pdb_extract

pdb_extract is a pre-deposition service for assembling structure files for wwPDB OneDep deposition .
Use this online tool (tutorials available) or download the standalone program to run on your local machine. This tool will:

Convert PDB format file to mmCIF format
Prepare a re-usable template file of your metadata via PDBj's mmCIF Editor for Xray, NMR, EM (*Note: click Editor's upper-left gear icon to save/download or access help). The template can be uploaded at the next step, and used for multiple entries.
Assemble coordinates and log files pertaining to your specific experimental methods.
Allow you to update the primary sequence of your protein/nucleotide chains to account for unresolved residues.

How to Run:

Select the experimental method you used to solve the structure
Select the type of structure model coordinates file to be uploaded
Upload the finally refined structure model coordinate file
Press the RUN button to start pdb_extract
The mmCIF files that you obtain can be used as input for wwPDB OneDep deposition and validation.

If you upload PDB format structure model coordinates file:

1. The column alignment for ATOM and/or HETATM record rows must be correct.

2. Please ensure that each polymer has a unique Chain ID in the file. If your uploaded file does not have chain ID, pdb_extract will try the best guess to add chain ID, and if so please review the chain ID addition on the next page.

3. A TER card must be present at the end of each complete polymer chain, but a TER card should not be placed in the middle of a polymer chain even if there is a main-chain break due to disordered residues not built in the model.

Note: If the file size is too large (e.g. >100 MB), you can upload gzipped (*.gz) or compressed (*.Z) file for faster loading.

Reference: Huanwang Yang, Vladimir Guranovic, Shuchismita Dutta, Zukang Feng, Helen M. Berman and John D. Westbrook (2004), Acta Cryst. D60, 1833-18399

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