Opened 2 months ago

Closed 2 months ago

#18701 closed defect (fixed)

pae is not a file in the archive

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-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/pae_4-1BB_costimulatory_receptor_449_model_0.npz

Failed opening file
/Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/pae_4-1BB_costimulatory_receptor_449_model_0.npz:  
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command structure option, for example  
  
open
/Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/pae_4-1BB_costimulatory_receptor_449_model_0.npz
structure #1  
  
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as  
  
open mole_channels.json format mole  

> open
> /Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/4-1BB_costimulatory_receptor_449_model_0.cif

4-1BB_costimulatory_receptor_449_model_0.cif title:  
. [more info...]  
  
Chain information for 4-1BB_costimulatory_receptor_449_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Color 4-1BB_costimulatory_receptor_449_model_0.cif by residue attribute
pLDDT_score  
Computing secondary structure  

> open
> /Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/confidence_4-1BB_costimulatory_receptor_449_model_0.json

JSON file
"/Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/confidence_4-1BB_costimulatory_receptor_449_model_0.json"
is not AlphaFold predicted aligned error data, expected a top level list  

> open
> /Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/confidence_4-1BB_costimulatory_receptor_449_model_0.json

JSON file
"/Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/confidence_4-1BB_costimulatory_receptor_449_model_0.json"
is not AlphaFold predicted aligned error data, expected a top level list  

> open
> /Users/adrian/Desktop/fold_2025_07_04_12_45/fold_2025_07_04_12_45_model_0.cif
> format mmcif

No such file/path:
/Users/adrian/Desktop/fold_2025_07_04_12_45/fold_2025_07_04_12_45_model_0.cif  

> open /Users/adrian/Desktop/1dif/1dif_model_0.cif format mmcif

Summary of feedback from opening /Users/adrian/Desktop/1dif/1dif_model_0.cif  
---  
warning | Unable to fetch template for 'LIG1': will connect using distance criteria  
  
1dif_model_0.cif title:  
. [more info...]  
  
Chain information for 1dif_model_0.cif #2  
---  
Chain | Description  
1dif | .  
  
Non-standard residues in 1dif_model_0.cif #2  
---  
LIG1 — (LIG1)  
  

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

Computing secondary structure  

> open
> /Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/4-1BB_costimulatory_receptor_449_model_0.cif
> format mmcif

4-1BB_costimulatory_receptor_449_model_0.cif title:  
. [more info...]  
  
Chain information for 4-1BB_costimulatory_receptor_449_model_0.cif #3  
---  
Chain | Description  
A | .  
  
Color 4-1BB_costimulatory_receptor_449_model_0.cif by residue attribute
pLDDT_score  
Computing secondary structure  

> open /Users/adrian/Desktop/1dif/pae_1dif_model_0.npz format pae

Opened AlphaFold PAE with values for 258 residues and atoms  

> open /Users/adrian/Desktop/1dif/pae_1dif_model_0.npz format pae

Opened AlphaFold PAE with values for 258 residues and atoms  

> open /Users/adrian/Desktop/1dif/pae_1dif_model_0.npz format pae

Opened AlphaFold PAE with values for 258 residues and atoms  

> open /Users/adrian/Desktop/tba/tba/tba_model_0.cif format mmcif

tba_model_0.cif title:  
. [more info...]  
  
Chain information for tba_model_0.cif #4  
---  
Chain | Description  
TBA | .  
  
Color tba_model_0.cif by residue attribute pLDDT_score  
Computing secondary structure  

> open /Users/adrian/Desktop/1dif/1dif_model_0.cif format mmcif

Summary of feedback from opening /Users/adrian/Desktop/1dif/1dif_model_0.cif  
---  
warning | Unable to fetch template for 'LIG1': will connect using distance criteria  
  
1dif_model_0.cif title:  
. [more info...]  
  
Chain information for 1dif_model_0.cif #5  
---  
Chain | Description  
1dif | .  
  
