NMR data deposition

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ECI: preparation of CCPN projects for deposition

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ECI Menus

The menu bar is only available if you run ECI as a stand-alone application. The menus are described below.

Project

The M:Project menu is used for actions that act on complete projects, such as creating, opening, saving projects and quitting. You can also import and export PDB and NMR-STAR files. The menu is similar to that found for analysis and details about those menus and any resulting popups, which are very similar to those used in ECI, can be found here.

New

Creates a new CCPN project. You need to create a CCPN project first or open an old one to edit any data in ECI. This will provide a popup for you to give the project a name that can be up to 32 characters consisting of alphanumerics and "_".

Open

Use this option to load an existing project that was previously stored on disk. Saved projects are identified by a directory which contains all of their data organised in various XML files. Note that any binary spectral matrices made with analysis are stored separately to the CCPN data, although a project will store references to where the spectra are located. These matrices are not normally sent for upload when you deposit your final CCPN project. This menu item will provide you with a popup where you can select valid CCPN projects in green. Valid backup project directories are highlighted in yellow, with the name of the xml file listed instead of "OK" in the "Status" column. Archive CCPN projects, which are list as "XML" format, can be searched for and downloaded from the BMRB NMR Restraints Grid (NRG) Server.

Close

Closes a CCPN project. If you have not already saved the project, you will be asked if you want to save it before ECI closes it.

Save

Saves the CCPN project with the name that was used to create it or open it with the M:Project:New or M:Project:Open options.

Save As

Saves the CCPN project with a new name, this is especially useful if you want to keep an old copy of the project prior to any new edits or operations that could result in data loss. Be careful though, as if you give the same name, then it will overwrite the old project data.

Import

This menu option has five sub-menus for importing Fasta, NMR-STAR and PDB files into a CCPN project.

Fasta Sequence

Useful for importing simple molecular systems into ECI. Use FormatConverter or Analysis for more complicated molecular systems or import a PDB file with the relevant molecular system information in the header.

NMR-STAR 2.1.1

This will import the data from NMR-STAR 2.1.1 files available from the BMRB site. Note import of project meta data is not supported as this format will soon become obsolete and so is not fully supported. NMR data sets can be downloaded from here.

NMR-STAR 3.1

This option imports data and meta data from NMR-STAR 3.1 files. This is very useful for people who want to do similar depositions as they have done previously as things like Authors and Spectrometers will be immediately populated correctly. NMR restraints files in NMR-STAR v3.1 format can be downloaded from the BMRB NMR Restraints Grid (NRG) Server.

PDB 3.20

Imports header data, molecular system, sequence and coordinates from the latest wwPDB files. You can search for these files on the PDBe web server PDBeView.

PDB Coords

Imports molecular system, sequence and coordinates from the PDB-like files but no other header information.

Export

This menu option has two sub-menus for exporting NMR-STAR and PDB files from a CCPN project. These functions can also be accessed from the bottom of the Main tab for users running ECI from CcpNmr Analysis or from the Extend-NMR GUI.

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.

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.

Quit

This menu option will close ECI. If you have not saved your CCPN project, you will be prompted if you wish to do so.

Version

Displays a pop-up indicating the version of ECI being run.

CcpNmr

The M:CcpNmr menu is used to open other software packages in the CcpNmr suite. If one of the programs is not available (for example, if you do not have the correct C libraries required to run Analysis), the menu option will also show the phrase "** NOT INSTALLED **".

Analysis

Opens CcpNmr Analysis. This is useful for deleting working objects from your CCPN project such as constraints lists and non-final structures.

Format Converter

Opens the desktop version of CcpNmr FormatConverter. This program can be used for importing and exporting CCPN data sets such as constraints, coordinates, chemical shift and peak lists into the most common NMR file formats available (possible formats are listed here.).

Data Shifter

Opens Data Shifter, which allows you to import objects from other CCPN projects into your deposition project. This is particularly useful for standard attributes that are shared by many projects such as People and NMR spectrometers

Options

This menu allows you to change the type and size of font used in CcpNmr ECI.