Update to AlphaFold 2.2.0

[Tom Goddard]

Update ChimeraX structure prediction from AlphaFold 2.1.0 to 2.2.0.

AlphaFold 2.2.0 came out March 10, 2022 and is said to reduce clashing atoms significantly. That could help reduce energy minimization time. Also they got rid of the prokaryote option saying it did not result in better structures.

[Tom Goddard]

Here are the changes I've made in updating the AlphaFold Colab script for the prediction capability.

1) Prokaryote option removed from the AlphaFold tool and alphafold predict command.
2) Energy minimization option added to AlphaFold tool and predict command, default true. Allows faster runs with no minimization and avoiding failures when minimization fails.
3) Made predicting monomers use the monomer_ptm AlphaFold parameters which produces the PAE matrix. Formerly it used the monomer parameters which did not provide PAE matrix.
4) Write best_model_pae.json to the results directory so the Error Plot button on the AlphaFold tool can easily find it.
5) Write sequence_coverage_N.png images to the results directory containing the plots showing sequence coverage for each sequence (N = 1,2,...).
6) Fixed a bug to make AlphaFold use a specific version of jax and jaxlib Python modules so future updates of those don't break alphafold.
7) Made the AlphaFold Run panel log which version of AlphaFold it is using.

These changes effect all daily builds since ChimeraX 1.3 came out but do not effect ChimeraX 1.3. All the 1.4 daily builds use the new script while ChimeraX 1.3 uses an older colab script that only handled monomers.

[Tom Goddard]

Done.