Non-standard residues in 1dif_model_0.cif #5  
---  
LIG1 — (LIG1)  
  

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

Computing secondary structure  

> color #2/1dif:28 lime

> color #2/1dif:129 magenta

> color #2/1dif:33 lime

> color #2/1dif:123 magenta

> color #2/1dif:67 lime

> color #2/1dif:111 magenta

> color #2/1dif:117 lime

> color #2/1dif:106 magenta

> color #2/1dif:148 lime

> color #2/1dif:106 magenta

> lighting simple

> color #2/1dif:179 lime

> color #2/1dif:20 magenta

> open /Users/adrian/Desktop/1dif/plddt_1dif_model_0.npz

Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command structure option, for example  
  
open /Users/adrian/Desktop/1dif/plddt_1dif_model_0.npz structure #1  
  
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as  
  
open mole_channels.json format mole  

> open /Users/adrian/Desktop/1dif/1dif_model_0.cif

Summary of feedback from opening /Users/adrian/Desktop/1dif/1dif_model_0.cif  
---  
warning | Unable to fetch template for 'LIG1': will connect using distance criteria  
  
1dif_model_0.cif title:  
. [more info...]  
  
Chain information for 1dif_model_0.cif #6  
---  
Chain | Description  
1dif | .  
  
Non-standard residues in 1dif_model_0.cif #6  
---  
LIG1 — (LIG1)  
  

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

Computing secondary structure  

> open /Users/adrian/Desktop/1dif/pae_1dif_model_0.npz

Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command structure option, for example  
  
open /Users/adrian/Desktop/1dif/pae_1dif_model_0.npz structure #1  
  
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as  
  
open mole_channels.json format mole  

> open /Users/adrian/Desktop/1dif/pde_1dif_model_0.npz

Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command structure option, for example  
  
open /Users/adrian/Desktop/1dif/pde_1dif_model_0.npz structure #1  
  
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as  
  
open mole_channels.json format mole  

> open /Users/adrian/Desktop/1dif/1dif_model_0.cif

Summary of feedback from opening /Users/adrian/Desktop/1dif/1dif_model_0.cif  
---  
warning | Unable to fetch template for 'LIG1': will connect using distance criteria  
  
1dif_model_0.cif title:  
. [more info...]  
  
Chain information for 1dif_model_0.cif #7  
---  
Chain | Description  
1dif | .  
  
Non-standard residues in 1dif_model_0.cif #7  
---  
LIG1 — (LIG1)  
  

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

> open /Users/adrian/Desktop/1dif/confidence_1dif_model_0.json

Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command structure option, for example  
  
open /Users/adrian/Desktop/1dif/confidence_1dif_model_0.json structure #1  
  
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as  
  
open mole_channels.json format mole  
Computing secondary structure  

> open /Users/adrian/Desktop/1dif/confidence_1dif_model_0.json structure #1

JSON file "/Users/adrian/Desktop/1dif/confidence_1dif_model_0.json" is not
AlphaFold predicted aligned error data, expected a top level list  

> open /Users/adrian/Desktop/1dif/pae_1dif_model_0.npz

Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command structure option, for example  
  
open /Users/adrian/Desktop/1dif/pae_1dif_model_0.npz structure #1  
  
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as  
  
open mole_channels.json format mole  

> close

> open /Users/adrian/Desktop/1dif/1dif_model_0.cif format mmcif

Summary of feedback from opening /Users/adrian/Desktop/1dif/1dif_model_0.cif  
---  
warning | Unable to fetch template for 'LIG1': will connect using distance criteria  
  
1dif_model_0.cif title:  
. [more info...]  
  
Chain information for 1dif_model_0.cif #1  
---  
Chain | Description  
1dif | .  
  
Non-standard residues in 1dif_model_0.cif #1  
---  
LIG1 — (LIG1)  
  

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

Computing secondary structure  

> select add #1

1574 atoms, 1604 bonds, 199 residues, 1 model selected  

> close

> open /Users/adrian/Desktop/1dif/confidence_1dif_model_0.json

Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command structure option, for example  
  
open /Users/adrian/Desktop/1dif/confidence_1dif_model_0.json structure #1  
  
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as  
  
open mole_channels.json format mole  

> open /Users/adrian/Desktop/1dif/confidence_1dif_model_0.json structure #1

Invalid "structure" argument: must specify 1 atomic structure, got 0 for "#1"  

