AlphaFold RFE: don't minimize by default

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
I noticed that the AlphaFold prediction tool has energy minimization on by default. For what it's worth I'd recommend against that: in places where the model is good its impacts will be minimal, while in places where the model is bad (or incomplete) the errors tend to be of the sort where energy minimisation will do more harm than good. Where AlphaFold has left space for a missing ligand the energy minimisation is likely to close the space (or at least shift the local geometry); where low-confidence regions or sequence-distance independent domains have caused major clashes, it'll blow apart geometry that *might* have been good. I think in general the better approach is to encourage the user to do some basic quality checks (and possible pruning of bad regions) before running minimisation.

OpenGL version: 3.3.0 NVIDIA 497.29
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: Notebook                        
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB

Installed Packages:
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    -himerax-isolde: 1.4b2
    absl-py: 1.0.0
    alabaster: 0.7.12
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    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
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    ChimeraX-AltlocExplorer: 1.0.2
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    ChimeraX-Atomic: 1.39.1
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    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
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[Tom Goddard]

Good point. I agree. But ChimeraX does not currently offer minimization even of these all standard amino acid AlphaFold models. So if the user gets an unminimized model it is not a simple button press or command to do it. I know they could get ISOLDE, but I think most AlphaFold uses are not cryoEM modeling so that is an obscure way to do minimization. Still I may turn minimization off by default. It also causes a fair number of AlphaFold failures when minimization fails.

[Tom Goddard]

One of the worst aspects of having minimization on by default is that if it failed then the prediction failed -- it did not even download the unminimized structure. I fixed that today, ticket #7258.

I'd still like to have energy minimization off by default, but I want to have a convenient way for the user to do the minimization in ChimeraX -- that should not be too hard since the AlphaFold models are only standard amino acids.

[Tom Goddard]

Done.

I changed the AlphaFold prediction energy minimization option to default false for both the command and gui. I also changed the predictions to use ColabFold which is about 10 times faster (ticket #7260). Colabfold makes the runs take just tens of minutes, so the user can rerun it with energy minimization if desired. Still would be nicer to have a button and command so ChimeraX can do the energy minimization with OpenMM.