View source for 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 [[How to predict structures with AlphaFold|AlphaFold model]] by using [http://firstglance.jmol.org FirstGlance in Jmol].
(Note that [https://alphafold.ebi.ac.uk/ AlphaFold Database] assigns the same pLDDT value to all atoms in an amino acid, while [https://alphafoldserver.com/ AlphaFold3] assigns different pLDDT values to each atom in an amino acid.) The procedure here will also report the average estimated error in &Aring; for subsets of residues in models predicted by [https://robetta.bakerlab.org/ RoseTTAFold].

* Download the predicted structure as a '''.pdb''' file (or '''.cif''' file if .pdb is not available). (For the example below, residues 126-761 of human ubiquitin protein ligase E3A [https://www.uniprot.org/uniprotkb/Q05086/entry Q05086] were submitted to AlphaFold3. See [[8jrp]] at [[User:Eric_Martz/AlphaFold3_case_studies#8JRP_Chain_A:_Partially_Untemplated|case studies]].)
* If only the .cif file is available, [[Converting AlphaFold3 CIF to PDB|convert it to .pdb format]].
* Go to [http://firstglance.jmol.org FirstGlance in Jmol], and [http://firstglance.jmol.org/where.htm#uploading Upload] the .pdb file.
* After the model is displayed in FirstGlance, in the ''Views'' tab, click ''Find..'' in the Focus Box:


[[Image:Firstglance-find-sequence-range.png|750px|border]]


* Enter the range of sequence numbers in the ''Find..'' slot. (Or enter multiple ranges separated by commas, for example <i>45-365, 380-682</i>.)
* Click ''List Found Atoms''.
* AlphaFold puts its predicted confidence ([[pLDDT]]) in the temperature column, labeled '''Conf''' in the listing. The Confidence/pLDDT statistics are at the bottom of the list:
[[Image:Firstglance-found-report-plddt.png|750px|border]]

==See Also==
*[[AlphaFold/Index]], a list of Proteopedia pages about AlphaFold.
*[[How to predict structures with AlphaFold]]