> ui windowfill toggle

[Repeated 1 time(s)]

> open /Users/adrian/Desktop/1dif/confidence_1dif_model_0.json structure #1

Invalid "structure" argument: must specify 1 atomic structure, got 0 for "#1"  

> open /Users/adrian/Desktop/1dif/confidence_1dif_model_0.cif

No such file/path: /Users/adrian/Desktop/1dif/confidence_1dif_model_0.cif  

> open /Users/adrian/Desktop/1dif/1dif_model_0.cif

Summary of feedback from opening /Users/adrian/Desktop/1dif/1dif_model_0.cif  
---  
warning | Unable to fetch template for 'LIG1': will connect using distance criteria  
  
1dif_model_0.cif title:  
. [more info...]  
  
Chain information for 1dif_model_0.cif #1  
---  
Chain | Description  
1dif | .  
  
Non-standard residues in 1dif_model_0.cif #1  
---  
LIG1 — (LIG1)  
  

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

Computing secondary structure  

> open
> /Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/confidence_4-1BB_costimulatory_receptor_449_model_0.json

Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command structure option, for example  
  
open
/Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/confidence_4-1BB_costimulatory_receptor_449_model_0.json
structure #1  
  
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as  
  
open mole_channels.json format mole  

> open mole_channels.json format mole

No such file/path: mole_channels.json  

> open
> /Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/pae_4-1BB_costimulatory_receptor_449_model_0.npz

Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command structure option, for example  
  
open
/Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/pae_4-1BB_costimulatory_receptor_449_model_0.npz
structure #1  
  
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as  
  
open mole_channels.json format mole  

> open
> /Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/pae_4-1BB_costimulatory_receptor_449_model_0.npz

Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command structure option, for example  
  
open
/Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/pae_4-1BB_costimulatory_receptor_449_model_0.npz
structure #1  
  
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as  
  
open mole_channels.json format mole  

> open /Users/adrian/Desktop/1dif/pae_1dif_model_0.npz

Opened AlphaFold PAE with values for 258 residues and atoms  

> color /1dif:5 lime

> color /1dif:92 magenta

> open
> /Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/4-1BB_costimulatory_receptor_449_model_0.cif

4-1BB_costimulatory_receptor_449_model_0.cif title:  
. [more info...]  
  
Chain information for 4-1BB_costimulatory_receptor_449_model_0.cif #2  
---  
Chain | Description  
A | .  
  
Color 4-1BB_costimulatory_receptor_449_model_0.cif by residue attribute
pLDDT_score  
Computing secondary structure  

> open
> /Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/pae_4-1BB_costimulatory_receptor_449_model_0.npz

Opened AlphaFold PAE with values for 95 residues and atoms  

> color #2/A:41-47 lime

> color #2/A:51 lime

> color #2/A:40 magenta

> color #2/A:31-46 lime

> color #2/A:34-41 lime

> open
> /Users/adrian/Desktop/4-1BB_costimulatory_receptor_449/pde_4-1BB_costimulatory_receptor_449_model_0.npz

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event  
if self.handle_drag_and_drop(event):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop  
mw.dropEvent(event)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 768, in dropEvent  
_open_dropped_file(self.session, p)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2154, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Applications/ChimeraX-1.10.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/__init__.py", line 129, in open  
pae = alphafold_pae(session, file = path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.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.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.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.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.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.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 - 89.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: 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: Mac14,7
      Model Number: MNEH3E/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.1 (24D70)
      Kernel Version: Darwin 24.3.0
      Time since boot: 1 day, 14 hours, 14 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 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: 3.5.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    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: 1.10
    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: 2.2.2
    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: 1.45.2
    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: 7.9.1
    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: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    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: 2.11.0
    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: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    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: 4.14.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (2)

comment:1 by Eric Pettersen, 2 months ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → pae is not a file in the archive

comment:2 by Tom Goddard, 2 months ago

Resolution: → fixed
Status: assigned → closed

The user tried to open a predicted distance error .npz file from Boltz as PAE data and this failed because it does not contain the "pae" key. The daily build gives a clearer error message than 1.10 where this user got a traceback.

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