or notes that you wish to convey to the curators about your deposition, and the type of NMR method employed (solution, solid-state, etc.). Also, you can select whether you are going to deposit to PDBe or BMRB. Changing this drop down menu will affect which fields are shown to be mandatory in the bottom frame.

On the bottom frame, there is a list of data/information that is mandatory for a deposition. Main items/sections (or objects such as a person or a citation) that still need to be completed are shown in red, while those that have been included are displayed in green. If a section is partially completed, then any incomplete fields (tags such as family name or journal title) are shown in orange, or yellow when not all objects of that type have a completed field.

Clicking on any missing data will take you to the correct tab so that you can add this information. Sometimes the report will take you to add some new data (like "Sample", "Sample Condition", "Shift List Experiments", "NMR Spectrometer" or "Chemical Shift References"), which may have been added but not linked. In these cases, you will need to set a link to this data - usually in the "Experiments" tab.

Buttons at the bottom of the Main tab

There are four buttons at the bottom of the Main tab. The two buttons for exporting your CCPN "Entry" object as NMR-STAR 3.1 or PDB coordinates have the same function as in the Project menu, and they are there if you are running ECI as a popup from CcpNmr Analysis or as a tab in the Extend-NMR GUI.

Add New Deposition Entry

Allows you to add a new deposition "Entry" object. If you do not have an "Entry" object you will need to add one. You can also create different "Entry" objects if you have data for more than one separate deposition in your CCPN project.

Remove Current Deposition Entry

Removes the currently selected "Entry" object as shown at the top of the Main tab in the pulldown menu for "Deposition Entry".

Export as NMR-STAR 3.1

Exports your CCPN project as a full NMR-STAR 3.1 file that can be uploaded at the ADIT-NMR deposition server at the BMRB. If you give an old file name, there will be a popup asking you if you want to overwrite the existing file.

Export PDB Coords

Exports the coordinates of your CCPN project into PDB format. This is more for convenience if you wish to check by looking in a program like Rasmol that the coordinates you are using look like the correct ones to be submitted. We do not support export of full header information as PDB files can lose important information from a project as only a sub-set of NMR meta data is archived in this format. If you give an old file name, there will be a popup asking you if you want to overwrite the existing file.

The Main tab of ECI


The top frame is for editing basic entry information and the bottom frame is to see what data has been completed (green) or is yet to be done (red, orange or yellow>; see text for an explanation of the colours).