AlphaFold PAE domain coloring IndexError

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-12.3.1-arm64-arm-64bit
ChimeraX Version: 1.4.dev202204210038 (2022-04-21 00:38:21 UTC)
Description
AlphaFold PAE domain coloring gives an error when shown on AlphaFold model matched to PDB structure 6pxv chain A because the alphafold model is trimmed to the range of the experimental sequence.

Log:
UCSF ChimeraX version: 1.4.dev202204210038 (2022-04-21)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6pxv format mmcif fromDatabase pdb

6pxv title:  
Cryo-EM structure of full-length insulin receptor bound to 4 insulin. 3D
refinement was focused on the extracellular region. [more info...]  
  
Chain information for 6pxv #1  
---  
Chain | Description | UniProt  
A C | Insulin receptor | INSR_HUMAN  
D E F G | Insulin | A6XGL2_HUMAN  
  

> alphafold match #1/A

1 AlphaFold model found using UniProt identifier: P06213 (chain A)  
AlphaFold chains matching 6pxv  
---  
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id  
A | INSR_HUMAN | P06213 | 30.76 | 1343 | 823 | 100  
  
Opened 1 AlphaFold model  

> ui tool show AlphaFold

> alphafold pae #2.1 uniprotId P06213

> alphafold pae #2.1 colorDomains true

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 343, in _color_domains  
self._pae.color_domains(log_command = True)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 509, in color_domains  
color_by_pae_domain(m.residues, self._clusters, colors=self._cluster_colors)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 672, in color_by_pae_domain  
cresidues = residues[array(list(c),int32)]  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molarray.py", line 160, in __getitem__  
ptrs = self._pointers[i].copy()  
IndexError: index 1343 is out of bounds for axis 0 with size 1343  
  

Populating font family aliases took 70 ms. Replace uses of missing font family
".AppleSystemUIFont" with one that exists to avoid this cost.  

IndexError: index 1343 is out of bounds for axis 0 with size 1343  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molarray.py", line 160, in __getitem__  
ptrs = self._pointers[i].copy()  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt runtime version: 6.2.4
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 7459.101.3
      OS Loader Version: 7459.101.3

Software:

    System Software Overview:

      System Version: macOS 12.3.1 (21E258)
      Kernel Version: Darwin 21.4.0
      Time since boot: 15 days 13:14

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      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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[Tom Goddard]

Made opening PAE matrix for a structure with a different number of residues give an explanatory error message that the number of residues must match.

This isn't the best solution. It would be nicer if an AlphaFold model remembered it original residue indexes so that even if residues get deleted we can still use the PAE plots. I could add a residue attribute "alphafold_residue_index" when the alphafold command trims a structure. But this would not fix the case when the user opens an AlphaFold model directly and deletes some residues. Still may be worth handling the trim case.

[Tom Goddard]

Fixed by making better error message.

Made ticket #6730 to try to allow coloring when residues deleted.