Benjamin Fry

icon location Cambridge, MA icon location Biophysics PhD Candidate @ Harvard GSAS; Computational protein design @polizzilab

Results 4 comments of Benjamin Fry

Success install but import error

Just ran into this as well

Covalently bound ligands with no CCD

It's a little hacky, but check out this notebook: https://github.com/benf549/boltz-generalized-covalent-modification

saved plDDT in CIF for ligand is only the first ligand atom's pLDDT

Thanks for pointing this out @tubiana, I've also noticed some weirdness working with the pLDDTs written to the bfactor columns of Boltz generated PDB and CIF files. I think this...

`compute_3d_conformer` takes a long time to run - Would it be reasonable to bypass it?

I haven't tried this myself at all but you might be able to modify this notebook I wrote to inject arbitrary covalently modified residues into the Boltz CCD to inject...