alphafold pae: KeyError: 'pae is not a file in the archive'

[o.bozkurt@…]

The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.10rc202505300032 (2025-05-30 00:32:35 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10rc202505300032 (2025-05-30)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/obozkurt/Downloads/X/predictions/X/X_model_0.cif

Summary of feedback from opening
/Users/obozkurt/Downloads/X/predictions/X/X_model_0.cif  
---  
warning | Atom C50 is not in the residue template for LIG /C:1  
  
X_model_0.cif title:  
. [more info...]  
  
Chain information for X_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Non-standard residues in X_model_0.cif #1  
---  
LIG — (LIG)  
  

No chain in structure corresponds to chain ID given in local score info (chain
'C')  

Computing secondary structure  

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> alphafold fetch Q86V81 pae true

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold Q86V81 from
https://alphafold.ebi.ac.uk/files/AF-Q86V81-F1-model_v3.cif  
Chain information for AlphaFold Q86V81 #2  
---  
Chain | Description | UniProt  
A | THO complex subunit 4 | THOC4_HUMAN 1-257  
  
Color AlphaFold Q86V81 by residue attribute pLDDT_score  
Fetching compressed AlphaFold PAE Q86V81 from
https://alphafold.ebi.ac.uk/files/AF-Q86V81-F1-predicted_aligned_error_v3.json  

> close #2

> import json

Unknown command: import json  

> from google.colab import files

Unknown command: from google.colab import files  

> with open('/content/results/ranking_summary.json') as f:

Unknown command: with open('/content/results/ranking_summary.json') as f:  

> data = json.load(f)

Unknown command: data = json.load(f)  

> attr_path = '/content/confidence_scores.attr'

Unknown command: attr_path = '/content/confidence_scores.attr'  

> with open(attr_path, 'w') as f:

Unknown command: with open(attr_path, 'w') as f:  

> f.write("attribute: confidence_score\n")

Unknown command: f.write("attribute: confidence_score\n")  

> f.write("recipient: model\n\n")

Unknown command: f.write("recipient: model\n\n")  

> force i, (pose_name, pose_data) in enumerate(data.items(), start=1):

force is provided by the uninstalled bundle SEQCROW versions 1.8.19 – 1.8.21  

> score = pose_data.get('confidence', 0.0)

Unknown command: score = pose_data.get('confidence', 0.0)  

> f.write(f"{i} {score:.4f}\n")

Unknown command: f.write(f"{i} {score:.4f}\n")  

> print(f"✅ Done! Attr file saved to: {attr_path}")

Unknown command: print(f"✅ Done! Attr file saved to: {attr_path}")  

> files.download(attr_path)

Unknown command: files.download(attr_path)  

> cartoon style protein thickness 3.4 width 3.4

> color bychain

> cartoon style protein thickness 2 width 2

> graphics silhouettes true

> lighting soft

> cartoon style protein thickness 1 width 2

> 1

Unknown command: 1  

> cartoon style protein thickness 3.4 width 3.4

> cartoon style protein thickness 1 width 3.4

> cartoon style protein thickness 1 width 1

> ui tool show "AlphaFold Error Plot"

> close

> open /Users/obozkurt/Desktop/boltz_INF-ERG3_1/INF-ERG3_model_0.cif

Summary of feedback from opening /Users/obozkurt/Desktop/boltz_INF-ERG3_1/INF-
ERG3_model_0.cif  
---  
warning | Atom C54 is not in the residue template for LIG /C:1  
  
INF-ERG3_model_0.cif title:  
. [more info...]  
  
Chain information for INF-ERG3_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Non-standard residues in INF-ERG3_model_0.cif #1  
---  
LIG — (LIG)  
  

No chain in structure corresponds to chain ID given in local score info (chain
'C')  

Computing secondary structure  

> alphafold pae #1 file /Users/obozkurt/Desktop/boltz_INF-ERG3_1/pae_INF-
> ERG3_model_0.npz

> color bfactor #1 palette alphafold

6936 atoms, 884 residues, atom bfactor range 31 to 98.3  

> color bychain

> cartoon style protein thickness 1 width 1

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> alphafold contacts /a toAtoms /b distance 4

Found 63 residue or atom pairs within distance 4  

> select /B:1-785

6191 atoms, 6321 bonds, 785 residues, 1 model selected  

> select /A:1-98

715 atoms, 724 bonds, 98 residues, 1 model selected  

> show sel surfaces

> select clear

> close

> open /Users/obozkurt/Desktop/boltz_INF-ERG3/INF-ERG3_model_0.cif

Summary of feedback from opening /Users/obozkurt/Desktop/boltz_INF-ERG3/INF-
ERG3_model_0.cif  
---  
warnings | Atom C54 is not in the residue template for LIG /B:1  
Atom C54 is not in the residue template for LIG /C:1  
Atom C54 is not in the residue template for LIG /D:1  
  
INF-ERG3_model_0.cif title:  
. [more info...]  
  
