You can create a PyMOL script from a protein crosslink.

Procedure

  1. Do one of the following:
  2. Download a protein structure file for the protein of interest from the RCSB PDB (Protein Data Bank) https://www.rcsb.org/.
  3. Use a structure model from a modeling program.
  4. The structure model must be in .pdb or .cif format.
  5. If more than one protein structure is available, store each file in a separate directory to create PyMOL scripts for each structure.
  6. After structures are available, open the Results page in the Proteome Discoverer application.
  7. Select the proteins for export, and select File > Export > To PyMOL.
  8. The PyMOL dialog box opens.
  9. For Model Folder, enter the path to the directory that contains the protein structures.
  10. (Optional) Select the Sequence Identity (%) Threshold value.
  11. For Export to Folder, enter the output directory.
  12. Select Export.
  13. To open the script in PyMOL, do the following:
  14. In PyMOL, open the generated file to retrieve distance information.

  15. NOTE

    The script contains the path to the .pdb or .cif structure file. Do not remove the file from the Model folder directory after the script is created.

If the protein structure contains more than one protein chain, the software treats the chains in the structure separately and creates a PyMOL script for each chain that meets the sequence identity threshold.

The software generates a file name for the script in the following format:

  • The accession ID of the protein in the Proteome Discoverer Results page
  • The structure file name
  • The chain (if more than one chain is present in the structure)
  • The chain identifier
  • The extension .py

For example: 6QS9ASerum_pdb6qs9pdbchainA.py

For information about using PyMOL, refer to the PyMOL documentation.