$TEMPLATE_MMCIF_DIR

[yuzimu1]

Hi OpenFold team,

I'm running OpenFold in a template-free mode using the finetuning_no_templ_ptm_1.pt checkpoint, and I expected that no template structures would be needed. However, I found that the script still requires me to provide a template_mmcif_dir, and I get errors like:

FileNotFoundError: [Errno 2] No such file or directory: '/path/to/template_dir/1h1a.cif'
Here's the command I'm using:

python3 run_pretrained_openfold.py
/home/rotation14/export/openfold/examples/monomer/fasta_dir
/home/rotation14/export/openfold/examples/template_free_empty4
--output_dir /home/rotation14/export/openfold/examples/monomer/output_dir
--use_precomputed_alignments /home/rotation14/export/openfold/examples/monomer/alignments
--config_preset model_3_ptm
--openfold_checkpoint_path /home/rotation14/export/openfold/openfold/resources/params/finetuning_no_templ_ptm_1.pt
--model_device cuda:0
--save_outputs
I want to clarify two things:

Is template_mmcif_dir still required even for template-free inference?

If so, is there a minimal valid .cif file I can use or a flag to completely bypass template usage?

Thanks a lot for your help, and thank you for the amazing work on OpenFold!

Best

[vaclavhanzl]

The directory is required and one totally empty file named whatever.cif in it makes it look legit enough for things to work.

[yuzimu1]

But I can only run the script once, and then the terminal tells me which .cif file is missing. I create an empty .cif file with that name, run it again, and then it complains about another missing .cif file. This keeps happening over and over again. Am I supposed to manually create empty .cif files one by one?
FileNotFoundError: [Errno 2] No such file or directory: '/home/rotation14/export/openfold/examples/template_free_empty4/1pvx.cif'
FileNotFoundError: [Errno 2] No such file or directory: '/home/rotation14/export/openfold/examples/template_free_empty4/5hxv.cif'.......

[yuzimu1]

This is the command I used.
python3 run_pretrained_openfold.py /home/rotation14/export/openfold/examples/monomer/fasta_dir /home/rotation14/export/openfold/examples/template_free_empty4 --output_dir /home/rotation14/export/openfold/examples/monomer/output_dir --use_precomputed_alignments /home/rotation14/export/openfold/examples/monomer/alignments --config_preset model_3_ptm --openfold_checkpoint_path /home/rotation14/export/openfold/openfold/resources/params/finetuning_no_templ_ptm_1.pt --model_device "cuda:0" \
I created an empty folder named 'template_free_empty4' to store the missing .cif files that the terminal reported. Whenever the terminal mentioned a missing .cif file, I just cre
ated an empty .cif file with that name in the folder."