Converting AlphaFold3 CIF to PDB

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Revision as of 02:16, 11 November 2024 by Eric Martz (Talk | contribs)
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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:

  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. Download the zip file from the AlphaFold3 Server.
  4. Double-click the zip file to unzip it.
  5. Drag the file with a name ending _model_0.cif into your working folder.[1]

Notes

  1. ↑ 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.

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Eric Martz

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