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

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202405031817 (2024-05-03 18:17:29 UTC)
Description
Loading PAE data for AlphaFold3 run that had a ligands and ions fails with this error, wrong number of residues in structure.

Log:
UCSF ChimeraX version: 1.8.dev202405031817 (2024-05-03)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

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> registration file ~/Desktop/reg2.html

Expected name of a file to open/read; a name of 'browse' will bring up a file
browser or a keyword  

> open 4xv9

Summary of feedback from opening 4xv9 fetched from pdb  
---  
warning | Cannot find consistent set of bond orders for ring system containing atom C19 in residue 1OO /A:801  
  
4xv9 title:  
B-Raf Kinase domain in complex with PLX5568 [more info...]  
  
Chain information for 4xv9 #1  
---  
Chain | Description | UniProt  
A | Serine/threonine-protein kinase B-raf | BRAF_HUMAN 442-705  
  
Non-standard residues in 4xv9 #1  
---  
1OO —
N-{3-[(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)carbonyl]-2,4-difluorophenyl}-4-(trifluoromethyl)benzenesulfonamide  
SO4 — sulfate ion  
  
4xv9 mmCIF Assemblies  
---  
1| author_defined_assembly  
  
53 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> close

> open 8jk9

Summary of feedback from opening 8jk9 fetched from pdb  
---  
note | Fetching compressed mmCIF 8jk9 from http://files.rcsb.org/download/8jk9.cif  
  
8jk9 title:  
SP1746 in complex with GDP [more info...]  
  
Chain information for 8jk9 #1  
---  
Chain | Description | UniProt  
A | bis(5'-nucleosyl)-tetraphosphatase (symmetrical) | A0A0H2URF8_STRPN 1-197  
  
Non-standard residues in 8jk9 #1  
---  
FE — Fe (III) ion  
GDP — guanosine-5'-diphosphate  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
  
8jk9 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
15 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select :FE

2 atoms, 2 residues, 1 model selected  

> select :GDP

28 atoms, 30 bonds, 1 residue, 1 model selected  

> select :MG

2 atoms, 2 residues, 1 model selected  

> open
> /Users/goddard/Downloads/fold_2024_05_08_15_09/fold_2024_05_08_15_09_model_0.cif

Chain information for fold_2024_05_08_15_09_model_0.cif #2  
---  
Chain | Description  
A B | .  
  

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8jk9, chain A (#1) with fold_2024_05_08_15_09_model_0.cif, chain A
(#2), sequence alignment score = 1114.4  
RMSD between 194 pruned atom pairs is 0.339 angstroms; (across all 195 pairs:
0.385)  
  

> sym #1 assembly 1

Made 2 copies for 8jk9 assembly 1  

> view

> hide #!3 models

> show #!3 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #!3 models

> hide #2 models

> show #2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> ui tool show "AlphaFold Error Plot"

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 62, in <lambda>  
sf.widget.menu().triggered.connect(lambda action, self=self:
self._guess_for_source())  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 132, in _guess_for_source  
pae_path = _matching_pae_file(structure_path)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 316, in _matching_pae_file  
mfile = _longest_matching_prefix(filename, pkl_files, min_length = min_length)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 328, in _longest_matching_prefix  
mfilename = m[0][1] if m[0][0] >= min_length and m[0][0] > m[1][0] else None  
~^^^  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 328, in _longest_matching_prefix  
mfilename = m[0][1] if m[0][0] >= min_length and m[0][0] > m[1][0] else None  
~^^^  
  
See log for complete Python traceback.  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #2 file
> /Users/goddard/Downloads/fold_2024_05_08_15_09/fold_2024_05_08_15_09_full_data_0.json

Number of residues in structure "fold_2024_05_08_15_09_model_0.cif #2" is 440
which does not match PAE matrix size 494.  
  
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 Metal - 88
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
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: 10151.101.3
      OS Loader Version: 10151.101.3

Software:

    System Software Overview:

      System Version: macOS 14.4.1 (23E224)
      Kernel Version: Darwin 23.4.0
      Time since boot: 1 day, 19 hours, 22 minutes

Graphics/Displays:

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      Total Number of Cores: 60
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          Online: Yes
          Rotation: Supported


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[Tom Goddard]

The AlphaFold 3 PAE json file has rows that are individual atoms for ligands and ions, and rows that are residues for protein and nucleic acid polymers. AlphaFold 2 only had residues. Reworking the PAE plot, PAE domains and alphafold contacts code to handle a mix of residues and atoms will require modifying a few hundred lines of code and will be more complex.

I think I should do this soon and include it in ChimeraX 1.8.

Oleg Kovalevskiy from DeepMind asked for this fix in #15135.

[Tom Goddard]

Fixed in ChimeraX daily build and 1.8 release candidates dated May 14, 2024 or later.

The predicted aligned error from AlphaFold 3 includes rows in the matrix for individual atoms of ligands, ions, glycans, and modified residues, while standard protein and nucleic polymers still have rows corresponding to whole residues as in AlphaFold 2. This ChimeraX fix allows handling the atom and residue PAE values in the AlphaFold Error Plot tool that shows a heatmap of PAE values, and also in the "alphafold contacts" command that color-coded shows lines connecting nearby residues or atoms to indicate PAE values.

Elaine could you update the AlphaFold Error Plot and alphafold contacts command documentation to indicate that they handle AlphaFold 3 output. The descriptions will need to be update to indicate the PAE values are assigned to both polymer residues (as before) and non-polymer atoms (new to AlphaFold 3).

The "alphafold contacts" command now takes arguments "atoms" and "toAtoms" instead of "residues" and "toResidues" so that PAE values to specific atoms can requested. The lines connecting PAE for individual atoms and residues go between the atom and the residue CA or P atom (principal backbone atom).