Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#7946 closed defect (nonchimerax)

partially initialized module 'jax._src.device_array' has no attribute 'DeviceArray

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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5rc202210312311 (2022-10-31 23:11:39 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5rc202210312311 (2022-10-31)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/jinueki/Downloads/relaxed_model_2_multimer_v2_pred_0.pdb format
> pdb

Chain information for relaxed_model_2_multimer_v2_pred_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> /Users/jinueki/Downloads/result_model_2_multimer_v2_pred_0.pkl

Traceback (most recent call last):  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 153, in _choose_pae_file  
self._open_pae()  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 166, in _open_pae  
self._open_pae_from_file(s)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 190, in _open_pae_from_file  
run(self.session, cmd)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 1090, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 778, in __init__  
self._pae_matrix = read_pae_matrix(pae_path)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 905, in read_pae_matrix  
return read_pickle_pae_matrix(path)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 962, in read_pickle_pae_matrix  
p = pickle.load(f)  
ModuleNotFoundError: No module named 'jax'  
  
ModuleNotFoundError: No module named 'jax'  
  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 962, in read_pickle_pae_matrix  
p = pickle.load(f)  
  
See log for complete Python traceback.  
  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> pip install jax

Collecting jax  
Using cached jax-0.3.23-py3-none-any.whl  
Requirement already satisfied: typing-extensions in
/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from jax) (4.4.0)  
Collecting absl-py  
Using cached absl_py-1.3.0-py3-none-any.whl (124 kB)  
Requirement already satisfied: scipy>=1.5 in
/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from jax) (1.9.0)  
Collecting opt-einsum  
Using cached opt_einsum-3.3.0-py3-none-any.whl (65 kB)  
Collecting etils[epath]  
Using cached etils-0.9.0-py3-none-any.whl (140 kB)  
Requirement already satisfied: numpy>=1.20 in
/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from jax) (1.23.1)  
Requirement already satisfied: zipp in
/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from etils[epath]->jax) (3.10.0)  
Collecting importlib_resources  
Using cached importlib_resources-5.10.0-py3-none-any.whl (34 kB)  
Installing collected packages: opt-einsum, importlib_resources, etils, absl-
py, jax  
Successfully installed absl-py-1.3.0 etils-0.9.0 importlib_resources-5.10.0
jax-0.3.23 opt-einsum-3.3.0  
  
  
[notice] A new release of pip available: 22.2.2 -> 22.3  
[notice] To update, run:
/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/MacOS/ChimeraX
-m pip install --upgrade pip  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> /Users/jinueki/Downloads/result_model_2_multimer_v2_pred_0.pkl

Traceback (most recent call last):  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/_src/lib/__init__.py", line 38, in <module>  
import jaxlib as jaxlib  
ModuleNotFoundError: No module named 'jaxlib'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 166, in _open_pae  
self._open_pae_from_file(s)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 190, in _open_pae_from_file  
run(self.session, cmd)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 1090, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 778, in __init__  
self._pae_matrix = read_pae_matrix(pae_path)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 905, in read_pae_matrix  
return read_pickle_pae_matrix(path)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 962, in read_pickle_pae_matrix  
p = pickle.load(f)  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/__init__.py", line 35, in <module>  
from jax import config as _config_module  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/config.py", line 17, in <module>  
from jax._src.config import config  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/_src/config.py", line 29, in <module>  
from jax._src import lib  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/_src/lib/__init__.py", line 40, in <module>  
raise ModuleNotFoundError(  
ModuleNotFoundError: jax requires jaxlib to be installed. See
https://github.com/google/jax#installation for installation instructions.  
  
ModuleNotFoundError: jax requires jaxlib to be installed. See
https://github.com/google/jax#installation for installation instructions.  
  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/_src/lib/__init__.py", line 40, in  
raise ModuleNotFoundError(  
  
See log for complete Python traceback.  
  

> pip install jaxlib

Collecting jaxlib  
Downloading jaxlib-0.3.22-cp39-cp39-macosx_10_14_x86_64.whl (69.2 MB)  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 69.2/69.2 MB 11.7 MB/s eta 0:00:00  
Requirement already satisfied: scipy>=1.5 in
/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from jaxlib) (1.9.0)  
Requirement already satisfied: numpy>=1.20 in
/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from jaxlib) (1.23.1)  
Requirement already satisfied: absl-py in /Users/jinueki/Library/Application
Support/ChimeraX/1.5/site-packages (from jaxlib) (1.3.0)  
Installing collected packages: jaxlib  
Successfully installed jaxlib-0.3.22  
  
