No such file or directory: '.../pdb_mmcif/mmcif_files/XXXX.cif'

[biomolecule]

Now l'm running AF2 multimer with "run_alphafold.py" . Both MSAs' generation for two chains are success, as well as the template search for the first chain. BUT python report an error during that of the second:

FileNotFoundError: [Errno 2] No such file or directory: '.../pdb_mmcif/mmcif_files/7xiv.cif'

The publication date of the 7xiv is 2022-06, but the download date of pdb_mmcif is earlier, so, as my concerned, the most simple solution is to set the AF2's paramater "max_template_date" even earlier than database download, such as

--max_template_date=2020-05-14

But the error occurs again. Update pdb_mmcif might be another solution, but it is unacceptable to upgrade it everytime running AF2. It seems the " --max_template_date" does not work.

What should l do to avoid such error?

Regards

[benediktsinger]

I am expierencing the same issue with another protein not being found (7nvm) even though max_template_date is set.

[Htomlinson14]

Hi thanks for raising this. Have you updated the pdb_seqres file more recently than the PDB mmcif files? This error is likely to happen when they are out of sync. In the future we can add a more informative error message.

[phpeters]

I am experiencing the same issue and first tried changing the max_template_date, but that didn't help. Then I re-ran both download_pdb_mmcif.sh and download_pdb_seqres.sh yesterday. But the error persists, mmcif_files/6ek0.cif is missing. What I found is that 6ek0 appears in the obsolete.dat. Any idea how to proceed? Thanks and best! Philipp

[Maiya19724]

I am experiencing the same issue and first tried changing the max_template_date, but that didn't help. Then I re-ran both download_pdb_mmcif.sh and download_pdb_seqres.sh yesterday. But the error persists, mmcif_files/6ek0.cif is missing. What I found is that 6ek0 appears in the obsolete.dat. Any idea how to proceed? Thanks and best! Philipp

https://files.wwpdb.org/pub/pdb/data/structures/divided/mmCIF/ek/6eko.cif.gz

[Maiya19724]

I am experiencing the same issue and first tried changing the max_template_date, but that didn't help. Then I re-ran both download_pdb_mmcif.sh and download_pdb_seqres.sh yesterday. But the error persists, mmcif_files/6ek0.cif is missing. What I found is that 6ek0 appears in the obsolete.dat. Any idea how to proceed? Thanks and best! Philipp

or sync the PDB mmcif files

[phpeters]

Hej @Maiya19724, Thanks a lot for our help! Sadly, this is not the missing file - 6ek0 (with a zero) is not in the pdb ek-folder.

or sync the PDB mmcif files This is what download_pdb_mmcif.sh is doing, right? I did this and 6ek0 was not in there.

Thanks and best! Philipp

[Maiya19724]

Hej @Maiya19724, Thanks a lot for our help! Sadly, this is not the missing file - 6ek0 (with a zero) is not in the pdb ek-folder.

or sync the PDB mmcif files This is what download_pdb_mmcif.sh is doing, right? I did this and 6ek0 was not in there.

Thanks and best! Philipp

sorry for that.