Abhinav
Abhinav
I am trying to predict the structures of multiple multimers but I find that if I fold them one after another, the memory consumption increases. For example, folding one multimer...
I tried to predict the structure of a protein that contains a selenocysteine. The unrelaxed pdb has a missing residue corresponding to the selenocysteine position and relaxation failed due to...
I thought random numbers are required to initialize a model during training. So, why does AlphaFold require a random seed during inference? Where is this randomness introduced? Are these models...
I tried to install openfold with the command: mamba env create -n openfold_env -f environment.yml and I get the following error: Downloading and Extracting Packages Preparing transaction: done Verifying transaction:...
Hi, Does the Open Protein Set comes with Uniprot hits for the PDB proteins? I could find Uniref90, Mgnify, and BFD hits but not the UniProt hits, which are required...
I am trying to finetune AF-multimer and I start with a mock dataset of just 3 proteins. I get the following error: torch.cuda.OutOfMemoryError: CUDA out of memory. Tried to allocate...
I am trying to train a multimer model resuming from jax weights and get the following error: Traceback (most recent call last): File "/work/10110/abhinav22/ls6/openfold/train_openfold.py", line 706, in main(args) File "/work/10110/abhinav22/ls6/openfold/train_openfold.py",...
Core dumped and crashed when running expand aln command using the recent mmseqs version. The following is what I ran: `#!/bin/bash -e MMSEQS="mmseqs" QUERY= BASE= DB1="database/mmseqs/uniref30/uniref30_2302_db" DB2="" DB3="" USE_ENV="0" USE_TEMPLATES="0"...
I want to use Mmseqs to generate MSAs against uniprot and use that with the default alphafold2-multimer pipeline. However, when I run the following script, the header in the sto...
`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...