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 coordinate validation and deposition to ADIT-NMR.

Step 1: Select the NMR option in the main panel at pdb-extract.rcsb.org/.

Step 2: Upload your fully refined coordinate file into the box provided.

Step 3: Select the file format (PDB or mmCIF) and program used to refine the coordinates.

Step 4: Click the run button to start pdb_extract.

The next series of forms will capture essential information about your structural determination process, including resulting
outputs/LOG files used for structural refinement. Items marked with an asterisk (*) are required.

Form 1: Information about Authors, spectrometer ...
You can either upload the file that you have filled out offline (available here), or you can complete it online
during the pdb_extract process by following the "click here to complete this entry on line" link.

Guidelines and examples for filling out the author information file are listed at the top of the file.

Form 2: Extract Information from NMR Structure Determination
Upload your resulting output/LOG files only. You do not have to give the coordinate file again since it was provided in the initial step.
• Upload the output file names exported from each application step.
• Select the program names that exported the file names.
• Select the file format (LOG or mmCIF formats).

Final Form: 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.
  Missing residues that appear as question marks "?" must be replaced with their actual amino acid composition.
• Confirm that the correct molecular entity chains exist
• Confirm that the polymer type is correct
• If this structure is a result of a structural genomics project, enter the Target ID here as well

Step 5: Begin the extraction!

• Click the RUN button in the bottom of the lower frame
• Processing takes approximately 5 minutes, 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.