The project is difficult to use

[KKKangKaiKK]

This is an interesting project with great potential for solving ligand-receptor pairing. However, I have encountered several issues that make it difficult for those who are not familiar with your code to use it effectively. Here are the problems I found:

1. There is a merge conflict in the compute_msa_parallel.sh file, specifically in lines 15-20. Please resolve this conflict.
2. In the run_parafold_no_template.sh script, you are passing the --data_dir argument to alphafold_script. However, it seems that ParallelFold/run_alphafold.py is unable to parse this argument correctly.
3. The ParallelFold/run_alphafold.py script requires the --parameter_pat argument, which is not being passed by run_parafold_no_template.sh.

I hope these suggestions help in resolving the issues.

[denizkavi]

Thank you for bringing this to our attention, I'll get to resolve them right away. Thank you for your interest!