FirstGlance/How to get average pLDDT from AlphaFold models

It is easy to get the average confidence (pLDDT) for any range of residues in an AlphaFold model by using FirstGlance in Jmol. (Note that AlphaFold Database assigns the same pLDDT value to all atoms in an amino acid, while AlphaFold3 assigns different pLDDT values to each atom in an amino acid.)

• Download the predicted structure as a .pdb file (or .cif file if .pdb is not available).
• If only the .cif file is available, convert it to .pdb format.
• Go to FirstGlance in Jmol, and Upload the .pdb file.
• After the model is displayed in FirstGlance, in the Views tab, click Find.. in the Focus Box:

• Enter the range of sequence numbers in the Find.. slot. (Or enter multiple ranges separated by commas, for example 45-365, 380-682.)
• Click List Found Atoms.
• AlphaFold puts its predicted confidence (pLDDT) in the temperature column. The confidence/pLDDT statistics are at the bottom of the list as "temperature":

See Also

• AlphaFold/Index, a list of Proteopedia pages about AlphaFold.
• How to predict structures with AlphaFold

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz