ScNPC2020

Welcome to the repository ScNPC2020 from Kosinski Lab (EMBL Hamburg), which includes all the custom code files used for integrative modeling of ScNPC as part of the following work:

"Allegretti, M., Zimmerli, C.E., Rantos, V., Wilfling, F., Ronchi, P., Fung, H.K., Lee, C.W., Hagen, W., Turonova, B., Karius, K. and Zhang, X., 2020. In cell architecture of the nuclear pore complex and snapshots of its turnover. bioRxiv."

The repository consists of the following directories:

• CR_Y_complex

  • README file for running the 'de novo' integrative modeling of wt CR Y-complex
  • parameters file & configuration file for 'de novo' integrative modeling of wt CR Y-complex
  • systematic_fits (directory):
    • parameters file for systematic fitting

• IR_asymmetric_unit_refinement

  • README file for running the 'refinement' integrative modeling of wt IR unit
  • parameters file & configuration file for 'refinement' integrative modeling of wt IR unit

• NR_Y_complex

  • README file for running the 'de novo' & 'refinement' integrative modeling of wt NR Y-complex
  • parameters file & configuration file for 'refinement' integrative modeling of wt NR Y-complex
  • NR_Y_complex_de_novo_run (directory):
    • parameters file & configuration file for 'de novo' integrative modeling of wt NR Y-complex
  • systematic_fits (directory):
    • parameters file for systematic fitting

• P_complex_neg_stain_fitting

  • README file for running the systematic fitting of the negtive stain map of the ScNup159 complex (P-complex)
  • parameters file for systematic fitting

• Nup116delta25C

  • README file for running the 'refinement' integrative modeling of Nup116delta25C ScNPC
  • parameters file & configuration file for 'refinement' integrative modeling of Nup116delta25C ScNPC

• Nup116delta37C

  • README file for running the 'refinement' integrative modeling of Nup116delta37C ScNPC
  • parameters file & configuration file for 'refinement' integrative modeling of Nup116delta37C ScNPC

• software (directory with bundled packages essential for running integrtive modeling & systematic fitting)

  • SuperConfig
  • pyxlinks
  • pdb_utils
  • imp_utils1
  • efitter

• For questions/support please contact: [email protected] or [email protected]