[chimerax-users] alphafold in Google colab

[Tom Goddard]

Hi Roberto,

  I have fixed ChimeraX AlphaFold prediction.  You do not need a new version of ChimeraX, the fix was in the Colab script that installs AlphaFold and ChimeraX gets that script from GitHub whenever you run a prediction.  Unfortunately Google changed the location of a Python package called jaxlib that AlphaFold requires.  I updated to use the new location.

  Thanks for alerting me to the problem!

	Tom


> On Jun 20, 2022, at 11:48 AM, Roberto Marabini via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> 
>    Starting today, when I try to execute AlphaFold calculations using
> Google Colab, I get the message:
> 
> ======
> ERROR: pip's dependency resolver does not currently take into account
> all the packages that are installed. This behaviour is the source of
> the following dependency conflicts.
> kapre 0.3.7 requires tensorflow>=2.0.0, which is not installed.
> xarray-einstats 0.2.2 requires numpy>=1.21, but you have numpy 1.19.5
> which is incompatible.
> datascience 0.10.6 requires folium==0.2.1, but you have folium 0.8.3
> which is incompatible.
> albumentations 0.1.12 requires imgaug<0.2.7,>=0.2.5, but you have
> imgaug 0.2.9 which is incompatible.
> Successfully installed absl-py-0.13.0 biopython-1.79 chex-0.0.7
> dm-haiku-0.0.4 dm-tree-0.1.6 docker-5.0.0 flatbuffers-1.12 gast-0.4.0
> grpcio-1.34.1 immutabledict-2.0.0 jax-0.2.14
> keras-nightly-2.5.0.dev2021032900 ml-collections-0.1.0 numpy-1.19.5
> pandas-1.3.4 scipy-1.7.0 tensorflow-cpu-2.5.0
> tensorflow-estimator-2.5.0 typing-extensions-3.7.4.3
> websocket-client-1.3.3 wrapt-1.12.1
> + pip3 install --upgrade jaxlib==0.3.2+cuda11.cudnn82 -f
> https://storage.googleapis.com/jax-releases/jax_releases.html
> Looking in indexes: https://pypi.org/simple,
> https://us-python.pkg.dev/colab-wheels/public/simple/
> Looking in links: https://storage.googleapis.com/jax-releases/jax_releases.html
> ERROR: Could not find a version that satisfies the requirement
> jaxlib==0.3.2+cuda11.cudnn82 (from versions: 0.1.23, 0.1.29, 0.1.32,
> 0.1.40, 0.1.41, 0.1.42, 0.1.43, 0.1.44, 0.1.46, 0.1.50, 0.1.51,
> 0.1.52, 0.1.55, 0.1.56, 0.1.57, 0.1.58, 0.1.59, 0.1.60, 0.1.61,
> 0.1.62, 0.1.63, 0.1.64, 0.1.65, 0.1.66, 0.1.67, 0.1.68, 0.1.69,
> 0.1.70, 0.1.71, 0.1.72, 0.1.73, 0.1.74, 0.1.75, 0.1.76, 0.3.0, 0.3.2,
> 0.3.5, 0.3.7, 0.3.8, 0.3.10)
> ERROR: No matching distribution found for jaxlib==0.3.2+cuda11.cudnn82
> =======
> The error seems to be obvious but, can someone point me towards a solution?
> 
>    Thanks
> 
>       Roberto
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