Update/download of pdb_mmcif in alphafold2/2022-02-02

IFB Core Cluster Tool or data bank request
1

Hello @team.bank @team.alphafold,

AlphaFold-Multimer is giving an error when searching for templates:

File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.1.1/lib/python3.8/site-packages/alphafold/data/templates.py", line 681, in _read_file
with open(path, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/shared/bank/alphafold2/current/pdb_mmcif/mmcif_files/7olc.cif'
srun: error: gpu-node-03: task 0: Exited with exit code 1

In fact, the pdb_mmcif databank has not been updated concomitantly with pdb_seqres in /shared/bank/alphafold2/2022-02-02 as indicated in the AlphaFold-Multimer documentation (extract below):

  • Remove <DOWNLOAD_DIR>/pdb_mmcif. It is needed to have PDB SeqRes and PDB from exactly the same date. Failure to do this step will result in potential errors when searching for templates when running AlphaFold-Multimer.
  • Run scripts/download_pdb_mmcif.sh <DOWNLOAD_DIR>.
  • Run scripts/download_pdb_seqres.sh <DOWNLOAD_DIR>.

Would be possible to fix it? Thank you very much!

Andreas

2

Hello,

Yes the directory alphafold2/2022-02-02 is not ready yet.

I have started the download after your message here: Demande installation banque données pour AlphaFold 2.1 (Multimer)

As you can see I don't answer to it :wink: because it always failed on pdb_mmcif download so this directory is not ready for use now.

3

Hello,

I have noticed that pdb_mmcif was empty that why in my command line I am pointing to the pdb_mmcif directory under current. I realized I had this error, because I am using pdb_seqres in 2022-02-02/, so if alphafold finds a similarity in pdb_seqres with a recently solved structure (i.e 7olc), it will not find the corresponding structure file in current/pdb_mmcif.

If the match correspond to a template from a "old" structure, alphafold runs smoothly and provides predicted models.

If the download of the most recent pdb_mmcif is still giving issues (timeout?), could it be possible to retrieve an older version of pdb_seqres (if available)?

4

Hello,

I donwload it on my own personnel computer and transfert it to the cluster after that, I think the db is ok now, please confirm or not.

I also update the current link.