Alphafold prediction PAE matrix includes X residues while structure does not: can't load PAE

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.1.2-arm64-arm-64bit
ChimeraX Version: 1.8.dev202312190520 (2023-12-19 05:20:12 UTC)
Description
The AlphaFold prediction PAE matrix size is 34 while the predicted structure is 32 residues for 1a0m dimer.  The trouble is that the 2 sequences for 1a0m contain an unknown residue X that does not get modeled.  But apparently it includes PAE entries for the X residues.

Log:
UCSF ChimeraX version: 1.8.dev202312190520 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1a0m format mmcif fromDatabase pdb

1a0m title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]  
  
Chain information for 1a0m #1  
---  
Chain | Description | UniProt  
A B | ALPHA-CONOTOXIN [TYR15]-EPI | CXA1_CONEP 1-16  
  
Non-standard residues in 1a0m #1  
---  
NH2 — amino group  
  

> ui tool show AlphaFold

> alphafold predict #1

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/goddard/Downloads/ChimeraX/AlphaFold/prediction_79  

> open
> /Users/goddard/Downloads/ChimeraX/AlphaFold/prediction_79/best_model.pdb

Chain information for best_model.pdb #2  
---  
Chain | Description  
A B | No description available  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #2 file
> /Users/goddard/Downloads/ChimeraX/AlphaFold/prediction_79/best_model_pae.json

Number of residues in structure "best_model.pdb #2" is 32 which does not match
PAE matrix size 34.  
  
This can happen if chains were deleted from the AlphaFold model or if the PAE
data was applied to a structure that was not the one predicted by AlphaFold.
Use the full-length AlphaFold model to show predicted aligned error.  

> select #2

238 atoms, 242 bonds, 32 residues, 1 model selected  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
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: 10151.41.12
      OS Loader Version: 10151.41.12

Software:

    System Software Overview:

      System Version: macOS 14.1.2 (23B92)
      Kernel Version: Darwin 23.1.0
      Time since boot: 24 days, 7 hours, 34 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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