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'''). These files<ref name="best">Each job produces 5 .cif files. The file with a name ending &nbsp; _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]] 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.


In 2024, [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 most of them* can be converted to PDB format:
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.
 
==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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   </ol>
   </ol>
<li> Double-click Jmol.jar to run it.
<li> Double-click Jmol.jar to run it.
<li> Drag the _model_0.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 af3-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> [http://firstglance.jmol.org/where.htm#uploading Upload] the af3-jobname.pdb to [http://firstglance.jmol.org FirstGlance in Jmol].
<li> Drag and drop ''jobname.pdb'' into [http://firstglance.jmol.org FirstGlance in Jmol].
</ol>
 
===Caution: Ligand Names May Be Wrong===
 
If your .cif file had 5-character ligand codes (instead of or in addition to 3-character ligand codes), conversion will truncate those 5-character codes to their first three characters.
(5-character ligand names were introduced after all 3-character codes were in use.)
For example, the ligand code [https://www.rcsb.org/ligand/A1EJM A1EJM] in [[9l63|9L63]] will be truncated to A1E in the converted PDB file. FirstGlance will handle it correctly except that under ''Ligands and Non-Standard Residues'' (in the Molecule Information Tab), '''the link (=?) will display the wrong chemical structure'''; namely, it will display ligand A1E instead of A1EJM.
 
To display the chemical structure of a ligand with a 5-character code, go to [http://rcsb.org RCSB.org] and enter the 5-character code into the search slot at the top, then press Enter.
 
To list all the ligand codes in your .cif file, after dropping the .cif file into the black window of Jmol.jar, enter these two '''bold commands''' in the white window (example is [[9dos]]):
 
<br>
<span style="color:magenta;">$</span> '''select hetero'''
<br>
94 atoms selected
<br>
<span style="color:magenta;">$</span> '''show residues'''
<br>
<span style="color:blue;">[GOL]501:A
<br>
[A1A8V]502:A
<br>
[A1A8V]501:B
<br>
[A1A8V]501:C
<br>
[A1A8V]501:D</span>
 
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==
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==Notes==
==Notes==
<nowiki>*</nowiki>Models with > 99,999 atoms or > 62 chains will not fit in the legacy PDB format.
<!--<nowiki>*</nowiki>Models with > 99,999 atoms or > 62 chains will not fit in the legacy PDB format.-->
<references />
<references />
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