pdb_extract - Tutorial

Tutorial for using the pdb_extract web interface for NMR

The pdb_extract online tool extracts key information from NMR applications. By providing the necessary files, you will receive one file in return: one mmCIF file containing coordinates, annotations, and refinement statistics (pdb_extract_coord_#.cif). This file is then used as input for wwPDB OneDep coordinate validation and deposition.

Step 1: Select the NMR option in the main panel.

Step 2: Select the file format (PDB or mmCIF) and program used to refine the coordinates.

Step 3: Upload your fully refined coordinate file into the box provided.

Step 4: Click the run button to start pdb_extract.

Form for Information about Authors, spectrometer ...
You can upload the template file that you have filled out offline, or you can complete it online
during the pdb_extract process

Form for Confirmation of macromolecular sequence and other information
• Confirm that the number of molecular entities (unique) is correct
• Modify the chemical sequence in the molecular entity group to match the full protein sequence used in this experiment.
• Confirm that the correct molecular entity chains exist
• Confirm that the polymer type is correct

Step 5: Begin the extraction!

• Click the RUN button in the bottom of the lower frame
• Processing takes a while, perhaps longer if your files are very large
• Save the mmCIF file (pdb_extract_coord_#.cif) onto your local computer

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