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]''' | 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''''' (or later) available via '''[http://firstglance.jmol.org firstglance.jmol.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]]. | ||
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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. | ||
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. | 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. | 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. | ||
==Conversion Procedure== | ==Conversion Procedure== | ||
You do not need this procedure to make AlphaFold Server .cif files compatible with FirstGlance in Jmol (see above). You can drop those .cif files directly into the [http://firstglance.jmol.org FrontDoor of FirstGlance]. | |||
The procedure below could be used, for example, to convert molecular models in XYZ format to PDB format. Most* CIF-only models from the [[wwPDB]] can also be converted (see ''Caution'' below). | |||
<ol> | <ol> | ||
<li> Get the Jmol.jar Java application running on your computer by following the instructions at [[Jmol/Application]]. | <li> Get the Jmol.jar Java application running on your computer by following the instructions at [[Jmol/Application]]. | ||
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<li> Drag the .cif file and drop it into the black window of Jmol. The model should appear. | <li> Drag the .cif file and drop it into the black window of Jmol. The model should appear. | ||
<li> In the white ''Jmol Script Console'', enter the command '''write jobname.pdb''', where ''jobname'' is a unique identifier for this model. | <li> In the white ''Jmol Script Console'', enter the command '''write jobname.pdb''', where ''jobname'' is a unique identifier for this model. | ||
<li> | <li> Drag and drop ''jobname.pdb'' into [http://firstglance.jmol.org FirstGlance in Jmol]. | ||
</ol> | </ol> | ||
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GOL is a 3-character ligand code (for glycerol), and A1A8V is a 5-character ligand code. "501:D" means residue number 501 in chain D. | GOL is a 3-character ligand code (for glycerol), and A1A8V is a 5-character ligand code. "501:D" means residue number 501 in chain D. | ||
==See Also== | ==See Also== | ||
