plotly
Can't display ESMFold Protein Predictions
I'm trying to use HuggingFace's ESMFold to predict 3D protein structures from the protein sequence. I've got a PDB output that loads just fine on the RCSB Viewer but doesn't work with the Dash Bio dashbio.Molecule3dViewer.
From what I can tell in the examples, the Dash PdbParser utility is expecting "BOND" information. The only thing I have is "ATOM" information. I've attached the PDB file.
What am I missing? Thanks. -Tony prediction_dash_pdb.txt
The Dash PdbParser is built on ParmEd and uses the parmed load_files() function to read input pdbs. This should automatically generate bond information even if it is not provided in the input file. Trying to open your PDB file using parmed, it seems that the issue is the first line PARENT N/A is not recognized by parmed as pertaining to a specific file type. If you remove that line it loads in ATOM and BOND information just fine and it should be able to load them into dashbio.Molecule3dViewer.
