google-deepmind
Help info should indicate that a filename argument is needed
https://github.com/google-deepmind/alphafold/blob/020cd6d6cb16540114a084f9dbb8f21f811f9d21/run_alphafold.py#L92
The help/usage info currently states
--pdb_seqres_database_path: Path to the PDB seqres database for use by hmmsearch.
This option seems to require a filename argument where the other database specification options require a directory. It would be helpful for the help info to be more explicit in what is required for an input argument, especially since the error will take 15-20 minutes to occur.
The help text for the pdb_seqres_database_path flag was unclear—it did not specify that a full file path (not just a directory) is required.
I updated the help text in run_alphafold.py to clearly state that the full file path to the PDB seqres database file must be provided, making it less confusing for users.
Please reply if I made any mistake !
@Augustin-Zidek I believe we can close this: https://github.com/google-deepmind/alphafold/pull/1083#issuecomment-3214795671
Fixed by @rpachauri in https://github.com/google-deepmind/alphafold/commit/e57fba02b18a33334b1304846830021b9e46f8af. Thanks!
