AlphaFold error plot tool does not suggest PAE file

[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
Bringing up alphafold error plot tool does not suggest any PAE file to open unless I choose from the menu PAE from file even though it starts with that menu choice chosen.

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_3/boltz_results_mg_249_dna/predictions/mg_249_dna/mg_249_dna_model_0.cif
> format mmcif logInfo false

> boltz predict protein #1 dna #1 name mg_249_dna recycles 10 seed 1 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 0.74, pTM 0.88, ipTM 0.98, pLDDT 0.68  
Confidence score 0.71, pTM 0.61, ipTM 0.95, pLDDT 0.65  
Confidence score 0.71, pTM 0.69, ipTM 0.95, pLDDT 0.65  
Confidence score 0.71, pTM 0.44, ipTM 0.92, pLDDT 0.65  
Confidence score 0.69, pTM 0.75, ipTM 0.93, pLDDT 0.63  
Boltz prediction completed in 673 seconds (start boltz 6 sec, sequence search
0 sec, load weights 11 sec, structure inference 655 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_6/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 = 2492  
RMSD between 56 pruned atom pairs is 1.282 angstroms; (across all 497 pairs:
30.877)  
  

> open
> /Users/goddard/Desktop/boltz/boltz_mg_249_dna_6/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 = 2411.6  
RMSD between 94 pruned atom pairs is 0.878 angstroms; (across all 497 pairs:
39.657)  
  

> open
> /Users/goddard/Desktop/boltz/boltz_mg_249_dna_6/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 = 2444  
RMSD between 179 pruned atom pairs is 1.062 angstroms; (across all 497 pairs:
23.184)  
  

> open
> /Users/goddard/Desktop/boltz/boltz_mg_249_dna_6/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 = 2415.8  
RMSD between 86 pruned atom pairs is 0.389 angstroms; (across all 497 pairs:
28.315)  
  

> open
> /Users/goddard/Desktop/boltz/boltz_mg_249_dna_6/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 = 2434.4  
RMSD between 166 pruned atom pairs is 0.796 angstroms; (across all 497 pairs:
36.986)  
  

> hide #1 models

> hide #6 models

> hide #5 models

> hide #4 models

> hide #3 models

> ui tool show "AlphaFold Error Plot"

> alphafold pae #2 file
> /Users/goddard/Desktop/boltz/boltz_mg_249_dna_6/boltz_results_mg_249_dna/predictions/mg_249_dna/pae_mg_249_dna_model_0.npz

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

Found 92 residue or atom pairs within distance 5  

> alphafold contacts #2/A toAtoms #2/B,C distance 8

Found 234 residue or atom pairs within distance 8  

> ui tool show "AlphaFold Error Plot"




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:

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      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: 47 days, 28 minutes

Graphics/Displays:

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[Tom Goddard]

Seems to happen only when opening multiple predictions from same directory.

[Tom Goddard]

Fixed.

The code was only showing the file suggestion if it recognizes the structure as an AlphaFold prediction. It doesn't know how to recognize a Boltz predicted structure. In fact the mmCIF for a Boltz prediction does not contain any mention of Boltz. I changed the error plot gui so even if it does not recognize the structure as a prediction it tries to find a PAE file in the same directory.