OPM is a program to predict the location of transmembrane planes in protein structures, utilizing the atomic coordinates. ssbio provides a wrapper to submit PDB files to the web server, cache, and parse the results.


  1. Use the function ssbio.protein.structure.properties.opm.run_ppm_server() to upload a PDB file to the PPM server.


  • How can I install OPM?

    • OPM is only available as a web server. ssbio provides a wrapper for the web server and allows you to submit protein structures to it along with caching the output files.
  • How do I cite OPM?

    • Lomize MA, Pogozheva ID, Joo H, Mosberg HI & Lomize AL (2012) OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res. 40: D370–6 Available at: http://dx.doi.org/10.1093/nar/gkr703
  • I’m having issues running OPM…

    • See the ssbio wiki for (hopefully) some solutions - or add yours in when you find the answer!


ssbio.protein.structure.properties.opm.run_ppm_server(pdb_file, outfile, force_rerun=False)[source]

Run the PPM server from OPM to predict transmembrane residues.

  • pdb_file (str) – Path to PDB file
  • outfile (str) – Path to output HTML results file
  • force_rerun (bool) – Flag to rerun PPM if HTML results file already exists

Dictionary of information from the PPM run, including a link to download the membrane protein file

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