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