Chain information for INF-ERG3_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Non-standard residues in INF-ERG3_model_0.cif #1  
---  
LIG — (LIG)  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

Computing secondary structure  

> close

> open /Users/obozkurt/Desktop/boltz_INF-lipid_1/INF-lipid_model_0.cif

Summary of feedback from opening /Users/obozkurt/Desktop/boltz_INF-
lipid_1/INF-lipid_model_0.cif  
---  
warning | Atom C54 is not in the residue template for LIG /B:1  
  
INF-lipid_model_0.cif title:  
. [more info...]  
  
Chain information for INF-lipid_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Non-standard residues in INF-lipid_model_0.cif #1  
---  
LIG — (LIG)  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

Computing secondary structure  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file /Users/obozkurt/Desktop/boltz_INF-lipid_1/pae_INF-
> lipid_model_0.npz

> color bfactor #1 palette alphafold

745 atoms, 99 residues, atom bfactor range 55.9 to 97.6  

> show surfaces

> hide surfaces

> Movie record

Unknown command: Movie record  

> movie record

> roll y 2 180

> show surfaces

> roll x 2 180

> hide surfaces

> show surfaces

> color #fffffff4

> color #fffffff3

[Repeated 1 time(s)]

> color #fffffff2

> color #ffffffe9

> color #ffffffdf

> color #ffffffde

[Repeated 1 time(s)]

> color #ffffffd6

> color #ffffffd3

> color #ffffffce

> color #ffffffcd

[Repeated 2 time(s)]

> color #ffffffce

> color #ffffffe2

> color #ffffffe3

> color #ffffffea

> color #fffffffb

> color #ffffffff

> color #7d90ffff

> color #90a0ffff

> color #90a0fffe

> color #90a0fffb

> color #90a0ffe6

> color #90a0ffd5

> color #90a0ffd3

> color #90a0ffcb

> color #90a0ffc3

> color #90a0ffb8

> color #90a0ffb4

> color #90a0ffb3

[Repeated 1 time(s)]

> color #90a0ffb2

> color #90a0ffb1

> color #90a0ffaf

> color #90a0ffad

> color #90a0ffa3

> color #90a0ffa0

> color #90a0ff9f

> color #90a0ff9c

> color #90a0ff9b

> color #90a0ff9a

> color #90a0ff93

> color #90a0ff8e

> color #90a0ff8d

[Repeated 1 time(s)]

> color #90a0ff8c

> color #90a0ff8b

> color #90a0ff89

> color #90a0ff86

> color #90a0ff77

> color #90a0ff75

> color #90a0ff6a

> color #90a0ff69

> color #90a0ff63

> color #90a0ff61

> color #90a0ff60

> color #90a0ff59

> color #90a0ff58

> color #90a0ff57

> color #90a0ff56

> color #90a0ff55

[Repeated 1 time(s)]

> color #90a0ff54

> color #90a0ff50

> color #90a0ff4f

[Repeated 1 time(s)]

> color #90a0ff4e

> color #90a0ff4d

[Repeated 1 time(s)]

> color #90a0ff4c

> color #90a0ff4b

[Repeated 1 time(s)]

> color #90a0ff4a

> color #90a0ff48

[Repeated 1 time(s)]

> color #90a0ff47

> color #90a0ff46

[Repeated 1 time(s)]

> color #90a0ff44

> color #90a0ff37

> color #90a0ff30

[Repeated 1 time(s)]

> color #90a0ff2f

> color #90a0ff31

> color #90a0ff5f

> color #90a0ff62

> color #90a0ff64

> color #90a0ff66

> color #90a0ff69

> color #90a0ff6a

> color #90a0ff6f

[Repeated 1 time(s)]

> color #90a0ff72

> color #90a0ff78

> color #90a0ff7e

> color #90a0ff85

> color #90a0ff8c

> color #90a0ffeb

> color #90a0ffff

> movie stop

> movie encode output mymovie.mp4

Movie saved to mymovie.mp4  
  

> hide surfaces

> color bfactor #1 palette alphafold

745 atoms, 99 residues, 1 surfaces, atom bfactor range 55.9 to 97.6  

> alphafold pae #1 colorDomains true

> color bychain

> movie record

> rock y

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file /Users/obozkurt/Desktop/boltz_INF-lipid_1/pae_INF-
> lipid_model_0.npz

