FirstGlance/How to get average pLDDT from AlphaFold models: Difference between revisions
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(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.) | (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.) | ||
* 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 [[User:Eric_Martz/AlphaFold3_case_studies|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. | ||
