ADIT deposition tool
| deposit your structures to the PDB
ADIT FAQ |
Deposition FAQ |
Depositing large structures?
If your structure exceeds the size of the traditional PDB file format limits
(>62 chains or >99,999 atoms), please prepare your
deposition as a single PDBx/mmCIF file using recent versions of CCP4
(REFMAC > 5.8) or Phenix (> 1.8.2) before submitting your structure with
the wwPDB Deposition System.
NOTICE FOR REFMAC USERS - details for
generating total B factors when TLS used
For structures solved by Electron Microscopy, first deposit the 3D map at
EMDB and then follow the link provided to deposit the coordinates.
To start a new ADIT session, select the
experimental method and the molecular structure type. Then press the BEGIN button.
To continue a session from an earlier
date, enter your session restart ID and press the CONTINUE
instructions that describe how to deposit X-ray,
Microscopy structures are available. Coordinates may be deposited
as either mmCIF or PDB formatted files.
To ensure that all tools will work with minimal error, the format requirements for depositing structures in PDB format 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
- 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.
- The sf file can either be in mmCIF, ASCII, or mtz formats and should at least include h, k, l, F, SigmaF (and/or I and SigmaI) and test flags.
Definitions and format are available in DOC (48 KB) and PDF (24 KB) format.
The guidelines for
are available at http://www.wwpdb.org.
Question, Comments, and suggestions should be sent to firstname.lastname@example.org.