boltz
boltz copied to clipboard
jwohlwend
Official repository for the Boltz biomolecular interaction models
I encountered a `KeyError: 'test_'` when running Boltz-1 with a custom FASTA file. The traceback indicates the issue arises from the chain name not matching the expected keys in `chain_to_msa`....
There's a bug where timed out MSA submission requests from the mmseqs2 API result in an infinite loop since the error count code is not properly referenced. This PR addresses...
A major limitation of Boltz is that it uses a lot of GPU memory compared say to AlphaFold 3 so predictions run out of memory. This is especially problematic on...
It seems that boltz1x steering only calculates residue_constraints when handling non-standard residues, without considering standard residues to impose physical constraints. What is the reasoning behind this? https://github.com/jwohlwend/boltz/blob/091b424cb40c09a77c67786f45260bddb38e84bf/src/boltz/data/parse/schema.py#L647
Hi, I'm attempting to reproduce the results on **macOS**, but since the [last merge](https://github.com/jwohlwend/boltz/commit/b8b6373842e7295d03ea347c20729967c487f745), it's no longer possible to install the environment directly from the GitHub repository due to a...
Hello, I'm trying to install Boltz-1 on a M2 Mac. I have been using homebrew for installing other things, and I think it may be the cause of an error...
CIF output of predictions truncates lines at 79 characters [ETA: actually 80 characters], introducing a newline. Example: ``` ... ATOM 1057 C CB . THR 135 135 ? A -8.90867...
Output of `boltz predict` gives the pLDDT as percent (0,100) when reported in the B-factor column, but as a fraction (0,1) in the `_ma_qa_metric_local` loop.
As noted by @jbderoo in a comment on PR #249 (and related to #243), training with `fk_steering` and `guidance_update` set to `True` results in a `KeyError`. This is because `compute_constraint_features`...
Hi, I am not able to make reproducible predictions with fixed pytorch seeds and random.seed. What can I do for stable predictions? ``` from pytorch_lightning import seed_everything import random seed...
