Converting AlphaFold3 CIF to PDB

From Proteopedia

The AlphaFold3 Server predicts models only in the 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 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.

Conversion Procedure

In 2025, 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).

1. Get the Jmol.jar Java application running on your computer by following the instructions at Jmol/Application.
2. Create a working folder (directory), and put Jmol.jar in it.
3. Get the .cif file to convert. If you have downloaded a .cif file from the wwPDB, you can skip the next 3 steps.
   1. Download the zip file from the AlphaFold3 Server.
   2. Double-click the zip file to unzip it.
   3. In the newly unzipped folder, find the file with a name ending _model_0.cif. Drag it into your working folder.^[1]
4. Double-click Jmol.jar to run it.
5. Drag the .cif file and drop it into the black window of Jmol. The model should appear.
6. In the white Jmol Script Console, enter the command write jobname.pdb, where jobname is a unique identifier for this model.
7. Upload jobname.pdb to FirstGlance in Jmol.

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 A1EJM in 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 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:

For example 9dos:
$ select ligands
94 atoms selected
$ show residues
[GOL]501:A
[A1A8V]502:A
[A1A8V]501:B
[A1A8V]501:C
[A1A8V]501: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

• How to predict structures with AlphaFold
• AlphaFold/Index

Notes

*Models with > 99,999 atoms or > 62 chains will not fit in the legacy PDB format.

1. ↑ 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.