FirstGlance/How to get average pLDDT from AlphaFold models: Difference between revisions

Revision as of 20:55, 29 December 2025

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":

Revision as of 15:55, 14 November 2024 view source Eric Martz (talk \| contribs) ConfirmAccount, Editor, Print3D, Tester, Bureaucrats, journal, Administrators 30,134 edits No edit summary ← Older edit		Revision as of 20:55, 29 December 2025 view source Eric Martz (talk \| contribs) ConfirmAccount, Editor, Print3D, Tester, Bureaucrats, journal, Administrators 30,134 edits No edit summary Newer edit →
Line 1:		Line 1:
	It is easy to get the average confidence ([[pLDDT]]) for any range of residues in an AlphaFold model by using [http://firstglance.jmol.org FirstGlance in Jmol].		It is easy to get the average confidence ([[pLDDT]]) for any range of residues in an [[How to predict structures with AlphaFold\|AlphaFold model]] by using [http://firstglance.jmol.org FirstGlance in Jmol].

	* Download the predicted structure as a '''.pdb''' file (or '''.cif''' file if .pdb is not available).		* Download the predicted structure as a '''.pdb''' file (or '''.cif''' file if .pdb is not available).