openfold

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 The training loss is significant, with shaking and no decrease

yzb123789

Support for ESMfold with newer Ubuntu and CUDA version

9

Hi, First of all, thanks for all works put in. The system I have is Ubuntu 22.04 My issue is as follow. I am trying to use ESMfold which is...

Wan8uq1

Running the Openfold Inference for PDB 6KWC

1

I am confused as to why its asking for a separate pdb's cif file ``` (openfold_env) MATTERHORN ~/workdir/openfold/bin $ ./first_test/predict_test_prealigned.sh [2025-06-23 15:57:36,689] [INFO] [real_accelerator.py:203:get_accelerator] Setting ds_accelerator to cuda (auto detect)...

TonnarCastellano

Average LDDT-Cα and TM-Score on CAMEO

2

Hi, thanks for your great work on this open-source implementation of AlphaFold2! I am trying to reproduce performance on the CAMEO validation set using OpenFold, and I am struggling to...

tyler-hayes

`def chain_center_of_mass_loss( all_atom_pred_pos: torch.Tensor, all_atom_positions: torch.Tensor, all_atom_mask: torch.Tensor, asym_id: torch.Tensor, clamp_distance: float = -4.0, weight: float = 0.05, eps: float = 1e-10, **kwargs ) -> torch.Tensor: ca_pos = residue_constants.atom_order["CA"] all_atom_pred_pos...

abhinavb22

Why isn't there an additional broadcast dimension over the atom indices? Won't this code only calculate pairwise distances between the same atom types in different residues instead of all pairwise...

tsjain

Hi, I've been running some folding with OpenFold Multimer using custom inputs, and have found some strange discrepancies between OpenFold outputs and AlphaFold outputs. In the process of tracking this...

eswan01

Potential bug in DataPipelineMultimer when there are chains with the same sequence

1

This is based on my limited understanding of the codebase so please correct me if I am wrong. When inspecting the code, it appears to me that there is a...

dxu16

openfold3

1

Hi, When the openfold3 will be released ?

wangjiawen2013

installation fails with newer flash-attn version

1

Installation of openfold didn't work for me with cuda 12.4 and latest flash-attention: ``` Failed to build flash-attn Pip subprocess error: Running command git clone --filter=blob:none --quiet https://github.com/NVIDIA/dllogger.git /tmp/pip-req-build-zrt57w23 error:...

jotech