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Evolutionary Scale Modeling (esm): Pretrained language models for proteins
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Folded structure from `esm-fold` has overlapping atoms #560

Open em255 opened 1 year ago

em255 commented 1 year ago

Bug description I installed esm using the conda environment I Folded many proteins using the esm-fold command, however I have found some proteins with physically impossible structure.

Reproduction steps input fasta test.txt output pdb test_pdb.txt clipped out first 9 residues for image model image Trying with the whole PDB will only crash your viewer

Expected behavior Expected 3D structure with physically possible coordinates

Logs Please paste the command line output: 23/05/11 02:23:45 | INFO | root | Predicted structure for testAA with length 1046, pLDDT 29.2, pTM 0.999 in 126.8s. 31536 / 32805 completed

Additional context I do not udnerstand how to specify model used by ESM-fold command (maybe there are no other options for this command?). I'm supposing that this could be due to trying to fold a protein with > 1000 AA, but the limits of the folder are not very explicit. Like maybe there's a 400 AA limit, but that's mentioned and then quickly glazed over.

Ieremie commented 1 year ago

I have a similar problem, where the predicted structure has missing residues.