Data preparation

Download the data for this tutorial from here

Create a directory for your project and gather your data there. For this tutorial the data files are organized as follows:

Elongator/

    # Electron microscopy map
    EM_data/
        emd_4151_binned.mrc

    #input structures for modeling
    in_pdbs/
        Elp1.CTD.on5cqs.5cqr.model_ElNemo_mode7.pdb
        Elp1_NTD_1st_propeller.pdb
        Elp1_NTD_2nd_propeller.pdb
        Elp2.pdb
        Elp3.flex_helix.pdb
        Elp3.helix4.pdb
        Elp3.mono.pdb

    #FASTA-formatted file with sequences of all subunits
    elp_sequences.fasta

    #Crosslink files in xQuest or Xlink Analyzer format
    xlinks/
        DSS/
            inter_run3_190412.clean_strict.csv
            intra_run3_190412.clean_strict.csv
            loop_run3_190412.clean_strict.csv
            mono_run3_190412.clean_strict.csv
            sg1-inter.clean_strict.csv
            sg1-intra.clean_strict.csv
            sg1-loop.clean_strict.csv
            sg2-3-inter.clean_strict.csv
            sg2-3-intra.clean_strict.csv
            sg2-3-loop.clean_strict.csv
            sg2-3-mono.clean_strict.csv
        DSG/
            inter_dsg.clean_strict.csv
            inter_dsg_repeat.clean_strict.csv
            intra_dsg.clean_strict.csv
            intra_dsg_repeat.clean_strict.csv
            loop_dsg.clean_strict.csv
            loop_dsg_repeat.clean_strict.csv
            mono_dsg.clean_strict.csv
            mono_dsg_repeat.clean_strict.csv