georgkempf

I don't understand the purpose of the following except block: https://github.com/deepmind/alphafold/blob/c42a96f3a5b6179484b5f0b936e3dd0c9b08fde1/alphafold/data/templates.py#L716 When strict_error_check is set to False then the result would still be empty because below the conditional another empty...

[BUG]: Problems with using previous dataset splits

1

I wanted to train other models with sklearn_train using the same train, val, test indices from a previous training (with chemprop_train) where I used --save_smiles_splits option (which seems to write...

seq_length dimension different to AlphaFold-multimer

2

In case of the original AlphaFold pipeline, the "seq_length" array in the feature_dict seems to get flattened in multimer mode (in monomer mode it stays a 1-D array). As far...

AutoChunk

2

Hello, I was wondering whether AutoChunk described in https://arxiv.org/pdf/2203.00854v3.pdf is already implemented? Will this avoid manually setting the chunk_size?

Illegal memory access error after get_chi_atom_indices

12

I tried to predict a 5 subunit complex (in total ~5000 aa) and get the following error with various settings (1-4x A100 80GB, w/ and w/o --inplace, w/ and w/o...

Hi, I wanted to ask whether modeled ligands or PTMs (e.g. phosphorylated residues) that are in the same chain as the polypeptide are included in the descriptor calculation?