esm

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Embedding with multiple GPUs

1

I understand this is for ESM3, but I am encountering an issue with embedding in ESM2. I have two GPUs, and while performing embedding, I consistently run out of memory...

aimilkveg

first sequence than structure or the other way around

1

Thanks for providing this comprehensive model open-source. I was wondering what the correct sequence of predictions is: In your examples, e.g. with the Carbonic Anhydrase (2vvb) the following order is...

l-i-g

error getting sequence embeddings.

4

Hi, I am processing lots of sequences in a fasta file but esm3-small model failed on the sequence "EHVAATHKTGLDALAELTGAALNSVEKLSELQFQTVRASLEDSTEQGKRVFDARSLHELTALQSEVSQPTEKLVAYGRHLYQIAAGTHAEWRKVAQTRA". I tried reducing the sequence to see where exactly it failed...

santule

multichain protein structure predicrion

5

How can i input 2 chains into ESM3 to predict structure? I tried ":" in the sequence like esm2, but returned an error

InvincibleZZH

Question About Residue Annotations vocabulary file

3

Not found Residue Annotations vocabulary file data/uniref90_and_mgnify90_residue_annotations_gt_1k_proteins.csv in repo.

wukong1992

Sidechains in output

6

Would it be possible to implement a function to generate all-atom PDB outputs including sidechains?

BJHardy

from_pretrained() Error. Cannot use a path to import local model?

5

my code like this: > model = ESM3.from_pretrained(model_name = "./huggingface/hub/models--EvolutionaryScale--esm3-sm-open-v1/snapshots/66ecd636588d3100e13598a5720678db6583d01c/", device=torch.device("cpu")) and give the error: `--------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In [27], [line 1](vscode-notebook-cell:?execution_count=27&line=1) ----> [1](vscode-notebook-cell:?execution_count=27&line=1) model...

1830416002

How can we get attention weights from example sequence and structure?

2

How can we get attention weights from example sequence and structure? There were no arguments to get attention weights in transformer blocks, unlike esm2.

what-is-what

Problems when loading esm3 model

2

Hi, when using esm3 model to generate embeddings, I face a new error: ``` File "/gpfs/radev/scratch/ying_rex/tl688/esm3/esm/test_esm3.py", line 1, in from esm.models.esm3 import ESM3 File "/gpfs/radev/scratch/ying_rex/tl688/esm3/esm/esm/models/esm3.py", line 13, in from esm.layers.regression_head...

HelloWorldLTY

where is attention_contacts in esm2?

3

Hi, thank you for the great job! There is a return which contains attention_contacts in esm2, and the code is: results = model(batch_tokens, repr_layers=[33], return_contacts=True). However, i cannot find similar...

linshuxi