ADITBeta deposition tool | submit your structures to the PDB


Tutorial | ADIT FAQ | Deposition FAQ | pdb_extract | Ligand Expo

Thank you for choosing ADITBeta to deposit your structures to the PDB.
Please check the instructions below to ensure that your coordinate files have the correct format for deposition. This version of ADIT indicates file format errors with suggestions for solutions, automatically validates the structure; checks for consistency between sequence and coordinates; allows easier organization of sequence information and simplifies the way for entering author, title and citation information. ADITBeta will replace the current ADIT tool in 2008.

Effective February 1, 2008, structure factor amplitudes/intensities (for crystal structures) and restraints (for NMR structures) are mandatory requirements for PDB deposition. This policy is published at http://www.wwpdb.org/news.html.


Polypeptide structures containing 24 or more residues and polynucleotide structures with 4 or more residues are accepted by the wwPDB.

Structures solved by Electron Microscopy should deposit their maps to the EMDB first, and should supply the EMD-id as an associated entry with their ADIT deposition.


To start a new ADIT session, select the experimental method and the molecular structure type. Then press the BEGIN button.

New ADIT Session
Method:
 X-ray
NMR
Electron Microscopy
Structure Type:
 Protein
Nucleic acid
Nucleic acid/protein complex

To continue a session from an earlier date, enter your session restart ID and press the CONTINUE SESSION button.


Continue Previous ADIT Session*
Session Restart ID:
example: 2006-07-01.serverhostname.9999.12345678

* If you have started an ADIT-NMR session, you can continue at ADIT-NMR (http://deposit.bmrb.wisc.edu/bmrb-adit/)


Detailed instructions that describe how to deposit X-ray, NMR and Electron Microscopy structures are available. Coordinates may be deposited as either mmCIF or PDB formatted files. Depositions in mmCIF format should be prepared using pdb_extract. To ensure that all tools will work with minimal error, first check that your coordinate files contains the following format requirements:

  • Each polymer must be assigned a unique alphanumeric chain ID (A-Z, 0-9, a-z) in column 22.
  • Each residue must be assigned a unique residue number within that chain ID.
  • If there are alternate conformations in the structure, the alternate conformation indicator must be provided in column 17.
  • Atoms with the same coordinates may not be present in the same MODEL.
  • All polymer chains should have a TER card at the end. No TER cards should be included at the end of non-polymer residues (such as ions, ligands, waters).
  • There should be only one END card at the end of the file.
  • Each record must start in the first column.
  • Record types (such as COMPND, ATOM, SEQRES) must be capitalized.
  • If the entry contains ANISOU, SIGATM, or SIGUIJ lines, there must be a corresponding ATOM record.
  • Depositions with multiple models should include MODEL and ENDMDL cards. The models should be sequentially numbered in columns 11-14.
  • Chain IDs used in the SEQRES records should correspond to those in the coordinates

Starting August 1, 2007 data depositions processed by the wwPDB follow the Protein Data Bank Contents Guide (Version 3.1) and the latest PDB Exchange dictionary (PDBx).  The guidelines for data processing and policies are also available.


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