AlphaFold3 with ligands PAE json file: number of structure residues does not match matrix size

[jdzimian@…]

The following bug report has been submitted:
Platform:        macOS-13.6.6-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
The AlphaFold Error Plot function fails for an AlphaFold3 predicted glycoprotein with the following message:

Number of residues in structure "fold_tas20_model_0.cif #1" is 1551 which does not match PAE matrix size 1980.

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.

I suspect this may be due to AlphaFold3 providing matrix values for glycans on an atom-by-atom basis rather than residue-by-residue.

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/John/Documents/UCSC/Research/Influenza/InfA/Manuscripts/H3/AlphaFold3/fold_tas20/fold_tas20_model_0.cif
> format mmcif

Chain information for fold_tas20_model_0.cif #1  
---  
Chain | Description  
A B C | .  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> /Users/John/Documents/UCSC/Research/Influenza/InfA/Manuscripts/H3/AlphaFold3/fold_tas20/fold_tas20_full_data_0.json

Number of residues in structure "fold_tas20_model_0.cif #1" is 1551 which does
not match PAE matrix size 1980.  
  
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.  




OpenGL version: 4.1 INTEL-20.7.2
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.

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:

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      Model Identifier: MacBookPro14,1
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Software:

    System Software Overview:

      System Version: macOS 13.6.6 (22G630)
      Kernel Version: Darwin 22.6.0
      Time since boot: 20 days, 4 hours, 51 minutes

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[Eric Pettersen]

Reported by John Dzimianski

[Eric Pettersen]

Duplicate of #15144; adding reporter to recipient list for that ticket.

[Tom Goddard]

You are right. The AlphaFold 3 PAE matrix has rows for individual atoms for ligands, glycans, ions while AlphaFold 2 only has rows for amino acid residues. I will be fixing ChimeraX to handle AlphaFold 3 PAE, but probably not until Monday or Tuesday since I am on vacation Thursday and Friday. The fix will be in the daily builds and you will get email about it.

If you use AlphaFold 3 for protein-only predictions then I think current ChimeraX PAE display will work in that simple case.