RosettaCommons
Traceback (most recent call last)
I encountered the following error while executing the task. Does anyone know how to resolve it? Thank you.
./scripts/run_inference.py scaffoldguided.target_path=../IL10/IL10RA.pdb inference.output_prefix=IL10_outputs/design_ppi_scaffolded scaffoldguided.scaffoldguided=True 'ppi.hotspot_res=[S44,S76,S96,S101,S190,S191]' scaffoldguided.target_pdb=True scaffoldguided.scaffold_dir=./ppi_scaffolds/ inference.num_designs=5 denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0
Error executing job with overrides: ['scaffoldguided.target_path=./IL10/IL10RA.pdb', 'inference.output_prefix=IL10_outputs/design_ppi_scaffolded', 'scaffoldguided.scaffoldguided=True', 'ppi.hotspot_res=[S44,S76,S96,S101]', 'scaffoldguided.target_pdb=True', 'scaffoldguided.scaffold_dir=./ppi_scaffolds/', 'inference.num_designs=5', 'denoiser.noise_scale_ca=0', 'denoiser.noise_scale_frame=0'] Traceback (most recent call last): File "/home/L/RFdiffusion/./scripts/run_inference.py", line 84, in main x_init, seq_init = sampler.sample_init() File "/home/L/RFdiffusion/rfdiffusion/inference/model_runners.py", line 776, in sample_init self.L, self.ss, self.adj = self.blockadjacency.get_scaffold() File "/home/L/RFdiffusion/rfdiffusion/inference/utils.py", line 891, in get_scaffold item = random.choice(self.scaffold_list) File "/home/L/miniconda3/envs/SE3nv/lib/python3.9/random.py", line 346, in choice return seq[self._randbelow(len(seq))] IndexError: list index out of range
Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.
I know how to solve it now. It was a path specification error in the code, and I hope it can be a reference for future generations
Hello, could you share how you solve this problem, I'm also encountering the same problem. Thank you for your help!
It's not immediately obvious, but the directory passed to scaffoldguided.scaffold_dir must contain *_ss.pt and *_adj.pt files (not raw PDB files). See examples/design_timbarrel.sh and the associated examples/tim_barrel_scaffold/ directory for an example. -- I think you're getting the error you are because there are no such files in your specified directory.
As mentioned in the Fold Conditioning section of the README, these can be created with the make_secstruc_adj.py helper script.
