search

evolutionaryscale / esm

Other
1.32k stars 155 forks source link

Missing side-chain info for predicted structure #124

Closed ahof1704 closed 2 weeks ago

ahof1704 commented 1 month ago

Hi,

I would like to predict structures for some given sequences using ESM3. I am using the following code snippet for it

structure_prediction_config = GenerationConfig(
    track="structure",  # We want ESM3 to generate tokens for the structure track
    num_steps=len(sequence_generation) // 8,
    temperature=0.7,
)
structure_prediction_prompt = ESMProtein(sequence=sequence_generation.sequence)
structure_prediction = model.generate(
    structure_prediction_prompt, structure_prediction_config
)

# Convert the generated structure to a back into a ProteinChain object
structure_prediction_chain = structure_prediction.to_protein_chain()
pdb_to_input_seq = structure_prediction_chain.to_pdb_string()

However, I don't see side-chain information in the resulting pdb. Is there a parameter that needs to be set to force the side-chain prediction?

Thank you in advance!

ebetica commented 2 weeks ago

Side-chains are currently only possible through the API. We have not open sourced the all-atom decoder.