Output sequences in json format for running alphafold3

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.9.dev202407260123 (2024-07-26 01:23:22 UTC)
Description
Add an outputJson option to alphafold monomers and dimers commands to produce input for Google's AlphaFold 3 server.

Log:
UCSF ChimeraX version: 1.9.dev202407260123 (2024-07-26)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> usage alpha dimer

alphafold dimers sequences [withSequences sequences] [homodimers true or
false] [maxLength an integer] [recycles an integer] [models models]
[outputFasta name of a file to save/write; a name of 'browse' will bring up a
file browser] [outputJson name of a file to save/write; a name of 'browse'
will bring up a file browser]  
— Setup AlphaFold predictions for all dimers for a set of sequences using
colabfold_batch  
sequences: sequences  
models: some integers  

> alphafold dimers data/cncalcium_monomers.fasta homodimers false outputJson
> data/dimers_af3.json

10 dimers with lengths 772-4678.  
Estimated prediction time 1 day 10 hours using Nvidia 3090 GPU.  
5 monomer sequences with lengths 149-2352:  
CAM1_CNAG_01557 (149), CCH1_CNAG_01208 (2106), CNAG_01613 (2352), CNAG_06362
(2326), MID1_CNAG_03751 (623)  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.0, Qt 6.7.1
Qt runtime version: 6.7.2
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: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 56 days, 18 hours, 28 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 3
      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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[Tom Goddard]

Done.

There is a new outputJson option for both the alphafold monomers and alphafold dimers command. The output file can be uploaded by Google's AlphaFold 3 server

​https://alphafoldserver.com

[Tom Goddard]

Added outputJson option to alphafold monomers and alphafold dimers commands.