Opened 4 months ago

Closed 4 months ago

#18127 closed defect (duplicate)

PAE file: Operation not permitted

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech Tools/Discovery/Structures -
> AnkZip/AnkryinBTest3/AnkyrinBTest3/AnkyrinBTest3_model_0.pdb"

Summary of feedback from opening
/Users/johnteare/Library/CloudStorage/OneDrive-
Personal/Documents/johntearebio/Biotech Tools/Discovery/Structures -
AnkZip/AnkryinBTest3/AnkyrinBTest3/AnkyrinBTest3_model_0.pdb  
---  
warning | Ignored bad PDB record found on line 1642  
  
Chain information for AnkyrinBTest3_model_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> set bgColor white

> close

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech Tools/Discovery/Structures -
> AnkZip/AmZTest5/AmZTest5/AmZTest5_model_0.pdb"

Summary of feedback from opening
/Users/johnteare/Library/CloudStorage/OneDrive-
Personal/Documents/johntearebio/Biotech Tools/Discovery/Structures -
AnkZip/AmZTest5/AmZTest5/AmZTest5_model_0.pdb  
---  
warning | Ignored bad PDB record found on line 1925  
  
Chain information for AmZTest5_model_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> close

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech Tools/Discovery/Structures -
> AnkZip/AnkyrinBTest1/AnkyrinBTest1/AnkyrinBTest1_model_0.pdb"

Summary of feedback from opening
/Users/johnteare/Library/CloudStorage/OneDrive-
Personal/Documents/johntearebio/Biotech Tools/Discovery/Structures -
AnkZip/AnkyrinBTest1/AnkyrinBTest1/AnkyrinBTest1_model_0.pdb  
---  
warning | Ignored bad PDB record found on line 3124  
  
Chain information for AnkyrinBTest1_model_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> close

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech Tools/Discovery/Structures -
> AnkZip/AnkyrinBTest1/AnkyrinBTest1/AnkyrinBTest1_model_24.pdb"

Summary of feedback from opening
/Users/johnteare/Library/CloudStorage/OneDrive-
Personal/Documents/johntearebio/Biotech Tools/Discovery/Structures -
AnkZip/AnkyrinBTest1/AnkyrinBTest1/AnkyrinBTest1_model_24.pdb  
---  
warning | Ignored bad PDB record found on line 3124  
  
Chain information for AnkyrinBTest1_model_24.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> select /A:1-208

1574 atoms, 1603 bonds, 208 residues, 1 model selected  

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech Tools/Discovery/Structures -
> AnkZip/AnkyrinBTest1/AnkyrinBTest1/AnkyrinBTest1_model_11.pdb"

Summary of feedback from opening
/Users/johnteare/Library/CloudStorage/OneDrive-
Personal/Documents/johntearebio/Biotech Tools/Discovery/Structures -
AnkZip/AnkyrinBTest1/AnkyrinBTest1/AnkyrinBTest1_model_11.pdb  
---  
warning | Ignored bad PDB record found on line 3124  
  
Chain information for AnkyrinBTest1_model_11.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> hide #1 models

> close

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech Tools/Discovery/Structures -
> AnkZip/Ankyrin34_35Op1/drive-download-20250117T163156Z-001/ranked_0.pdb"

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> close

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech Tools/Discovery/Structures -
> AnkZip/AnkZip34/drive-download-20250110T154709Z-001/ranked_0.pdb"

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> close

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech Tools/Discovery/Sequences/Boltz1
> fasta/Structures/AZ34V2/drive-
> download-20250409T021039Z-001/AZ34V2_model_0.pdb"

Summary of feedback from opening
/Users/johnteare/Library/CloudStorage/OneDrive-
Personal/Documents/johntearebio/Biotech Tools/Discovery/Sequences/Boltz1
fasta/Structures/AZ34V2/drive-download-20250409T021039Z-001/AZ34V2_model_0.pdb  
---  
warning | Ignored bad PDB record found on line 2008  
  
Chain information for AZ34V2_model_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> close

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech Tools/Discovery/Sequences/Boltz1
> fasta/Structures/AZ34V2/drive-
> download-20250409T021039Z-001/AZ34V2_model_0.pdb" format pdb

Summary of feedback from opening
/Users/johnteare/Library/CloudStorage/OneDrive-
Personal/Documents/johntearebio/Biotech Tools/Discovery/Sequences/Boltz1
fasta/Structures/AZ34V2/drive-download-20250409T021039Z-001/AZ34V2_model_0.pdb  
---  
warning | Ignored bad PDB record found on line 2008  
  
Chain information for AZ34V2_model_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> sequence chain /A

Alignment identifier is 1/A  

> select /B:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /B

998 atoms, 1015 bonds, 130 residues, 1 model selected  

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech
> Tools/Discovery/Structures/07-2025/First Tests/AnkyrinBTest1_model_0.cif"

AnkyrinBTest1_model_0.cif title:  
. [more info...]  
  
