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CcpNmr ECI


Contents

  1. Downloading and installing ECI
  2. Menu options
  3. Main
  4. People
  5. References
  6. NMR Data
  7. Shifts
  8. Molecules
  9. Sources
  10. Samples
  11. NMR Conditions
  12. Instruments
  13. Experiments
  14. Structures
  15. After saving your changes in ECI

ECI allows you to easily add an "Entry" object to your CCPN project. An "Entry" object contains all the information that you wish to deposit with your submission. You can also select chemical shift lists, peak lists, structural restraints, ensembles, etc. and all at the click of a button. In addition, you can add all the meta data that is required for submissions to the PDB and BMRB. This can be done securely on your desktop computer over the duration of your NMR project.

In ECI, when hovering with a mouse over the titles of tabs and tables as well as widgets like pulldown menus, a tool tip will pop up presenting some brief help text (see all tool tips here). Fields that are editable are indicated with a small "E" in the bottom left corner. Sometimes data lines are shown in colour - for example, green is often used to indicate that the data will be submitted with your deposition.

ECI is tabbed based, and below are a list of the tabs together with short explanations and a link to a separate page about each tab and an example screenshot. This page gives a overview of all tabs: follow the accompanying links for more information.

Downloading and installing ECI

This link shows how to download and install ECI on your computer. At the moment, you need to download the main CcpNmr program Analysis. Run Analysis on your computer either with a new CCPN project or an existing one, and then you can open an ECI window from the analysis menu M:Structure:ECI: Database Deposition. It is also available as a tab in the Extend-NMR GUI. In addition, you can run ECI as a standalone application where you will get access to its menus as well. The location of the script to do this is in the same location as the analysis and formatConverter scripts of the analysis release and is called "eci".

Menu options

The menu bar is only available if you run ECI as a standalone application. Here there is a choice of:

Main

In this tab, you can add a new "Entry" for your project. It is also possible to add basic information about your study including a PDB title, study keywords, whether the deposition is for the PDB or BMRB, setting the molecular system (a "MolSystem" object in CCPN terminology) and special instructions for the curators of your data.

In the bottom frame there is a report to say how complete your "Entry" is. Finished data is shown in green. Clicking on any missing data (shown in red, orange, or yellow) 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" 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.

For more details go to the Main tab page.

People

This tab allows you to add people involved in your study and select them as authors and contact people. For each contact person, it is also possible to add address information in the bottom frame, such as email address, mailing address, email, etc.

For detailed information go to the People page.

References

This tab allows you to set information about citations and software of relevance to your study.

Read more on the References page for detailed information.

NMR Data

Here, you can select the different NMR measurements and data derivations in your CCPN project. The tab allows you to set, for example, a type of measurement, such as chemical shift list, peak lists, etc. It is still possible to import data from other software formats at this stage of your submission using FormatConverter.

Read more on the NMR Data page for detailed information.

Shifts

This tab allows you to add chemical shift references and provides quality control of the input data.

For more information go to the Shifts page.

Molecules

The molecules tab allows you to check the information about the molecule and chains in the "MolSystem" selected on the Main tab. You can also edit some physical properties about the chains and review information about ligands, metal ions and non-standard monomers in your polymers.

Go to the Molecules page for detailed information.

Sources

This tab is for experimental and biological (natural) sources for all the polymers in your "MolSystem".

Further information is provided on the Sources page.

Samples

The samples frame allows you to add sample information for the NMR experiments in your study.

More detailed information is provided on the Samples page.

NMR Conditions

This tab is for the NMR experimental conditions used in your experiments such as temperature or pH.

Read more on the NMR Conditions page for detailed information.

Instruments

This tab allows for the editing of NMR spectrometer and probe information.

See the Instruments page for extra help.

Experiments

On this tab, it is possible to add information about the experiments run and associate other experimental information on an experiment by experiment basis edited in the earlier tabs.

Further information is in the Experiments page.

Structures

The final tab is for adding structures and restraints used for calculating those structures.

For more details go to the Structures page.

After saving your changes in ECI

Finally, save the project directory as a .tar.gz file (see this page for help), which can be submitted to AutoDep.

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