AlphaFold prediction on Google Colab fails due to failed tensorflow import

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-26.4.1-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
AlphaFold prediction on Google Colab fails importing tensorflow.  Probably Google Colab updated some packages.  I'll attach the traceback from Colab.


Log:
Startup Messages  
---  
note | CubeNTube: sphere eraser undo support enabled  
  
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1fav format mmcif fromDatabase pdb

1fav title:  
The structure of an hiv-1 specific cell entry inhibitor In complex with the
hiv-1 GP41 trimeric core [more info...]  
  
Chain information for 1fav #1  
---  
Chain | Description | UniProt  
A | HIV-1 ENVELOPE PROTEIN CHIMERA | GCN4_YEAST 1-29, ENV_HV1BR 30-79  
C | PROTEIN (TRANSMEMBRANE GLYCOPROTEIN) | ENV_HV1BR 125-154  
  
Non-standard residues in 1fav #1  
---  
3PA — 3-cyclopentyl-propionic acid  
4BA — 4-[(2-carboxy-ethylamino)-methyl]-benzoic acid  
  
1fav mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
33 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show AlphaFold

> alphafold predict #1/C

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  

Populating font family aliases took 63 ms. Replace uses of missing font family
"Google Sans Text" with one that exists to avoid this cost.  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 Performance and 8 Efficiency)
      Memory: 64 GB
      System Firmware Version: 18000.101.7
      OS Loader Version: 18000.101.7

Software:

    System Software Overview:

      System Version: macOS 26.4.1 (25E253)
      Kernel Version: Darwin 25.4.0
      Time since boot: 3 days, 6 hours, 24 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


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File attachment: colab_error.txt

colab_error.txt​

[goddard@…]

Added by email2trac

[Tom Goddard]

Reported by Ju Fang Chang on the mailing list

​https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/thread/YYZA7LLGRUCQ6XMNMNQWURP56IEIKFEJ/

[Tom Goddard]

Fixed.

The problem is that importing tensorflow fails after colabfold is installed. It works before colabfold is installed. I updated colabfold to version 1.6.1 (March 16, 2026) and jax to 0.7.2 since that is what the standard Colabfold notebook is using but I still got the error. If I import tensorfold before installing ColabFold then I don't get the error. I wasn't able to get to the bottom of why this fixes it. I think it must be that the import before install loads the library containing the missing symbol, but after the install somehow it is unable to load that symbol. There was a line in the ChimeraX colabfold install script that deleted a seemingly unrelated tensorflow .so needed a year ago to fix some other tensorflow bug. I commented that removal out.

I'm going to go with the pre-install import tensorfold fix with the updated ColabFold. Maybe I just need a newer tensorfold, it is using 2.20.0 but the standard Colabfold notebook somehow gets 2.21.0.