Data preparation ================ .. note:: The data needed to follow the ScNPC modelling tutorial can be obtained from our git repository `ScNPC_tutorial git repository `__. Create a directory for your project and gather all your data there. For this tutorial the corresponding data files are organized per modelling target (e.g. CR Y-complex, NR Y-complex etc.) and Assembline modelling mode (sub-pipeline) that was used (see following sections of the tutorial). This repository includes the following modelling project directories (repository architecture): :: scnpc_tutorial/ # CR Y-complex data CR_Y_complex/ # Electron microscopy maps EM/ P-complex_fit1_0.86_search_100000_correlation_600_0.3_CR_with_Y_no_env_map_best.mrc membrane_cerevisiae_no_neg_relative.mrc CR_with_Y_no_env_relative.mrc #input structures for modeling input_PDB/ ScNup84_437-726_ScNup133C_490_1155_renamed_relative_3I4R.pdb ScNup133N_56-480_renamed.pdb 4XMM.renamed.noAb_Seh1_Nup85_47_544_3F3F.pdb 4XMM.renamed.noAb_Nup145c_149-550_Sec13_Nup84_7-436_3IKO_updated.pdb 4XMM.renamed.noAb_Nup120_715-1036_Nup85_553-744_Nup145c_92-99_554-712_remaining_updated.pdb 4XMM.renamed.noAb_Nup120_2-711_3F7F_updated.pdb #FASTA-formatted file with sequences of all subunits ScNPC_sequences.fasta # IR asymmetric unit data IR_asymmetric_unit_refinement/ # Electron microscopy maps EM/ IR_relative_no_env.mrc #input structures for modeling input_PDB/ ScNup192_NTD_nucl_in.pdb ScNup192_NTD_cyt_in.pdb ScNup192_CTD_nucl_in.pdb ScNup192_CTD_cyt_in.pdb ScNup188_NTD_nucl_out.pdb ScNup188_NTD_cyt_out.pdb ScNup188_CTD_nucl_out.pdb ScNup188_CTD_cyt_out.pdb ScNup170_NTD_nucl_in.pdb ScNup170_NTD_cyt_in.pdb ScNup170_CTD_nucl_in.pdb ScNup170_CTD_cyt_in.pdb ScNup157_NTD_nucl_out.pdb ScNup157_NTD_cyt_out.pdb ScNup157_CTD_nucl_out.pdb ScNup157_CTD_cyt_out.pdb ScNsp1_complex_nucl_out.pdb ScNsp1_complex_nucl_in.pdb ScNsp1_complex_cyt_out.pdb ScNsp1_complex_cyt_in.pdb ScNic96_CTD_nucl_out.pdb ScNic96_CTD_nucl_in.pdb ScNic96_CTD_cyt_out.pdb ScNic96_CTD_cyt_in.pdb #FASTA-formatted file with sequences of all subunits ScNPC_sequences.fasta # NR Y-complex data (master dir with refinement & global optimization data) NR_Y_complex/ # Electron microscopy maps for refinement EM/ NR_merged_unerased_tail_relative_clean_v1.3.mrc membrane_cerevisiae_no_neg_relative_NR_v3.mrc #input structures for refinement NR_Y_complex_de_novo_model_PDBs/ ScNup84_506-726_ScNup133C_882_1155_renamed_relative_3CQC_new_1.pdb ScNup133N_56-480_renamed_1.pdb ScNup133C_490_881_renamed_relative_3CQC_1.pdb 4XMM.renamed.noAb_Seh1_Nup85_47_544_3F3F_1.pdb 4XMM.renamed.noAb_Nup145c_149-550_Sec13_Nup84_7-436_3IKO_updated_1.pdb 4XMM.renamed.noAb_Nup120_715-1036_Nup85_553-744_Nup145c_92-99_554-712_remaining_updated_1.pdb 4XMM.renamed.noAb_Nup120_2-711_3F7F_updated_1.pdb #FASTA-formatted file with sequences of all subunits ScNPC_sequences.fasta #NR Y-complex data (dir with global optimization data) NR_Y_complex_de_novo_run/ # Electron microscopy maps for global optimization EM/ NR_merged_unerased_tail_relative_clean_v1.3.mrc membrane_cerevisiae_no_neg_relative_NR_v3.mrc #input structures for global optimization input_PDB/ ScNup84_506-726_ScNup133C_882_1155_renamed_relative_3CQC_new.pdb ScNup133N_56-480_renamed.pdb ScNup133C_490_881_renamed_relative_3CQC.pdb 4XMM.renamed.noAb_Seh1_Nup85_47_544_3F3F.pdb 4XMM.renamed.noAb_Nup145c_149-550_Sec13_Nup84_7-436_3IKO_updated.pdb 4XMM.renamed.noAb_Nup120_715-1036_Nup85_553-744_Nup145c_92-99_554-712_remaining_updated.pdb 4XMM.renamed.noAb_Nup120_2-711_3F7F_updated.pdb #FASTA-formatted file with sequences of all subunits ScNPC_sequences.fasta # Nup116k.o. ScNPC (at 25C) data Nup116delta25C/ # Electron microscopy maps EM/ Spoke_116d_25C_1fold_new.mrc membrane_cerevisiae_wt_relative_to_Spoke_116d_25C_1fold_new.mrc #input structures for modeling input_PDB/ ScNup84_506-726_ScNup133C_882_1155_renamed_relative_3CQC_new_NR.pdb ScNup84_506-726_ScNup133C_882_1155_renamed_relative_3CQC_CR.pdb ScNup192_NTD_nucl_in.pdb ScNup192_NTD_cyt_in.pdb ScNup192_CTD_nucl_in.pdb ScNup192_CTD_cyt_in.pdb ScNup188_NTD_nucl_out.pdb ScNup188_NTD_cyt_out.pdb ScNup188_CTD_nucl_out.pdb ScNup188_CTD_cyt_out.pdb ScNup170_NTD_nucl_in.pdb ScNup170_NTD_cyt_in.pdb ScNup170_CTD_nucl_in.pdb ScNup170_CTD_cyt_in.pdb ScNup157_NTD_nucl_out.pdb ScNup157_NTD_cyt_out.pdb ScNup157_CTD_nucl_out.pdb ScNup157_CTD_cyt_out.pdb ScNup133N_56-480_renamed_NR.pdb ScNup133N_56-480_renamed_CR.pdb ScNup133C_490_881_renamed_relative_3CQC_NR.pdb ScNup133C_490_881_renamed_relative_3CQC_CR.pdb ScNsp1_complex_nucl_out.pdb ScNsp1_complex_nucl_in.pdb ScNsp1_complex_cyt_out.pdb ScNsp1_complex_cyt_in.pdb ScNic96_CTD_nucl_out.pdb ScNic96_CTD_nucl_in.pdb ScNic96_CTD_cyt_out.pdb ScNic96_CTD_cyt_in.pdb 4XMM.renamed.noAb_Seh1_Nup85_47_544_3F3F_NR.pdb 4XMM.renamed.noAb_Seh1_Nup85_47_544_3F3F_CR.pdb 4XMM.renamed.noAb_Nup145c_149-550_Sec13_Nup84_7-436_3IKO_updated_NR.pdb 4XMM.renamed.noAb_Nup145c_149-550_Sec13_Nup84_7-436_3IKO_updated_CR.pdb 4XMM.renamed.noAb_Nup120_715-1036_Nup85_553-744_Nup145c_92-99_554-712_remaining_updated_NR.pdb 4XMM.renamed.noAb_Nup120_715-1036_Nup85_553-744_Nup145c_92-99_554-712_remaining_updated_CR.pdb 4XMM.renamed.noAb_Nup120_2-711_3F7F_updated_NR.pdb 4XMM.renamed.noAb_Nup120_2-711_3F7F_updated_CR.pdb #FASTA-formatted file with sequences of all subunits ScNPC_sequences.fasta # Nup116k.o. ScNPC (at 37C) data Nup116delta37C/ # Electron microscopy maps EM/ Nup116_37C_unmasked.mrc NR_116d37.mrc membrane_116d37C_relative_to_unmasked.mrc membrane_116d37C.mrc #input structures for modeling input_PDB/ ScNup84_506-726_ScNup133C_882_1155_renamed_relative_3CQC_new_NR.pdb ScNup188_NTD_nucl_out.pdb ScNup188_CTD_nucl_out.pdb ScNup157_NTD_nucl_out.pdb ScNup157_CTD_nucl_out.pdb ScNup133N_56-480_renamed_NR.pdb ScNup133C_490_881_renamed_relative_3CQC_NR.pdb ScNsp1_complex_nucl_out.pdb ScNic96_CTD_nucl_out.pdb 4XMM.renamed.noAb_Seh1_Nup85_47_544_3F3F_NR.pdb 4XMM.renamed.noAb_Nup145c_149-550_Sec13_Nup84_7-436_3IKO_updated_NR.pdb 4XMM.renamed.noAb_Nup120_715-1036_Nup85_553-744_Nup145c_92-99_554-712_remaining_updated_NR.pdb 4XMM.renamed.noAb_Nup120_2-711_3F7F_updated_NR.pdb #FASTA-formatted file with sequences of all subunits ScNPC_sequences.fasta