Read Boltz-1 .npz PAE files

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.10.dev202502060236 (2025-02-06 02:36:00 UTC)
Description
Make alphafold error plot and alphafold pae command able to read Boltz .npz files.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202502060236 (2025-02-06)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/goddard/ucsf/data/alphafold3/boltz_results_nipah_zmr/predictions/nipah_zmr/nipah_zmr_model_0.cif
> format mmcif

nipah_zmr_model_0.cif title:  
. [more info...]  
  
Chain information for nipah_zmr_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Non-standard residues in nipah_zmr_model_0.cif #1  
---  
ZMR — (ZMR)  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

Computing secondary structure  

> open
> /Users/goddard/ucsf/data/alphafold3/boltz_results_nipah_zmr/predictions/nipah_zmr/pae_nipah_zmr_model_0.npz

Opened AlphaFold PAE with values for 626 residues and atoms  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: MK1H3LL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 156 days, 12 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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[Tom Goddard]

ChimeraX currently can read .npy files produced by Chai-1 but not .npz PAE files produced by Boltz-1.

[Tom Goddard]

Done.

The AlphaFold Error Plot tool now will find .npz PAE files for Boltz predictions. Also the "alphafold pae" command "file" option will accept .npz files. And the open command will accept .npz PAE files.

[Tom Goddard]

Elaine, can you add the .npz PAE file support to the documentation? Thanks!