ChimeraX AlphaFold pLDDT Coloring

ChimeraX colors AlphaFold, Boltz, ESMFold and OpenFold predictions by pLDDT confidence scores using a different coloring than the EBI coloring for AlphaFold predictions. The ChimeraX colors are as follows:

• 100 to 90 – high accuracy expected
• 90 to 70 – backbone expected to be modeled well
• 70 to 50 – low confidence, caution
• 50 to 0 – should not be interpreted, may be disordered

The colors are linearly interpolated (in red, green, blue components) over the specified value ranges using pLDDT values in the bfactor field of mmCIF and PDB format atomic model files. This coloring is shown initially when a prediction is made within ChimeraX. It can be shown later if the predicted structure is reopened using the command

color bfactor #1 palette alphafold

EBI AlphaFold pLDDT Coloring

The EBI Alphafold Database uses a different pLDDT coloring. Their color scheme uses the same color for large ranges of pLDDT scores:

• 90 to 100 – very high confidence
• 70 to 90 – high confidence
• 50 to 70 – low confidence
• 0 to 50 – very low confidence

Scores in the range 70-90 are light blue and described as “high confidence” while scores in the range of 50-70 are yellow and described as “low confidence.” This makes predictions that have scores slightly above 70 look deceptively more confident than predictions with scores slightly less than 70. For this reason we discourage use of the EBI AlphaFold color scheme.