Converting AlphaFold3 CIF to PDB: Difference between revisions
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The [https://alphafoldserver.com AlphaFold3 Server] predicts models only in the [[Mmcif format|mmCIF format]] (filename ending '''.cif'''). These files<ref name="best">Each job produces 5 .cif files. The file with a name ending _model_0.cif is one of those with the highest overall [https://alphafoldserver.com/faq pTM quality score]. The pTM quality score is in the corresponding '''_summary_confidences_0.json''' file. Open this file in a [[Help:Plain text editors|text editor]]. Look for the third-from-last line, which begins "ptm": (including the quotes) followed by the overall pTM confidence value. See the FAQ at the [https://alphafoldserver.com AlphaFold3 Server] for how to interpret pTM.</ref> can be visualized & analyzed using ''FirstGlance in Jmol '''version 4.6''''' available via [http://firstglance.jmol.org firstglance.jmol.org] (but not yet installed at proteopedia.org). These mmCIF files can also be uploaded to [[iCn3D]], or displayed in [[PyMOL]] or [[ChimeraX]]. | The [https://alphafoldserver.com AlphaFold3 Server] predicts models only in the [[Mmcif format|mmCIF format]] (filename ending '''.cif'''). These files<ref name="best">Each job produces 5 .cif files. The file with a name ending _model_0.cif is one of those with the highest overall [https://alphafoldserver.com/faq pTM quality score]. The pTM quality score is in the corresponding '''_summary_confidences_0.json''' file. Open this file in a [[Help:Plain text editors|text editor]]. Look for the third-from-last line, which begins "ptm": (including the quotes) followed by the overall pTM confidence value. See the FAQ at the [https://alphafoldserver.com AlphaFold3 Server] for how to interpret pTM.</ref> can be visualized & analyzed using ''FirstGlance in Jmol '''version 4.6''''' available via '''[http://firstglance.jmol.org firstglance.jmol.org]''' (but not yet installed at proteopedia.org). These mmCIF files can also be uploaded to [[iCn3D]], or displayed in [[PyMOL]] or [[ChimeraX]]. | ||
Only [http://firstglance.jmol.org FirstGlance in Jmol] and [[iCn3D]] automatically color AlphaFold-predicted models by confidence/[[pLDDT]] correctly ('''{{Font color|blue|blue for high confidence}}, {{Font color|red|red for low confidence}}'''). See [[How_to_predict_structures_with_AlphaFold#Visualizing_Predicted_Structures|Visualizing Predicted Structures]]. | Only [http://firstglance.jmol.org FirstGlance in Jmol] and [[iCn3D]] automatically color AlphaFold-predicted models by confidence/[[pLDDT]] correctly ('''{{Font color|blue|blue for high confidence}}, {{Font color|red|red for low confidence}}'''). See [[How_to_predict_structures_with_AlphaFold#Visualizing_Predicted_Structures|Visualizing Predicted Structures]]. | ||
Revision as of 15:30, 7 March 2026
The AlphaFold3 Server predicts models only in the mmCIF format (filename ending .cif). These files[1] can be visualized & analyzed using FirstGlance in Jmol version 4.6 available via firstglance.jmol.org (but not yet installed at proteopedia.org). These mmCIF files can also be uploaded to iCn3D, or displayed in PyMOL or ChimeraX.
Only FirstGlance in Jmol and iCn3D automatically color AlphaFold-predicted models by confidence/pLDDT correctly (blue for high confidence, red for low confidence). See Visualizing Predicted Structures.
FirstGlance also makes it easy to get the average pLDDT for any range of residues that you specify.
The original version of this article discussed a method for converting AlphaFold 3 .cif models to .pdb format. That is no longer necessary. FirstGlance in Jmol version 4.6 accepts AlphaFold 3 .cif files directly via drag and drop.
About 5% of the models in the wwPDB are available only in mmCIF format ("CIF-only"). These are more complicated than AlphaFold models, and are not yet supported by FirstGlance. Support is expected later in 2026.
See Also
Notes
- ↑ Each job produces 5 .cif files. The file with a name ending _model_0.cif is one of those with the highest overall pTM quality score. The pTM quality score is in the corresponding _summary_confidences_0.json file. Open this file in a text editor. Look for the third-from-last line, which begins "ptm": (including the quotes) followed by the overall pTM confidence value. See the FAQ at the AlphaFold3 Server for how to interpret pTM.
