** How to prepare inputs for complex modeling **

1. Generate multiple sequence alignments for each subunit

2. Make paired alignments
   - It is important to generate "good" paired sequence alignments to extract coevolution signal properly.
   - For bacterial proteins, you may use "make_joint_MSA_bacterial.py" script to generate paired alignments. It pairs the sequences having similar UniProt accession code.
   - For eukaryotes, there's no easy way to generate paired alignments. Good luck!

3. Filter the paired alignment using hhfilter
   - hhfilter -i paired.a3m -o filtered.a3m -id 90 (or 95) -cov 75 (or 50)

3. If you want to incorporate complex template information, please make npz
file that contains input template features for RoseTTAFold. It should contain
the following keys ("xyz_t", "t1d", "t0d").
   - xyz_t: N, CA, C coordinates of complex templates (# of templ, # of residue, 3 (for N, Ca, C), 3 (xyz coord))
            For the unaligned region, it should be NaN.
   - t1d: 1-D features from HHsearch results (score, SS, probab column from atab file) (T, L, 3).
          For the unaligned region, it should be zeros
   - t0d: 0-D features from HHsearch (Probability/100.0, Ideintities/100.0, Similarity fro hhr file) (T, 3)

4. Run complex structure prediction
   - python network/predict_complex.py -i filtered.a3m -o complex -Ls 218 310 
   - Set the numeric parameters after -Ls argument to the lengths of each individual subunit, in the order that they were paired.
      - In this example, the aa length of subunit1 was 218, subunit2 was 310.

5. You may want to run Rosetta fastrelax w/ coordinate restraints to add sidechains.