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AutoDep Input Tool Tutorial Examples

This tutorial provides examples on how to deposit structures into Protein Data Bank using ADIT (AutoDep Input Tool). The first two examples demonstrate how to use the ADIT editor on previously-loaded deposition. The third example allows users to upload their files for practice.

A complete guide on using ADIT functions is available at http://deposit.rcsb.org/adit/docs/tutorial.html.

None of the examples below will create a real PDB deposition. If you are ready to make an official deposition, please deposit your structure at http://deposit.rcsb.org/adit/.

Questions, comments, and suggestions about data deposition and processing should be sent to deposit@deposit.rcsb.org.

Example 1

Practice on a completed deposition using the structure data of 1QAV. Click the "BEGIN EXAMPLE 1" button on the right.

The coordinate file has been loaded for you, with required information filled in. The ADIT editor page is divided into four frames or panels: The top frame with logo and buttons of general commands; The left frame listing all category items for depositor to choose from; The middle-right frame showing the content of the user-selected category and allowing users to edit; The bottom-right frame showing the diagnostics once editing is saved. To practice, select any category item in the left frame to view the pre-filled information.

Feel free to edit the catetory items, and any change can be saved by clicking the "SAVE" button for each category. The information will then be displayed in the bottom frame when DISPLAY AS TABLE is selected. At any time you may view all information about the entry by clicking the "PREVIEW ENTRY" button.

After you go through all categories you wish to review, you may click the "DEPOSIT" button, which will bring you to a final review on the completeness of the entry's information. At this point you may go back to editing or click the DEPOSIT confirmation button to finish the practice session.

Example 2

Practice on an incomplete deposition using the structure data of 1KIP. Click the "BEGIN EXAMPLE 2" button on the right.

The pre-loaded structural file contains only the basic symmetry information (SCALE records and CRYST records) and the coordinates. To practice, select any of the categories in the left frame to view the information needed

Detailed direction for example 2

Example 3

This practice allows you to upload your own structure into the ADIT Editor. The files to be used should be on the same machine that you are running ADIT from.

To practice ADIT deposition with your data:

  • Select the experimental method (X-ray or NMR) in the small window below;
  • Select the molecular type (protein, nucleic acid, or nucleic acid/protein complex);
  • Click the "BEGIN EXAMPLE 3" button, then you will be asked to load the data.
New ADIT Session
Method:
Structure Type:

This practice will not create an actual deposition into the Protein Data Bank.

Additional information about ADIT are available at http://deposit.rcsb.org/.

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