OpenFold3

A fully open source biomolecular structure prediction model based on AlphaFold3 OpenFold3 Homepage

Available Modules

module load OpenFold3/0.4.4-foss-2026-CUDA-13.2.1

Warning

Description

Referencing

Setting up OpenFold3

Downloading the parameters files

If you are using OpenFold3 for the first time on Mahuika, you will need to download the OpenFold3 model parameters to your directory.

1. Load OpenFold3:

   module load OpenFold3
   

2. Run setup_openfold in the terminal:

   setup_openfold
   

   • You will need to write out in full the direct path to where you want to store OpenFold3 files.
   • Please specify the OpenFold cache directory: Best idea to change this to your project folder. Example: /nesi/project/<PROJECT_ID>/<USERNAME>/openfold3
   • Please specify the directory for parameter download: This should default to your cache directory. Example /nesi/project/<PROJECT_ID>/<USERNAME>/openfold3
   • Select parameters to download: Download whatever parameters you would like.
   • Force re-download parameters even if they already exist?: Set this to yes
   • Run integration tests?: no

   The setup should look something like this

   user.name@login03:~$ setup_openfold
   [2026-08-11 17:54:31,291] [WARNING] [real_accelerator.py:199:get_accelerator] Setting accelerator to CPU. If you have GPU or other accelerator, we were unable to detect it.
   Setting up OpenFold3...
   Please specify the OpenFold cache directory (default: /home/user.name/.openfold3): /nesi/project/nesi12345/user.name/openfold3
   Please specify the directory for parameter download (default: /nesi/project/nesi12345/user.name/openfold3): 
   Select parameters to download:
   1) Download only the default checkpoint (openfold3-p2-155k)
   2) Download all parameters (openfold3-p2-145k, openfold3-p2-155k)
   3) Download a specific parameter by name
   Enter your choice (1/2/3, default: 1): 2
   Force re-download parameters even if they already exist? (yes/no, default: no) yes
   Run integration tests? (yes/no) no
   Parameters directory set to: /nesi/project/nesi12345/user.name/openfold3
   Starting parameter download...
   Downloading s3://openfold3-data/openfold3-parameters/of3-p2-145k.pt (2.13 GB) to /nesi/project/nesi12345/user.name/openfold3/of3-p2-145k.pt...
   of3-p2-145k.pt: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2.29G/2.29G [00:19<00:00, 115MB/s]
   Download complete.
   Downloading s3://openfold3-data/openfold3-parameters/of3-p2-155k.pt (2.13 GB) to /nesi/project/nesi12345/user.name/openfold3/of3-p2-155k.pt...
   of3-p2-155k.pt: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2.29G/2.29G [00:19<00:00, 116MB/s]
   Download complete.
   Download completed successfully.
   Starting Biotite CCD setup...
   Biotite CCD file at /opt/nesi/zen3/OpenFold3/0.4.4-foss-2026-CUDA-13.2.1/lib/python3.14/site-packages/biotite/structure/info/components.bcif is up-to-date with s3://openfold3-data/components.bcif, skipping.
   Skipping integration tests.
   Setup configuration saved to /nesi/project/nesi12345/user.name/openfold3/setup_config.json
   

   Warning

   If you get an error message relating to Biotite CCD, get in touch with support.

3. Add the following line to your .bashrc and source it. Make sure you change OPENFOLD_CACHE to what you gave in step 2:

   # Change the OPENFOLD_CACHE to what you used in step 2.
   OPENFOLD_CACHE=/nesi/project/<PROJECT_ID>/<USERNAME>/openfold3
   printf '\n# Path to your OpenFold3 Cache\nexport OPENFOLD_CACHE='${OPENFOLD_CACHE}'\n' >> ~/.bashrc
   source ~/.bashrc
   

   Check that your OPENFOLD_CACHE path is correct:

   echo $OPENFOLD_CACHE
   

   If this doesn't look right, you will need to change your ~/.bashrc file by using nano or vim.

