Cannot get example for CIF direct templates to work

[astromick71]

Hi,

I've been trying to run CIF direct template example from the documentation:-

{
"queries": {
"my_protein": {
"chains": [
{
"molecule_type": "protein",
"chain_ids": ["A", "B"],
"sequence": "XRMKQLEDKVEELLSKNYHLENEVARLKKLVGER",
"template_cif_paths": [
"templates/1dgc.cif",
"templates/1ysa.cif",
"templates/1zta.cif"
]
}
]
}
}
}

However, I log the following error message:

Traceback (most recent call last):
File "/apps/conda_envs/openfold3/bin/run_openfold", line 6, in
sys.exit(cli())
~~~^^
File "/apps/conda_envs/openfold3/lib/python3.13/site-packages/click/core.py", line 1524, in call
return self.main(*args, **kwargs)
~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/apps/conda_envs/openfold3/lib/python3.13/site-packages/click/core.py", line 1445, in main
rv = self.invoke(ctx)
File "/apps/conda_envs/openfold3/lib/python3.13/site-packages/click/core.py", line 1912, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/apps/conda_envs/openfold3/lib/python3.13/site-packages/click/core.py", line 1308, in invoke
return ctx.invoke(self.callback, **ctx.params)
~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/conda_envs/openfold3/lib/python3.13/site-packages/click/core.py", line 877, in invoke
return callback(*args, **kwargs)
File "/apps/conda_envs/openfold3/lib/python3.13/site-packages/openfold3/run_openfold.py", line 191, in predict
query_set = InferenceQuerySet.from_json(query_json)
File "/apps/conda_envs/openfold3/lib/python3.13/site-packages/openfold3/projects/of3_all_atom/config/inference_query_format.py", line 98, in from_json
return cls.model_validate_json(data)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
File "/apps/conda_envs/openfold3/lib/python3.13/site-packages/pydantic/main.py", line 782, in model_validate_json
return cls.pydantic_validator.validate_json(
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
json_data, strict=strict, extra=extra, context=context, by_alias=by_alias, by_name=by_name
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
pydantic_core._pydantic_core.ValidationError: 1 validation error for InferenceQuerySet
queries.my_protein.chains.0.template_cif_paths
Extra inputs are not permitted [type=extra_forbidden, input_value=['/home/mick.knaggs/OpenF...ggs/OpenFold3/1zta.cif'], input_type=list]
For further information visit https://errors.pydantic.dev/2.13/v/extra_forbidden

I am running this under Rocky 8.10 (Green Obsidian) on a RTX 4090GPU in a conda env using python version 3.13.13 and the command used to obtain the above error message is:

srun $(which run_openfold) predict
--query_json=./test_cif.json
--use-msa-server=false
--use-templates=true
--runner-yaml=./low_mem.yml
--inference-ckpt-path=/apps/miniforge3/base/envs/openfold3/.openfold/of3-p2-155k.pt
--num-diffusion-samples=25
--num_model_seeds=10
--output_dir=$OUTDIR

Cheers,

Mick

[jandom]

Hi there @astromick71 and thanks for reporting this – this is a real issue with the pip package, you've followed the documentation correctly.

We have fixed this bug, it's currently fixed on the 'main' but not yet released on PYPI. If you're familiar with git and pixi, you can clone this repo and use pixi to create an appropriate environment and get this to work, for example

pixi shell      -e openfold3-cuda12
run_openfold predict ...

Or inside a slurm submit script

eval "$(pixi shell-hook --manifest-path PATH/TO/YOUR/CHECKOUT/openfold3-main -e openfold3-cuda12)"
srun $(which run_openfold) predict

All the best, let's keep this open - we can close when we release

[astromick71]

Hi @jandom, thank you responding so quickly to this issue.

I did get it working with the main repo using pixi with the instructions you provided.

Cheers,

Mick