Converting AlphaFold3 CIF to PDB: Difference between revisions

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Eric Martz (talk | contribs)
ConfirmAccount, Editor, Print3D, Tester, Bureaucrats, journal, Administrators
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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]], or they can be converted to PDB format for analysis in [[FirstGlance in Jmol]].
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 ("CIF-only"). 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]].
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