PDB_extract Quick Tutorial

The PDB_extract online tool extracts essential information from each step of your structure determination process in preparation for PDB deposition. Refinement statistics, for the most part, will be extracted from the header of your coordinate file. However, if it does not list specific statistics, the LOG files you provide within PDB_extract should supply these extra values.

To start PDB_extract:

• Select experimental method (X-Ray or NMR).
• Enter the name of the coordinate file obtained from final structure refinement.
• Select the file type (PDB or mmCIF).
• Select the program name which was used to obtain the coordinate file. Select OTHER if yours is not listed.
• Press the RUN button to start this operation.

Note: If the file size is large, it is recommended to upload gzipped (*.gz) or compressed (*.Z) file for faster loading.

For structures solved by X-ray crystallography:
After you enter the coordinate file and start the operation, you will have several forms to fill in. By providing the necessary files and information, you will receive two files in return: one mmCIF file with coordinate and refinement statistics (pdb_extract_coord_#.cif), and the other contains your structure factors (pdb_extract_sf_#.cif). The two files can be used as input for Validation and deposition to ADIT or ADITBeta.

For structures solved by NMR:
After you enter the coordinate file and start the operation, you will have several forms to fill in. By providing the necessary files and information, you will receive one file in return: one mmCIF file containing coordinate and refinement statistics (pdb_extract_coord_#.cif). This file is then used as input for coordinate validation and deposition to ADIT-NMR.

Please refer to the help files in either interface for further details.

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