4. Test that your setup was successful. In the terminal, copy the following json file from openfold3:

   cat > query_ubiquitin.json << 'EOF'
   {
     "queries": {
       "ubiquitin": {
         "chains": [
           {
             "molecule_type": "protein",
             "chain_ids": ["A"],
             "sequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG"
           }
         ]
       }
     }
   }
   EOF
   

   Then run the following in your terminal:

   python - <<'EOF'
   import os, pathlib, zipfile
   
   import openfold3
   from openfold3.projects.of3_all_atom.config.inference_query_format import InferenceQuerySet
   print("[ok] openfold3 imports")
   
   import biotite.structure.info as info
   print(f"[ok] CCD: {len(info.all_residues())} components, "
         f"ALA={info.residue('ALA').array_length()} atoms")
   
   cache = pathlib.Path(os.environ.get("OPENFOLD_CACHE", pathlib.Path.home() / ".openfold3"))
   ckpts = sorted(cache.glob("*.pt"))
   assert ckpts, f"no checkpoint in {cache}"
   for c in ckpts:
       print(f"[ok] checkpoint {c.name}: {c.stat().st_size/1e9:.2f} GB, "
             f"intact={zipfile.is_zipfile(c)}")
   
   InferenceQuerySet.from_json("query_ubiquitin.json")
   print("[ok] query JSON validates against this version's schema")
   EOF
   

   If successful, you will get the following output:

   [2026-08-11 18:03:24,289] [WARNING] [real_accelerator.py:199:get_accelerator] Setting accelerator to CPU. If you have GPU or other accelerator, we were unable to detect it.
   [ok] openfold3 imports
   [ok] CCD: 49282 components, ALA=13 atoms
   [ok] checkpoint of3-p2-145k.pt: 2.29 GB, intact=True
   [ok] checkpoint of3-p2-155k.pt: 2.29 GB, intact=True
   [ok] query JSON validates against this version's schema
   

Downloading the database files

1. cd into the path where you would like to store your OpenFold3 databases. Ideally, this should be in your project directory:

   mkdir -p /nesi/project/<PROJECT_ID>/openfold3_databases
   cd /nesi/project/<PROJECT_ID>/openfold3_databases
   

2. Load OpenFold3:

   module load OpenFold3
   

3. Download the desired databases from the list below:

   aws s3 ls --no-sign-request --human-readable s3://openfold/alignment_databases/
   

   For example, the following will download and uncompress your desired databases:

   aws s3 cp --no-sign-request s3://openfold/alignment_databases/rfam.fasta.gz .
   aws s3 cp --no-sign-request s3://openfold/alignment_databases/pdb_seqres.fasta.gz .
   aws s3 cp --no-sign-request s3://openfold/alignment_databases/rnacentral.fasta.gz .
   aws s3 cp --no-sign-request s3://openfold/alignment_databases/nucleotide_collection.fasta.gz .
   aws s3 cp --no-sign-request s3://openfold/alignment_databases/uniref90.fasta.gz .
   aws s3 cp --no-sign-request s3://openfold/alignment_databases/uniprot.fasta.gz .
   aws s3 cp --no-sign-request s3://openfold/alignment_databases/mgnify.fasta.gz .
   aws s3 cp --no-sign-request s3://openfold/alignment_databases/uniref30.tar.gz .
   aws s3 cp --no-sign-request s3://openfold/alignment_databases/cfdb.tar.gz .
   aws s3 cp --no-sign-request s3://openfold/alignment_databases/bfd.tar.gz .
   

   Be mindful of the amount of space you will need before you download the databases:

   #	Database	Format	Size	Type
   1	pdb_seqres	.fasta.gz	55 MB	protein
   2	rfam	.fasta.gz	61 MB	RNA
   3	nucleotide_collection	.fasta.gz	2.3 GB	RNA
   4	rnacentral	.fasta.gz	4.2 GB	RNA
   5	uniref90	.fasta.gz	47 GB	protein
   6	uniprot	.fasta.gz	61 GB	protein
   7	mgnify	.fasta.gz	79 GB	protein
   8	uniref30	.tar.gz	141 GB	protein (HHblits)
   9	cfdb	.tar.gz	290 GB	protein (HHblits)
   10	bfd	.tar.gz	292 GB	protein (HHblits)

   Total download: ~918 GB — budget ~3–4 TB of filesystem for the decompressed set.

Quiz Progress

• Answered: 0 / 0 (0%)
• Correct: 0 / 0 (0%) Reset