ADIT Tutorial

Structures can be deposited using the AutoDep Input Tool (ADIT)
http://deposit.rcsb.org/adit/

The Auto Dep Input Tool (ADIT) was developed by the RCSB for depositing structures to the Protein Data Bank. ADIT also allows the user to check the format of coordinate and structure factor files and to perform a variety of validation tests on a structure prior to deposition in the database. These checks can be done without intervention by the database staff.

For the details about PDB format version 3.0 and 3.1, please see http://www.wwpdb.org/docs.html.

To deposit a structure, the user uploads the relevant coordinate and structure factor files and then adds any additional information to the submission using ADIT.

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The following tutorial is a guide to depositing a structure using all of the available ADIT functions.

Example "in progress" depositions are available at http://rcsb-deposit-demo-1.rutgers.edu.

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To begin a new ADIT session:

• From the pull-down menus provided at http://deposit.rcsb.org/adit/, select the experimental method used, molecular structure type, and press the BEGIN button.
  
  
• In the space provided, enter the name (including the path/location) of the coordinate and experimental data files. You may also use the Browse button to locate the file. Specify the file type using the pull-down menus provided.
  
  
• Select the operation you wish to perform (Precheck, Validate, or Deposit) and then press the BEGIN button. You may go directly to deposition without performing the validation steps, or you may check and validate the structure without going through the deposition steps.
  
  The advantage of performing the data format precheck and structure validation is to inform you of any potential changes you may wish to make to your structure before you deposit it.

Step 1: Data Format Precheck

• This check is run when the operation menu is set to Precheck and the BEGIN button is selected.

• A brief report is produced that identifies any changes that need to be made in your data files in order to obtain a validation report or to deposit a structure.

• Press the Continue to Validation or Deposition link to proceed.

• To continue working with this set of data files, select Validate from the operation menu and then press the BEGIN button.

• To begin a new session with another set of data files, select the ADIT Home Page link.

Step 2: Validation Precheck (Validation)

• This check is run when the operation menu is set to Validate and the BEGIN button is selected.

• In order to run this check, the coordinate file must be in either PDB or mmCIF format, including a complete CRYST card (unit cell and space group information) and TER cards at the end of each chain and chain IDs. If an alternate setting is being used for the space group symmetry then scale cards must be provided.

• The validation may take a few minutes depending on the size of your structure, so please be patient.

• Note: If atom names or ligand names are unrecognized by the dictionaries, validation results will not be optimal. If you wish to send us the definition for any new ligands we will include them in our dictionaries.

• When the validation process is complete, you will be presented with a validation report which includes an Atlas entry, a summary report, and a collection of structural diagnostics including bond distance and angle comparisons, torsion angle comparisons, base morphology comparisons (for nucleic acids), and a molecular graphics image of the crystal packing.

• Press Continue to proceed.

• To continue working with this set of data files, select Deposit from the operation menu and press the BEGIN button.

• To begin a new session with another set of data files, select the ADIT Home Page link.

Step 3: Data Deposition

You may wish to have the following information on hand:

citations of relevant references, sequences of macromolecules in your structure, molecular formulae of ligands, natural or genetic source of macromolecules, crystallization conditions, unit cell, space group, data collection parameters, refinement parameters, rms deviations

• A WWW editor is provided to help you enter and edit information about your structure. The information contained in the data files entered will be included in this editor.

• Be sure to note the Session Restart ID that will appear in the center of the browser window and again in the titlea of the browser. This ID can be used to continue the current deposition at a later time. The Session Restart ID will look like an address, i.e. inosine.rutgers.edu.6544.

• The data to be included in a deposition has been organized into different categories, which appear in the left frame of the Web browser.

• For each category, the user should enter information and then save the category:

  Entering information:

  • Select a category from the list on the left. The data items for this category will appear in the middle right frame.

  • Enter in any missing information in the spaces provided.

  Saving the category:

  • Before moving on to another category, select the SAVE button to enter the information. Switching to another category without saving your data will erase the information that you have entered.

  • To review the data currently entered in the selected category, press the DISPLAY AS TABLE button. A table including any information entered for the selected category will appear in the bottom frame.

• Proceed through the category list until you have entered all relevant information.

• You can review the data entered in all of the categories by selecting the PREVIEW ENTRY button located in the top frame.

• To deposit the structure, select the DEPOSIT button.

  You will be presented with an approximate measure of the completeness of your file for deposition and a table previewing your entry. If you wish to change or add any information, select Return to the Input Tool. If you have added all of the information you would like and do not want to make any changes, press the Deposit Now button. After selecting this button, you will not be able to change the entry any further using ADIT.

A previous ADIT deposition session can be continued at a later date as long as the structure has not been deposited.

To begin a previous ADIT session:

• From the ADIT home page at http://deposit.rcsb.org/adit/, enter the Session Restart ID Number and select CONTINUE SESSION in the space provided.

• The Session Restart ID appears in the center of the browser window when a deposition session is first begun, and then again in the titlea of the browser throughout the deposition session. The Session Restart ID will look like an address, i.e. inosine.rutgers.edu.6544.

• Once entered, the deposition session may be continued. You will be able to access your structure as many times as necessary until you deposit the structure.

Questions, comments, and suggestions should be sent to deposit@deposit.rcsb.org.