FirstGlance/How to get average pLDDT from AlphaFold models: Difference between revisions
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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]. | 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 Å 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). | * 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]]. | * 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. | * Go to [http://firstglance.jmol.org FirstGlance in Jmol], and [http://firstglance.jmol.org/where.htm#uploading Upload] the .pdb file. | ||
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* Enter the range of sequence numbers in the ''Find..'' slot. | * 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''. | * Click ''List Found Atoms''. | ||
* AlphaFold puts its predicted confidence ([[pLDDT]]) in the temperature column. The | * 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]] | [[Image:Firstglance-found-report-plddt.png|750px|border]] | ||
