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Data Deposition and Data Processing Procedures

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

Deposition Instructions

How Do I Submit Structures to the PDB?

Structures can be deposited using ADIT (AutoDep Input Tool), a new tool developed by the RCSB for data deposition. Nucleic acid crystal structures will be forwarded to the Nucleic Acid Database (http://ndbserver.rutgers.edu/ for processing.

ADIT is available at http://pdb.rutgers.edu/adit/.

Structures may also be deposited using either AutoDep or the PDB Deposition Form, which are available at http://www.pdb.bnl.gov/ and http://www2.ebi.ac.uk/pdb/.

What is ADIT?

ADIT, the AutoDep Input Tool, is used for data deposition, data processing, and data validation in the PDB. To deposit a structure, the user uploads the relevant coordinate and structure factor files and then adds any additional information. A session ID number is provided for depositions that occur over several sessions.

ADIT is available at http://pdb.rutgers.edu/adit/.

Who Is Processing the Data?

On January 27, 1999, the RCSB became responsible for the processing of all data received by the PDB. Brookhaven National Laboratory (BNL) is responsible for processing the files received prior to January 27, 1999.

After data is deposited, it is processed immediately by the RCSB and returned to the author. In most cases, files will be released within one week of their arrival at PDB or immediately following their release from a HOLD status. Files released by the RCSB are in a fully processed and final format.

How Do I Check the Status of an Unreleased File?

Currently, the status of all structures deposited at the PDB is available via the BNL pending/waiting/holding list at http://www.pdb.bnl.gov/pdb-bin/whsearch.

Questions and changes about unreleased files should be sent to deposit@rcsb.rutgers.edu.

What If I Have a Question About a Released File?

Questions and changes about released files should be sent to deposit@rcsb.rutgers.edu.

Validation Server (http://pdb.rutgers.edu/validate/)

The RCSB has released its Validation Server (http://pdb.rutgers.edu/validate/). The Validation Server can be used to check the format consistency of coordinates and to create validation reports about a structure before deposition. The validation report contains geometrical and experimental checks from the programs NUCheck1, PROCHECK2, and SFCHECK3.

While part of the ADIT system, the Validation Server can be used independently by the depositor.

Tutorials are available online.

1Zukang Feng, John Westbrook, and Helen M. Berman. (1998) Rutgers University, New Brunswick, NJ NDB-407.
2R.A. Laskowski, M.W. MacArthur, D.S. Moss and J.M. Thornton. (1993). J. Appl. Cryst., 26, 283-291.
3A.A. Vaguine, J. Richelle, and S.J. Wodak. (1999). Acta Cryst. D55, 191-205.