missing CIFS in pdb_mmcif?

[ryao-mdanderson]

Hello, Kalininalab support member!

I am trying alphafold 2.1.1 and this non docker version of set up. Thank you very much for providing this non-docker version, it helps us to set up on HPC cluster.

The testing I experienced is can't find CIFs,

(alphafold-2.1.1) [user@cdragon096 alphafold]$ bash run_alphafold.sh -d $HOME/alphafold/alphafold_data -o ./dummy_test/ -m model_1 -f $HOME/alphafold/alphafold_non_docker/example/query.fasta -t 2020-05-14 -g False Unknown model preset! Using default ('monomer') E1118 12:13:41.684854 46912496434880 templates.py:837] Could not find CIFs in $HOME/alphafold/alphafold_data/pdb_mmcif/mmcif_files Traceback (most recent call last): File "/home/ryao/alphafold/run_alphafold.py", line 427, in app.run(main) File "/risapps/rhel7/python/3.7.3/envs/alphafold-2.1.1/lib/python3.8/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/risapps/rhel7/python/3.7.3/envs/alphafold-2.1.1/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/home/ryao/alphafold/run_alphafold.py", line 341, in main template_featurizer = templates.HhsearchHitFeaturizer( File "$HOME/alphafold/alphafold/data/templates.py", line 838, in init raise ValueError(f'Could not find CIFs in {self._mmcif_dir}') ValueError: Could not find CIFs in $HOME/alphafold_data/pdb_mmcif/mmcif_files (alphafold-2.1.1)

Would you please advise if I have missing anything?

Regards, Rong

[ryao-mdanderson]

Please ignore my message. I figured out 2 places to be fixed

1, I should use "-t 2021-11-01" to do the testing; 2, refer to https://github.com/deepmind/alphafold/issues/54 there is a bug fix, in data directory mgnify, set up symbolic link ln -s mgy_clusters.fa mgy_clusters_2018_12.fa

[sanjaysrikakulam]

Hi @ryao-mdanderson

Thank you for the solutions. Yes, mgnify database name should be corrected if you are using latest version of AF2. I also updated our download_db.sh accordingly in the latest update.