error on installing AF2complex on colab notebook

[herman-einstein]

When I try to run AF2complex on colab, I come across the following error. I will very much appreciate if you can solve this error for me.

[FreshAirTonight]

The reason for this error is because Colab updated their environment, which unforuntaly is incompatible with the current notebook. If you have direct access to a GPU node, you could try install AF2Complex and run it directly.

[herman-einstein]

I see. Thank you very much

[herman-einstein]

I am using school's server to run alphafold and command is somthing like the following

_module add singularity/3.10.0 SIMG=/share/apps/singularity/simg/alphafold/alphafold_2_3_1.sif singularity exec --nv --bind /data:/data,/share:/share,/home:/home $SIMG bash -c "ulimit -s unlimited; python /app/alphafold/run_alphafold.py --fasta_paths=/home/alphafold_analysis/output/query.fasta --max_template_date=2023-12-01 --model_preset=multimer --data_dir=/home/alphafold_analysis/alphafold_database --output_dir=/home/alphafold_analysis/output --uniref90_database_path=/home/alphafold_analysis/alphafold_database/uniref90/uniref90.fasta --mgnify_database_path=/home/alphafold_analysis/alphafold_database/mgnify/mgy_clusters_2022_05.fa --template_mmcif_dir=/home/alphafold_analysis/alphafold_database/pdb_mmcif/mmcif_files --obsolete_pdbs_path=/home/alphafold_analysis/alphafold_database/pdb_mmcif/obsolete.dat --pdb_seqres_database_path=/home/alphafold_analysis/alphafold_database/pdb_seqres/pdb_seqres.txt --uniprot_database_path=/home/alphafold_analysis/alphafold_database/uniprot/uniprot.fasta --db_preset=reduced_dbs --small_bfd_database_path=/home/alphafold_analysis/alphafold_database/small_bfd/bfd-first_non_consensus_sequences.fasta --use_gpurelax=False"

I only have limited access to Alphafold using the server. Moreover, I think I am using singularity to run Alphafold instead of docker. May I know where I should alter the command so that I can run af2complex propoerly?

[herman-einstein]

May I know what version of jaxlib I should have if I install jax==0.3.25 because I following the command you suggested

_CUDA=11.1.1 pip3 install --upgrade --no-cache-dir jax==0.2.14 \ jaxlib==0.1.69+cuda$(cut -f1,2 -d. <<< ${CUDA} | sed 's/.//g') \ -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html_

but there is other error like

I very much appreciate if you could suggest me the version of installing jax and jaxlib

[FreshAirTonight]

Please try:

cd af2complex directory
$ pip3 install -r requirements.txt
$ pip3 install jax==0.3.25 jaxlib==0.3.25+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

[herman-einstein]

Please try:

cd af2complex directory
$ pip3 install -r requirements.txt
$ pip3 install jax==0.3.25 jaxlib==0.3.25+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

Very much appreciate your help.

In addition, I find that scipy.spatial is needed in your modified alphafold script "confidence.py", line 532 but you did not import this package for the command.

Again, thank you very much for your help.