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'''). In addition, a small percentage of models in the [[wwPDB]] are available only in mmCIF format. These files can 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'''). In addition, a small percentage of models in the [[wwPDB]] are available only in mmCIF format. These files can be uploaded to [[iCn3D]], or displayed in [[PyMOL]] or [[ChimeraX]], or they can be converted to PDB format for analysis in [[FirstGlance in Jmol]]. | ||
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]]. | ||
FirstGlance also makes it [[FirstGlance/How to get average pLDDT from AlphaFold models|easy to get the average pLDDT]] for any range of residues that you specify. | FirstGlance also makes it [[FirstGlance/How to get average pLDDT from AlphaFold models|easy to get the average pLDDT]] for any range of residues that you specify. | ||
==Conversion Procedure== | |||
In 2025, [http://firstglance.jmol.org FirstGlance in Jmol] requires the older [[PDB format]]. If you wish to display AlphaFold3 predicted structures in FirstGlance, here is how they can be converted to PDB format. Most* CIF-only models from the [[wwPDB]] can also be converted (see ''Caution'' below). | In 2025, [http://firstglance.jmol.org FirstGlance in Jmol] requires the older [[PDB format]]. If you wish to display AlphaFold3 predicted structures in FirstGlance, here is how they can be converted to PDB format. Most* CIF-only models from the [[wwPDB]] can also be converted (see ''Caution'' below). | ||
