FirstGlance/How to get average pLDDT from AlphaFold models

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It is easy to get the average confidence (pLDDT) for any range of residues in an AlphaFold model by using FirstGlance in Jmol.

  • 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.
  • 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

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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