Supplementary data for Hutchins, et al, 2023. For questions or enquiries, please contact bioc-exec@bristol.ac.uk The following software is required to access and visualise data: - PyMOL (.pdb) - Chimera (.mrc) - Amber Tools 16-22 (.cpptraj) - VMD (.nc, .prmtop, .inpcrd) - Jupyter Lab (.ipynb) - Notepad or other text editor (.txt, .xml) - Adobe Photoshop, Illustrator, ImageJ, or other image viewing software (.png, .jpg) Datasets for the following are provided: - design and MD analysis of the monoheme m4D2 - MD analysis of the tetraheme e4D2 - low resolution cryo-EM maps of e4D2 - cryo-EM micrographs of e4D2 The files comprise: - representative models of m4D2 and e4D2 from MD simulations (.pdb) - Amber MD parameter files for apo-m4D2, heme-bound m4D2 and heme-bound e4D2 (.prmtop) - MD trajectory files (.nc) - Input coordinate files for MD simulations (.inpcrd) - Scripts for combining MD trajectories and for RMSF/RMSD analysis (.cpptraj) - Python scripts for RMSF/RMSD analysis (.ipynb) - Data files from RMSD/RMSF analysis (.dat) - Images from RMSD/RMSF analysis (.png) - Rosetta design scripts for Backrub, FastDesign and RelaxRepack protocols (.xml) - low resolution cryo-EM map of e4D2 (.mrc) - cryo-EM micrographs of e4D2 (.jpg) [Note: MD trajectories are split into 10 nanosecond files. To combine: $cpptraj -i $/e4D2/V1/traj100ns.cpptraj] File list: >m4D2 e4D2 >e4D2 e4D2.pdb (representative e4D2 model from MD simulations) >cryoEM >cryoEM_micrographs e4D2_micrograph_1.jpg e4D2_micrograph_2.jpg e4D2_micrograph_3.jpg e4D2_micrograph_4.jpg >cryoEM_maps e4D2_C1_cryomap.mrc e4D2_D2_cryomap.mrc >V1 100ns.nc e4D2_v1_100ns.pdb e4D2.inpcrd e4D2.prmtop refrmsd_backbone_helix.cpptraj refrmsd_backbone.cpptraj remsd_backbone_helix.dat rmsd_backbone.dat traj100ns.cpptraj >V2 100ns.nc e4D2_v2_100ns.pdb e4D2.inpcrd e4D2.prmtop refrmsd_backbone.cpptraj rmsd_backbone.dat traj100ns.cpptraj >V3 100ns.nc e4D2_v3_100ns.pdb e4D2.inpcrd e4D2.prmtop refrmsd_backbone.cpptraj rmsd_backbone.dat traj100ns.cpptraj >m4D2_apo_design_MD traj100ns.cpptraj >0-fullrmsd plotting.ipynb rmsd_backrub.dat rmsd_fast.dat rmsd_relax.dat rmsdca_backrub.png rmsdca_fast.png rmsdca_full.png rmsdca_relax.png >1-helix_rmsd helix_rmsd.png plotting.ipynb rmsd_backrub_h.dat rmsd_fast_h.dat rmsd_relax_h.dat rmsdca_backrub.png rmsdca_fast.png rmsdca_relax.png >2-rmsf rmsf_backrub.dat rmsf_backrub.png rmsf_fast.dat rmsf_fast.png rmsf_relax.dat rmsf.relax.png RMSF.ipynb >backrub_trajectory >1 4d2backrub.ipncrd 4d2backrub.prmtop md10.nc md20.nc md30.nc md40.nc md50.nc md60.nc md70.nc md80.nc md90.nc md100.nc >2 4d2backrub.ipncrd 4d2backrub.prmtop md10.nc md20.nc md30.nc md40.nc md50.nc md60.nc md70.nc md80.nc md90.nc md100.nc >3 4d2backrub.ipncrd 4d2backrub.prmtop md10.nc md20.nc md30.nc md40.nc md50.nc md60.nc md70.nc md80.nc md90.nc md100.nc >fastdesign_trajectory >1 4d2fastdesign.ipncrd 4d2fastdesign.prmtop md10.nc md20.nc md30.nc md40.nc md50.nc md60.nc md70.nc md80.nc md90.nc md100.nc >2 4d2fastdesign.ipncrd 4d2fastdesign.prmtop md10.nc md20.nc md30.nc md40.nc md50.nc md60.nc md70.nc md80.nc md90.nc md100.nc >3 4d2fastdesign.ipncrd 4d2fastdesign.prmtop md10.nc md20.nc md30.nc md40.nc md50.nc md60.nc md70.nc md80.nc md90.nc md100.nc >Analysis 1.nc 2.nc 3.nc 4d2fastdesign.inpcrd 4d2fastdesign.prmtop refrmsd_backbone_h.cpptraj refrmsd_backbone.cpptraj rms.dat rmsd_1.dat rmsd_1h.dat rmsd_2.dat rmsd_2h.dat rmsd_3.dat rmsd_3h.dat rmsd_fast_h.dat rmsd_fast.dat rmsf.cpptraj rmsf1.dat rmsf2.dat rmsf3.dat >relaxrepack_trajectory >1 4d2relaxrepack.ipncrd 4d2relaxrepack.prmtop md10.nc md20.nc md30.nc md40.nc md50.nc md60.nc md70.nc md80.nc md90.nc md100.nc >2 4d2relaxrepack.ipncrd 4d2relaxrepack.prmtop md10.nc md20.nc md30.nc md40.nc md50.nc md60.nc md70.nc md80.nc md90.nc md100.nc >3 4d2relaxrepack.ipncrd 4d2relaxrepack.prmtop md10.nc md20.nc md30.nc md40.nc md50.nc md60.nc md70.nc md80.nc md90.nc md100.nc >Analysis 1.nc 2.nc 3.nc 4d2relaxrepack.inpcrd 4d2relaxrepack.prmtop refrmsd_backbone_h.cpptraj refrmsd_backbone.cpptraj rms.dat rmsd_1.dat rmsd_1h.dat rmsd_2.dat rmsd_2h.dat rmsd_3.dat rmsd_3h.dat rmsd_fast_h.dat rmsd_fast.dat rmsf.cpptraj rmsf1.dat rmsf2.dat rmsf3.dat >m4D2_heme_MD m4D2.pdb (representative m4D2 model from MD simulations) >1 m4d2_backrub.ipncrd m4d2_backrub.prmtop md10.nc md20.nc md30.nc md40.nc md50.nc md60.nc md70.nc md80.nc md90.nc md100.nc >2 m4d2_backrub.ipncrd m4d2_backrub.prmtop md10.nc md20.nc md30.nc md40.nc md50.nc md60.nc md70.nc md80.nc md90.nc md100.nc >3 m4d2_backrub.ipncrd m4d2_backrub.prmtop md10.nc md20.nc md30.nc md40.nc md50.nc md60.nc md70.nc md80.nc md90.nc md100.nc >m4D2_Rosetta_scripts Backrub.xml FastDesign.xml RelaxRepack