Conditional sequence generation also updates structure coordinates?

[kentwait]

I am doing sequence generation conditioned on a known structure (code below)

protein_chain = ProteinChain.from_rcsb(pdb_id=pdb_id, chain_id=chain_id)
protein = ESMProtein.from_protein_chain(protein_chain)
original_sequence = protein.sequence

# Mask sequence, minimum example of 1 site masked, position indicated by `mask_pos`
protein.sequence = protein.sequence[:mask_pos] + '_' + protein.sequence[mask_pos+1:]
 
# Fill in mask conditioned on structure
model = ESM3.from_pretrained('esm3_sm_open_v1').to('cuda:0')
new_protein = model.generate(protein, GenerationConfig(track='sequence', num_steps=1, temperature=1.0)
new_sequence = new_protein.sequence

I noticed that the value of coordinates changes after conditional sequence generation. Comparing the before and after structures (via .to_pdb() and TM-align), TM-score is >0.95 but not identical.

My initial impression was structure is held constant since GenerationConfig specifies the sequence track. It seems that structure also updates? Can you elaborate more on what is happening here?

Thanks in advance for the help.