Can you give me a concrete example of how to do this?

[Jo-Hyung-Sik]

I recently came across this paper, and I think it introduces a really impressive feature.

I believe it could make a significant impact in my research field, particularly in predicting ternary complex structures.

Right now, I’m simply trying to create a PPI binding structure between two proteins.

However, the instructions for running the code are quite vague.

Even after modifying the run_peptides_helix.slurm file in the masif_seed_search folder of the main branch, I still get the following error:

masif-neosurf/masif_seed_search/data/masif_targets/targets/template/run_peptides_helix.slurm: 10: masif-neosurf/masif_seed_search/data/masif_targets/targets/template/run_peptides_helix.slurm: [[: not found
params_peptides_helix
Traceback (most recent call last):
  File "/home/masif-neosurf/masif_seed_search/source/masif_seed_search_nn.py", line 26, in <module>
    custom_params_obj = importlib.import_module(custom_params_fn, package=None)
  File "/usr/local/lib/python3.6/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 994, in _gcd_import
  File "<frozen importlib._bootstrap>", line 971, in _find_and_load
  File "<frozen importlib._bootstrap>", line 953, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'params_peptides_helix'

I was able to generate a search output using the Python code from the update branch.

I could visualize the .vert file in PyMOL

But I have no idea how to use the coordinates in Rosetta.

Could you please share a really simple working example?

[arneschneuing]

Hi @Jo-Hyung-Sik, thanks for message and your interest in our work. I indeed recommend the masif_search.py script from the update branch as the entry point for running a search. There should be a minimal example in the corresponding README.
What search parameters did you use in your case? For example, what was the database you searched against? If the search was successful, there should be sub-directories with all hits found in PDB format in the same folder as the .vert file.