alphafold contacts command says no PAE data open when Boltz Error Plot button used

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.11.dev202509171705 (2025-09-17 17:05:04 UTC)
Description
Boltz gui Error Plot button shows PAE plot but then "alphafold contacts" command claims the structure does not have PAE data opened.

Log:
UCSF ChimeraX version: 1.11.dev202509171705 (2025-09-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/goddard/Desktop/boltz/boltz_mg_249_dna_2/boltz_results_mg_249_dna/predictions/mg_249_dna/mg_249_dna_model_0.cif
> format mmcif logInfo false

> ui tool show Boltz

> boltz predict protein /A dna /B dna /C name mg_249_dna steering true samples
> 5

Running Boltz prediction of protein with 497 residues, 2 nucleic acid
sequences with 24 residues on gpu  
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/mg_249_dna  
Confidence score 0.73, pTM 0.84, ipTM 0.97, pLDDT 0.68  
Confidence score 0.72, pTM 0.90, ipTM 0.97, pLDDT 0.65  
Confidence score 0.71, pTM 0.77, ipTM 0.95, pLDDT 0.65  
Confidence score 0.69, pTM 0.83, ipTM 0.91, pLDDT 0.63  
Confidence score 0.66, pTM 0.50, ipTM 0.79, pLDDT 0.63  
Boltz prediction completed in 349 seconds (start boltz 5 sec, sequence search
0 sec, load weights 10 sec, structure inference 334 sec)  
Please cite Boltz-1 Democratizing Biomolecular Interaction Modeling. BioRxiv
https://doi.org/10.1101/2024.11.19.624167 if you use these predictions.  

> open
> /Users/goddard/Desktop/boltz/boltz_mg_249_dna_3/boltz_results_mg_249_dna/predictions/mg_249_dna/mg_249_dna_model_0.cif
> logInfo false

Matchmaker mg_249_dna_model_0.cif, chain A (#1) with mg_249_dna_model_0.cif,
chain A (#2), sequence alignment score = 2435  
RMSD between 195 pruned atom pairs is 0.964 angstroms; (across all 497 pairs:
25.188)  
  

> open
> /Users/goddard/Desktop/boltz/boltz_mg_249_dna_3/boltz_results_mg_249_dna/predictions/mg_249_dna/mg_249_dna_model_1.cif
> logInfo false

Matchmaker mg_249_dna_model_0.cif, chain A (#1) with mg_249_dna_model_1.cif,
chain A (#3), sequence alignment score = 2466.2  
RMSD between 107 pruned atom pairs is 0.991 angstroms; (across all 497 pairs:
22.326)  
  

> open
> /Users/goddard/Desktop/boltz/boltz_mg_249_dna_3/boltz_results_mg_249_dna/predictions/mg_249_dna/mg_249_dna_model_2.cif
> logInfo false

Matchmaker mg_249_dna_model_0.cif, chain A (#1) with mg_249_dna_model_2.cif,
chain A (#4), sequence alignment score = 2442.8  
RMSD between 179 pruned atom pairs is 0.948 angstroms; (across all 497 pairs:
33.563)  
  

> open
> /Users/goddard/Desktop/boltz/boltz_mg_249_dna_3/boltz_results_mg_249_dna/predictions/mg_249_dna/mg_249_dna_model_3.cif
> logInfo false

Matchmaker mg_249_dna_model_0.cif, chain A (#1) with mg_249_dna_model_3.cif,
chain A (#5), sequence alignment score = 2447  
RMSD between 140 pruned atom pairs is 0.985 angstroms; (across all 497 pairs:
24.748)  
  

> open
> /Users/goddard/Desktop/boltz/boltz_mg_249_dna_3/boltz_results_mg_249_dna/predictions/mg_249_dna/mg_249_dna_model_4.cif
> logInfo false

Matchmaker mg_249_dna_model_0.cif, chain A (#1) with mg_249_dna_model_4.cif,
chain A (#6), sequence alignment score = 2421.8  
RMSD between 196 pruned atom pairs is 1.171 angstroms; (across all 497 pairs:
17.731)  
  

> hide #6 models

> hide #5 models

> hide #4 models

> hide #3 models

> hide #1 models

> alphafold contacts #2/A toAtoms #2/B,C

Found 27 residue or atom pairs within distance 3  

> alphafold contacts #2/A toAtoms #2/B,C distance 5

Found 105 residue or atom pairs within distance 5  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
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: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 46 days, 22 hours, 52 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]

Fixed.

The alphafold pae command set the structure.alphafold_pae attribute but the Boltz Error Plot button did not do that.