FileNotFoundError:

[Ryosuke-254]

A FileNotFoundError: [Errno 2] No such file or directory: error occurs. This error appears when inputting long sequences or complex structures into the contigs. When generating proteins with simple structures, this error doesn't occur, so it's unlikely that the error is due to file path names. How should this be addressed? This is regarding the Colab version of RF diffusion.

[roccomoretti]

Including which file or directory is not found (should be the line after the message you quote) may help track down which particular part of the process is at issue, and thus the proper resolution.

[Ryosuke-254]

FileNotFoundError Traceback (most recent call last)
in

in run_diffusion(contigs, path, pdb, iterations, symmetry, order, hotspot, chains, add_potential, num_designs, visual)

/content/colabdesign/shared/protein.py in pdb_to_string(pdb_file, chains, models)
39 old_lines = pdb_file.split("\n")
40 else:
---> 41 with open(pdb_file,"rb") as f:
42 old_lines = [line.decode("utf-8","ignore").rstrip() for line in f]
43 for line in old_lines:

FileNotFoundError: [Errno 2] No such file or directory: '&WVS.pdb1'
FileNotFoundError Traceback (most recent call last)
in <cell line: 52>()
66 plot_pdb(dropdown.value)
67 else:
---> 68 plot_pdb()

in plot_pdb(num)
22 else:
23 pdb = f"outputs/{path}_{num}.pdb"
---> 24 pdb_str = open(pdb,'r').read()
25 view.addModel(pdb_str,'pdb',{'hbondCutoff':hbondCutoff})
26 if color == "rainbow":

FileNotFoundError: [Errno 2] No such file or directory: 'outputs/6WVS12_0.pdb'
I'm getting this error, but I don't know what to do. I've told you many times that this error doesn't occur for simple proteins. 6WVS is a protein example given in the paper, so the program should work fine. This time, I'm entering alpha helix and beta sheet coordinate information in contigs, 6WVS in pdb, 1 in num designs, cyclic in symmetry, and 8 in order.

[roccomoretti]

No such file or directory: '&WVS.pdb1'

I'm concerned about the & and 1 there. My guess is that however you're specifying your input PDB names, you're getting extra spurious characters, and that's causing issues.