Converting AlphaFold3 CIF to PDB
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# Double-click the zip file to unzip it. | # Double-click the zip file to unzip it. | ||
# Drag the file with a name ending '''_model_0.cif''' into your working folder.<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 pTM quality score.</ref> | # Drag the file with a name ending '''_model_0.cif''' into your working folder.<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 pTM quality score.</ref> | ||
| + | # Double-click Jmol.jar to run it. | ||
| + | # Drag the _model_0.cif file and drop it into the black window of Jmol. The model should appear. | ||
| + | # In the white ''Jmol Script Console'', enter the command '''write af3-jobname.pdb''', where ''jobname'' is a unique identifier for this model. | ||
| + | # [http://firstglance.jmol.org#where.htm#uploading Upload] the af3-jobname.pdb to [http://firstglance.jmol.org FirstGlance in Jmol]. | ||
==Notes== | ==Notes== | ||
<references /> | <references /> | ||
Revision as of 02:21, 11 November 2024
The AlphaFold3 Server predicts models only in the mmCIF format (filename ending .cif). These files can be uploaded to iCn3D, or displayed in PyMOL or ChimeraX.
In 2024, FirstGlance in Jmol requires the older PDB format. If you wish to display AlphaFold3 predicted structures in FirstGlance, here is how to convert them to PDB format:
- Get the Jmol.jar Java application running on your computer by following the instructions at Jmol/Application.
- Create a working folder (directory), and put Jmol.jar in it.
- Download the zip file from the AlphaFold3 Server.
- Double-click the zip file to unzip it.
- Drag the file with a name ending _model_0.cif into your working folder.[1]
- Double-click Jmol.jar to run it.
- Drag the _model_0.cif file and drop it into the black window of Jmol. The model should appear.
- In the white Jmol Script Console, enter the command write af3-jobname.pdb, where jobname is a unique identifier for this model.
- Upload the af3-jobname.pdb to FirstGlance in Jmol.
Notes
- ↑ Each job produces 5 .cif files. The file with a name ending _model_0.cif is one of those with the highest pTM quality score.
