Hi Julian, My understanding is that for the standard amino acid residues, namely the ones that can be shown as cartoon or ribbon segments, AF only assigns a single pLDDT value per residue. The output structure file has exactly the same pLDDT (bfactor) for each atom of that residue. Maybe it is different for AF3, but things like ligands don't have mainchain/sidechain, at least in ChimeraX. One way to take a look at this is to use color bfactor on all atoms, e.g. sticks, instead of the cartoon representation, or save a PDB file and look in the bfactor column. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 8, 2024, at 7:22 AM, julian--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Here's the command with AF color hex codes from the AF3 server website
color bfactor palette 0,#ef821e:49.99,#ef821e:50,#f6ed12:69.99,#f6ed12:70,#10cff1:89.99,#10cff1:90,#106dff:100,#106dff key true
Now it's very close except I'm noticing that some small regions colored very high confidence by AF3 look just confident in Chimerax. Digging into it a bit, it seems the difference is that AF3 colors a residue by either the max bfactor of its atoms or maybe averages just the main-chain atoms. ChimeraX averages all atoms of a residue to color the cartoon, so a couple of C-delta atoms in the 80's is sometimes enough to bring the whole residue below 90. I'm guessing there's not way to match that AF behavior