openfold

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Colab is broken. Please consider my PR #432 which makes it work again. Colab now fails with `module 'numpy' has no attribute 'object'` because the depricated `np.object` now throws error,...

vaclavhanzl

Rigid.from_3_points comment

3

Hi, it seems that `openfold.utils.rigid_utils.Rigid.from_3_points` module is actually different from the algorithm 21 in Alphafold paper. Your code seems to write as v1 = x2 - x1 and v2 =...

Zhu-Siqi

Frequently failed in training.

2

 I noticed that every time when 3 epochs training were done, the training process failed.  Here you can see the process is still running, and memories are...

C-de-Furina

Unable to create conda environment

4

I clone the repo, cd into it, run the provided command `mamba env create -n openfold_env -f environment.yml` and run into the following error: ``` Channels: - conda-forge - bioconda...

AlejandroSanchezCano

OpenFold seems to be required for a different software I want to run: LigandMPNN, however it seems like there's an issue with my openfold install: Programs\Python\Python310\lib\importlib\__init__.py", line 126, in import_module...

emilyrkang

Finetune from AF_Multimer parameters

7

Hi, I am encountering an issue similar to issue #421 where I attempted to fine-tune a model using the AF_multimer pretrained parameters (resume_from_jax_params: params_model_1_multimer_v3.npz). However, the loss is unusually high,...

tpdmskim

Finetune from AF parameters

11

Hi, I'm trying to train this model from an AF-multimer pretrained parameters. I notice that although it resumes from jax parameters, the loss is still pretty high and this model...

C-de-Furina

Pickling error in Docker?

1

When I build the docker image and try to run open fold this is my error. Has anyone else experienced this? what is the work around? [2024-03-28 16:02:57,801] [INFO] [real_accelerator.py:161:get_accelerator]...

tonyageall

Inference error using precomputed alignments

1

Dear OpenFold community, I was encountering an error when running inference using precomputed alignments. I precomputed the alignments by: ``` python3 scripts/precompute_alignments_mmseqs.py \ ${OPENFOLD_RESULTS}/input/T1050.fasta \ ${OPENFOLD_DB}/mmseqs_dbs \ uniref30_2103_db \ ${OPENFOLD_RESULTS}/output/alignments...

xuagu37

jkosinski