> color bfactor #1 palette alphafold

745 atoms, 99 residues, 1 surfaces, atom bfactor range 55.9 to 97.6  

> select /A:1-98

715 atoms, 724 bonds, 98 residues, 1 model selected  

> show sel surfaces

> select clear

> stop

> hide surfaces

> select /A:1-98

715 atoms, 724 bonds, 98 residues, 1 model selected  

> ui tool show Contacts

> contacts sel restrict cross distanceOnly 3.4999999999999996 interModel false
> intraMol false select true color #0c0d0c radius 0.085 reveal true

10 distances  

> rock y

> select clear

> movie stop

> stop

> movie encode output mymovie.mp4

Movie saved to mymovie.mp4  
  

> hide #1.2 models

> hide #1.1 models

> hide #!1 models

> show #!1 models

> color bychain

> movie record

> roll y 2 180

> show #1.1 models

> select add #1.1

715 atoms, 98 residues, 1 model selected  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file /Users/obozkurt/Desktop/boltz_INF-lipid_1/pae_INF-
> lipid_model_0.npz

> color bfactor #1 palette alphafold

745 atoms, 99 residues, 1 surfaces, atom bfactor range 55.9 to 97.6  

> roll y 2 180

> show #1.2 models

> select clear

> select /A:1-98

715 atoms, 724 bonds, 98 residues, 1 model selected  

> show sel surfaces

> roll x 2 180

> movie encode output mymovie.mp4

Movie saved to mymovie.mp4  
  

> open
> /Users/obozkurt/Desktop/boltz_INF2B_NtREL1B_Bsis_1/INF2B_NtREL1B_Bsis_model_0.cif

Summary of feedback from opening
/Users/obozkurt/Desktop/boltz_INF2B_NtREL1B_Bsis_1/INF2B_NtREL1B_Bsis_model_0.cif  
---  
warning | Atom C48 is not in the residue template for LIG /C:1  
  
INF2B_NtREL1B_Bsis_model_0.cif title:  
. [more info...]  
  
Chain information for INF2B_NtREL1B_Bsis_model_0.cif #2  
---  
Chain | Description  
A | .  
B | .  
  
Non-standard residues in INF2B_NtREL1B_Bsis_model_0.cif #2  
---  
LIG — (LIG)  
  

No chain in structure corresponds to chain ID given in local score info (chain
'C')  

Computing secondary structure  

> close

> open
> /Users/obozkurt/Desktop/boltz_INF2B_NtREL1B_Bsis_1/INF2B_NtREL1B_Bsis_model_0.cif

Summary of feedback from opening
/Users/obozkurt/Desktop/boltz_INF2B_NtREL1B_Bsis_1/INF2B_NtREL1B_Bsis_model_0.cif  
---  
warning | Atom C48 is not in the residue template for LIG /C:1  
  
INF2B_NtREL1B_Bsis_model_0.cif title:  
. [more info...]  
  
Chain information for INF2B_NtREL1B_Bsis_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Non-standard residues in INF2B_NtREL1B_Bsis_model_0.cif #1  
---  
LIG — (LIG)  
  

No chain in structure corresponds to chain ID given in local score info (chain
'C')  

Computing secondary structure  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> /Users/obozkurt/Desktop/boltz_INF2B_NtREL1B_Bsis_1/pae_INF2B_NtREL1B_Bsis_model_0.npz

> color bfactor #1 palette alphafold

7655 atoms, 981 residues, atom bfactor range 27.4 to 98.3  

> alphafold contacts /a toAtoms /b distance 4

Found 67 residue or atom pairs within distance 4  

> close

> open
> /Users/obozkurt/Desktop/boltz_INF2B-NtREL1B-Bsis/INF2B-NtREL1B-Bsis_model_0.cif

Summary of feedback from opening
/Users/obozkurt/Desktop/boltz_INF2B-NtREL1B-Bsis/INF2B-NtREL1B-Bsis_model_0.cif  
---  
warning | Atom C50 is not in the residue template for LIG /C:1  
  
INF2B-NtREL1B-Bsis_model_0.cif title:  
. [more info...]  
  