Chain information for AnkyrinBTest1_model_0.cif #2  
---  
Chain | Description  
A | .  
B | .  
  
Color AnkyrinBTest1_model_0.cif by residue attribute pLDDT_score  
Computing secondary structure  

> close

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech
> Tools/Discovery/Structures/07-2025/First Tests/AnkyrinBTest1_model_0.cif"
> format mmcif

AnkyrinBTest1_model_0.cif title:  
. [more info...]  
  
Chain information for AnkyrinBTest1_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Color AnkyrinBTest1_model_0.cif by residue attribute pLDDT_score  
Computing secondary structure  

> show atoms

> coulombic

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
/A GLY 208 OXT  
/B GLY 208 OXT  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AnkyrinBTest1_model_0.cif_A SES surface #1.1: minimum,
-20.61, mean -1.52, maximum 11.81  
Coulombic values for AnkyrinBTest1_model_0.cif_B SES surface #1.2: minimum,
-26.11, mean -7.56, maximum 7.25  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide surfaces

> close

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech
> Tools/Discovery/Structures/07-2025/boltz_results_AZ34V4/predictions/AZ34V4/AZ34V4_model_0.cif"

AZ34V4_model_0.cif title:  
. [more info...]  
  
Chain information for AZ34V4_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Color AZ34V4_model_0.cif by residue attribute pLDDT_score  
Computing secondary structure  

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech Tools/Discovery/Sequences/Boltz1
> fasta/Structures/AZ34V2/drive-
> download-20250409T021039Z-001/AZ34V2_model_0.pdb"

Summary of feedback from opening
/Users/johnteare/Library/CloudStorage/OneDrive-
Personal/Documents/johntearebio/Biotech Tools/Discovery/Sequences/Boltz1
fasta/Structures/AZ34V2/drive-download-20250409T021039Z-001/AZ34V2_model_0.pdb  
---  
warning | Ignored bad PDB record found on line 2008  
  
Chain information for AZ34V2_model_0.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 1 time(s)]  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 AZ34V4_model_0.cif, chain A (#1) with AZ34V2_model_0.pdb, chain A
(#2), sequence alignment score = 689.1  
RMSD between 63 pruned atom pairs is 0.254 angstroms; (across all 136 pairs:
13.449)  
  

> close

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech
> Tools/Discovery/Structures/07-2025/boltz_results_AZ34V4/predictions/AZ34V4/AZ34V4_model_0.cif"
> format mmcif

AZ34V4_model_0.cif title:  
. [more info...]  
  
Chain information for AZ34V4_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Color AZ34V4_model_0.cif by residue attribute pLDDT_score  
Computing secondary structure  

> ui tool show "Model-map Q-Score"

Must select a model and map first!  

> select add #1

1984 atoms, 2017 bonds, 263 residues, 1 model selected  
Must select a model and map first!  

> style #1 stick

Changed 1984 atom styles  

> color #1 byhetero

> select subtract #1

Nothing selected  

> select add #1

1984 atoms, 2017 bonds, 263 residues, 1 model selected  

> ui tool show Angles/Torsions

Either three or four atoms must be selected!  

> ui tool show "AlphaFold Error Plot"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 101, in _structure_chosen  
self._guess_pae_file_or_database_id()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 118, in
_guess_pae_file_or_database_id  
pae_path = _matching_pae_file(structure_path)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 311, in _matching_pae_file  
dfiles = listdir(dir)  
^^^^^^^^^^^^  
PermissionError: [Errno 1] Operation not permitted:
'/Users/johnteare/Library/CloudStorage/OneDrive-
Personal/Documents/johntearebio/Biotech
Tools/Discovery/Structures/07-2025/boltz_results_AZ34V4/predictions/AZ34V4'  
  
PermissionError: [Errno 1] Operation not permitted:
'/Users/johnteare/Library/CloudStorage/OneDrive-
Personal/Documents/johntearebio/Biotech
Tools/Discovery/Structures/07-2025/boltz_results_AZ34V4/predictions/AZ34V4'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 311, in _matching_pae_file  
dfiles = listdir(dir)  
^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> close

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/johnteare/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/chimerax/qscore/ui.py", line
307, in _toggle_save_button_enabled  
for atom in model.atoms:  
^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "selected model changed":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "/Users/johnteare/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/chimerax/qscore/ui.py", line
307, in _toggle_save_button_enabled  
for atom in model.atoms:  
^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> close #

Expected a models specifier or a keyword  

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech
> Tools/Discovery/Structures/07-2025/boltz_results_CD83/predictions/CD83/CD83_model_0.cif"

CD83_model_0.cif title:  
. [more info...]  
  
