ADIT deposition tool | deposit your structures to the PDB


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

Welcome to the ADIT deposition tool. Please check the instructions below to ensure that your coordinate files have the correct format for deposition. This tool will be replaced by ADITBeta in 2008.

Since 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.


Structures solved by Electron Microscopy should have their maps deposited 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.
Deposition is easier if your files are prepared in mmCIF format using pdb_extract, and take the time to validate your files using our Validation Server. To ensure that all tools will work with minimal error, the format requirements for depositing structures are:

  • 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 listed sequentially in columns 11-14.
  • Chain IDs used in the SEQRES records should correspond to those in the coordinates

Since 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.


Question, Comments, and suggestions should be sent to deposit@deposit.rcsb.org


If your question is about a particular entry, please include the RCSB ID in your message.