Chain information for INF2B-NtREL1B-Bsis_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Non-standard residues in INF2B-NtREL1B-Bsis_model_0.cif #1  
---  
LIG — (LIG)  
  

No chain in structure corresponds to chain ID given in local score info (chain
'C')  

Computing secondary structure  

> ui tool show Contacts

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> /Users/obozkurt/Desktop/boltz_INF2B-NtREL1B-Bsis/pae_INF2B-NtREL1B-Bsis_model_0.npz

> color bfactor #1 palette alphafold

8030 atoms, 1038 residues, atom bfactor range 27.7 to 98  

> alphafold contacts /a toAtoms /b distance 4

Found 150 residue or atom pairs within distance 4  

> color bychain

> select /A:1-169

1170 atoms, 1186 bonds, 169 residues, 1 model selected  

> color sel dim gray

> select /A:1-169

1170 atoms, 1186 bonds, 169 residues, 1 model selected  

> color sel white

> color sel dim gray

> select /B:1-868

6832 atoms, 6967 bonds, 868 residues, 1 model selected  

> color sel white

> select clear

> select :LIG

28 atoms, 31 bonds, 1 residue, 1 model selected  

> color sel black

> color sel cyan

> select clear

Alignment identifier is 1/A  
Alignment identifier is 1/B  

> select /A:39-40

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select /A:39-46

57 atoms, 57 bonds, 8 residues, 1 model selected  

> select /A:85-86

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:85-99

105 atoms, 105 bonds, 15 residues, 1 model selected  

> select clear

> movie record

> roll y 2 180

[Repeated 1 time(s)]

> select /A:169

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A

1170 atoms, 1186 bonds, 169 residues, 1 model selected  

> show sel surfaces

> select clear

> roll y 2 180

> movie encode output INF2B-NtREL1b-Bsis.mp4

Movie saved to INF2B-NtREL1b-Bsis.mp4  
  

> close

> open "/Users/obozkurt/Downloads/CF4_AVR4_Chitin_Colab1
> (1)/predictions/CF4_AVR4_Chitin_Colab1/CF4_AVR4_Chitin_Colab1_model_0.cif"

Summary of feedback from opening
/Users/obozkurt/Downloads/CF4_AVR4_Chitin_Colab1
(1)/predictions/CF4_AVR4_Chitin_Colab1/CF4_AVR4_Chitin_Colab1_model_0.cif  
---  
warning | Atom C44 is not in the residue template for LIG /C:1  
  
CF4_AVR4_Chitin_Colab1_model_0.cif title:  
. [more info...]  
  
Chain information for CF4_AVR4_Chitin_Colab1_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Non-standard residues in CF4_AVR4_Chitin_Colab1_model_0.cif #1  
---  
LIG — (LIG)  
  

No chain in structure corresponds to chain ID given in local score info (chain
'C')  

Computing secondary structure  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file "/Users/obozkurt/Downloads/CF4_AVR4_Chitin_Colab1
> (1)/predictions/CF4_AVR4_Chitin_Colab1/plddt_CF4_AVR4_Chitin_Colab1_model_0.npz"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 186, in _open_pae  
self._open_pae_from_file(s)  
File
"/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 212, in _open_pae_from_file  
run(self.session, cmd)  
File
"/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1462, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 980, in __init__  
self._pae_matrix = read_pae_matrix(pae_path)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1226, in read_pae_matrix  
return read_numpy_pae_matrix(path)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1287, in read_numpy_pae_matrix  
pae = pae['pae']  
~~~^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/npyio.py", line 263, in __getitem__  
raise KeyError(f"{key} is not a file in the archive")  
KeyError: 'pae is not a file in the archive'  
  
KeyError: 'pae is not a file in the archive'  
  
File
"/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/npyio.py", line 263, in __getitem__  
raise KeyError(f"{key} is not a file in the archive")  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,10
      Model Number: MRX53B/A
      Chip: Apple M3 Max
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 36 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 3 days, 2 hours, 31 minutes

Graphics/Displays:

    Apple M3 Max:

      Chipset Model: Apple M3 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.4
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10rc202505300032
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.8.2
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.1
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.5
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 26.4.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.13.2
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

[pett]

Reported by Tolga

[Tom Goddard]

The user tried to open the plddt .npz file instead of the pae .npz file from a Boltz run when trying to show a PAE plot. I should probably give a sane error message saying they chose the wrong file when numpy finds the specified .npz does not contain the key "pae".

[Tom Goddard]

They probably ran Boltz with a Colab server judging by the file names and probably it did not compute the PAE file since boltz option --write_full_pae is false by default. So the error message should probably say that the file is not pae, and that Boltz may not have produced the pae file and less it was requested.

[Tom Goddard]

Added in ChimeraX 1.11 a user friendly error message explaining that the .npz file given does not contain PAE data.