Chain information for CD83_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Color CD83_model_0.cif by residue attribute pLDDT_score  
Computing secondary structure  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 101, in _structure_chosen  
self._guess_pae_file_or_database_id()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 118, in
_guess_pae_file_or_database_id  
pae_path = _matching_pae_file(structure_path)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 311, in _matching_pae_file  
dfiles = listdir(dir)  
^^^^^^^^^^^^  
PermissionError: [Errno 1] Operation not permitted:
'/Users/johnteare/Library/CloudStorage/OneDrive-
Personal/Documents/johntearebio/Biotech
Tools/Discovery/Structures/07-2025/boltz_results_CD83/predictions/CD83'  
  
PermissionError: [Errno 1] Operation not permitted:
'/Users/johnteare/Library/CloudStorage/OneDrive-
Personal/Documents/johntearebio/Biotech
Tools/Discovery/Structures/07-2025/boltz_results_CD83/predictions/CD83'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 311, in _matching_pae_file  
dfiles = listdir(dir)  
^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> hbonds reveal true

92 hydrogen bonds found  

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech Tools/Discovery/Cancer/Immune
> Engagers/CT83/swissmodel/Human_CT83/models/01/model.pdb"

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Human CT83 [more info...]  
  
Chain information for model.pdb #2  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 1 time(s)]  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 CD83_model_0.cif, chain A (#1) with model.pdb, chain A (#2),
sequence alignment score = 516.5  
RMSD between 30 pruned atom pairs is 0.652 angstroms; (across all 112 pairs:
24.111)  
  

> hide #2 models

> show #!1 atoms

> show #2 models

> hide #!1 models

> show #2 atoms

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech
> Tools/Discovery/Structures/07-2025/boltz_results_LamininG1PEGO/predictions/LamininG1PEGO/LamininG1PEGO_model_0.cif"

LamininG1PEGO_model_0.cif title:  
. [more info...]  
  
Chain information for LamininG1PEGO_model_0.cif #3  
---  
Chain | Description  
A | .  
B | .  
  
Color LamininG1PEGO_model_0.cif by residue attribute pLDDT_score  
Computing secondary structure  

> close

> open "/Users/johnteare/Library/CloudStorage/OneDrive-
> Personal/Documents/johntearebio/Biotech
> Tools/Discovery/Structures/07-2025/boltz_results_LamininG1PEGO/predictions/LamininG1PEGO/LamininG1PEGO_model_0.cif"

LamininG1PEGO_model_0.cif title:  
. [more info...]  
  
Chain information for LamininG1PEGO_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Color LamininG1PEGO_model_0.cif by residue attribute pLDDT_score  
Computing secondary structure  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 101, in _structure_chosen  
self._guess_pae_file_or_database_id()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 118, in
_guess_pae_file_or_database_id  
pae_path = _matching_pae_file(structure_path)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 311, in _matching_pae_file  
dfiles = listdir(dir)  
^^^^^^^^^^^^  
PermissionError: [Errno 1] Operation not permitted:
'/Users/johnteare/Library/CloudStorage/OneDrive-
Personal/Documents/johntearebio/Biotech
Tools/Discovery/Structures/07-2025/boltz_results_LamininG1PEGO/predictions/LamininG1PEGO'  
  
PermissionError: [Errno 1] Operation not permitted:
'/Users/johnteare/Library/CloudStorage/OneDrive-
Personal/Documents/johntearebio/Biotech
Tools/Discovery/Structures/07-2025/boltz_results_LamininG1PEGO/predictions/LamininG1PEGO'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 311, in _matching_pae_file  
dfiles = listdir(dir)  
^^^^^^^^^^^^  
  
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 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,10
      Model Number: MRX53LL/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: 10 hours, 7 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: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    biopython: 1.85
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AllMetal3D: 0.8
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-clix: 0.2.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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
    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: 1.2.1
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBImages: 1.2
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-PICKLUSTER: 2.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RIBFIND: 0.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 1.18.1
    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
    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: 1.41
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    fsspec: 2025.3.2
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    gradio_client: 0.11.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    huggingface-hub: 0.31.2
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    MolecularDynamicsViewer: 1.6
    msgpack: 1.0.8
    narwhals: 1.33.0
    ndindex: 1.9.2
    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: 2.2.4
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    plotly: 6.0.1
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pyKVFinder: 0.7.3
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    PyYAML: 6.0.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    ribfind: 2.0.2
    scipy: 1.14.0
    Send2Trash: 1.8.3
    SEQCROW: 1.8.20
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    toml: 0.10.2
    tornado: 6.4.2
    tqdm: 4.67.1
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    websockets: 11.0.3
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (2)

comment:1 by pett, 4 months ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → PAE file: Operation not permitted

comment:2 by Tom Goddard, 4 months ago

Resolution: → duplicate
Status: assigned → closed

Same reporter, same error as #18125.

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