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 option NMR in the main panel at http://pdb-extract.rcsb.org/.

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

Step 3: Select the file format

• Select PDB if the coordinate file is in PDB format.
• Select mmCIF if the coordinate file is in mmCIF format.

Step 4: Click the RUN button.

Step 5: Extract the key details about the structure.
Please upload any LOG files. Please do not give the coordinate file again, since it was already provided in the main panel.

• 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).
• Modify the chemical sequence in the molecular entity group, if necessary.
• Provide the non-electronically extracted information (Authors, Title, ...). Use the HELP button to download the data_template.text file, if needed.
• Click the RUN button in the bottom of the lower frame to get the mmCIF file in the next page.
• Save the mmCIF file in your local computer

Step 6:  Upload this mmCIF file to ADIT-NMR for data submission.

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