Obtaining pLDDT values for predicted structure
Closed this issue · 2 comments
biotech70 commented
Is it possible to calculate the value of pLDDT for the predicted structures in PymolFold?
JinyuanSun commented
The pLDDT is labeled in the b-factor column in the pdb file returned from the ESMFold API.
To get the plddt, you may use biopython
or biotite
:
# biotite example
import biotite.structure.io as bsio
struct = bsio.load_structure("/path/to/test.pdb", extra_fields=["b_factor"])
pLDDT = struct[struct.atom_name == 'CA'].b_factor.mean()
I guess it will be great to print pLDDT in the pymol console. I will try to avoid the dependency to make it easy to run.
JinyuanSun commented
Try the updated version.
Also, feel free to reopen it or open a new issue if feel needed.