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Hello.
When running RoseTTAFold-All-Atom using the following input YAML config file, I observed that the inference code returned a `.pdb` file that contains a predicted protein structure with the f…
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Hi everyone! I am new to this, with computer science and programming I don't have much experience, so I apologise if my problem is stupid or I do not give enough information. I am trying tu run RFAA o…
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I am trying to run your example (biomedgpt_inference.ipynb) and the OpenBioMed/ckpts/protein_ckpts/esm2-3b/config.json file is not found. Actually, there are no json files in the ckpts folder. Are the…
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Hi this is JeongSoo Na
After installation in README file, I try this command
But this error is printed
```
(dynamicbind) PS C:\Users\jsna\Desktop\Github\DynamicBind> python .\run_single_pr…
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### Description of feature
In the DDA/label-free workflow (perhaps in others as well), it would be useful to get an output of the identification results at the end of the search/inference/filtering p…
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Hi,
I observed while running the command [ time python -m inference --config default_inference_args.yaml --protein_ligand_csv data/test_1.csv --out_dir results_L_cpu/user_predictions_small] the GPU …
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Hi,
First of all, thank you for developing such an excellent tool! I am encountering an issue during the `windowmasker `step while processing my target genome. The error message I receive is:
``…
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(RFAA1) [2200012187@hr-6-6-login RoseTTAFold-All-Atom]$ python -m rf2aa.run_inference --config-name protein
/gpfs/share/home/2200012187/mambaforge/envs/RFAA1/lib/python3.10/site-packages/hydra/_inter…
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Hi Will,
Thanks for your great tool!
I was trying to use mokapot in combination with sage outputs to look at enzyme free peptidomics samples. Unfortunately, when I run this with a simple subset an…
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What a great job! Only the SDF files of small molecules are output in the "results/user_predictions_small" folder when I infer with the example code：
`python -m inference --protein_ligand_csv data/…