  
[notice] A new release of pip available: 22.2.2 -> 22.3  
[notice] To update, run:
/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/MacOS/ChimeraX
-m pip install --upgrade pip  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> /Users/jinueki/Downloads/result_model_2_multimer_v2_pred_0.pkl

Traceback (most recent call last):  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 166, in _open_pae  
self._open_pae_from_file(s)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 190, in _open_pae_from_file  
run(self.session, cmd)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 1090, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 778, in __init__  
self._pae_matrix = read_pae_matrix(pae_path)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 905, in read_pae_matrix  
return read_pickle_pae_matrix(path)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 962, in read_pickle_pae_matrix  
p = pickle.load(f)  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/_src/device_array.py", line 25, in <module>  
import jax  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/__init__.py", line 63, in <module>  
from jax._src.api import (  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/_src/api.py", line 41, in <module>  
from jax import stages  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/stages.py", line 24, in <module>  
from jax._src.stages import (  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/_src/stages.py", line 48, in <module>  
from jax.interpreters import xla  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/interpreters/xla.py", line 78, in <module>  
DeviceArray = device_array.DeviceArray  
AttributeError: partially initialized module 'jax._src.device_array' has no
attribute 'DeviceArray' (most likely due to a circular import)  
  
AttributeError: partially initialized module 'jax._src.device_array' has no
attribute 'DeviceArray' (most likely due to a circular import)  
  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/interpreters/xla.py", line 78, in  
DeviceArray = device_array.DeviceArray  
  
See log for complete Python traceback.  
  

Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> python -m pip list | grep jax

Unknown command: python -m pip list | grep jax  

> -m pip list | grep jax

Unknown command: -m pip list | grep jax  

> import jax.numpy as jnp

Unknown command: import jax.numpy as jnp  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> /Users/jinueki/Downloads/result_model_2_multimer_v2_pred_0.pkl

Traceback (most recent call last):  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 166, in _open_pae  
self._open_pae_from_file(s)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 190, in _open_pae_from_file  
run(self.session, cmd)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 1090, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 778, in __init__  
self._pae_matrix = read_pae_matrix(pae_path)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 905, in read_pae_matrix  
return read_pickle_pae_matrix(path)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 962, in read_pickle_pae_matrix  
p = pickle.load(f)  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/_src/device_array.py", line 25, in <module>  
import jax  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/__init__.py", line 63, in <module>  
from jax._src.api import (  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/_src/api.py", line 41, in <module>  
from jax import stages  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/stages.py", line 24, in <module>  
from jax._src.stages import (  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/_src/stages.py", line 48, in <module>  
from jax.interpreters import xla  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/interpreters/xla.py", line 78, in <module>  
DeviceArray = device_array.DeviceArray  
AttributeError: partially initialized module 'jax._src.device_array' has no
attribute 'DeviceArray' (most likely due to a circular import)  
  
AttributeError: partially initialized module 'jax._src.device_array' has no
attribute 'DeviceArray' (most likely due to a circular import)  
  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/interpreters/xla.py", line 78, in  
DeviceArray = device_array.DeviceArray  
  
See log for complete Python traceback.  
  

> select add #1

12229 atoms, 12393 bonds, 750 residues, 1 model selected  

> select subtract #1

Nothing selected  

> alphafold pae #1 file
> /Users/jinueki/Downloads/result_model_2_multimer_v2_pred_0.pkl

Traceback (most recent call last):  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 166, in _open_pae  
self._open_pae_from_file(s)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 190, in _open_pae_from_file  
run(self.session, cmd)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 1090, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 778, in __init__  
self._pae_matrix = read_pae_matrix(pae_path)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 905, in read_pae_matrix  
return read_pickle_pae_matrix(path)  
File
"/private/var/folders/sz/zg34l4h93bs0kw_93scj2b2m0000gn/T/AppTranslocation/12E0653E-A753-4EBF-821C-CB1DD98AA6F1/d/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 962, in read_pickle_pae_matrix  
p = pickle.load(f)  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/_src/device_array.py", line 25, in <module>  
import jax  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/__init__.py", line 63, in <module>  
from jax._src.api import (  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/_src/api.py", line 41, in <module>  
from jax import stages  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/stages.py", line 24, in <module>  
from jax._src.stages import (  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/_src/stages.py", line 48, in <module>  
from jax.interpreters import xla  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/interpreters/xla.py", line 78, in <module>  
DeviceArray = device_array.DeviceArray  
AttributeError: partially initialized module 'jax._src.device_array' has no
attribute 'DeviceArray' (most likely due to a circular import)  
  
AttributeError: partially initialized module 'jax._src.device_array' has no
attribute 'DeviceArray' (most likely due to a circular import)  
  
File "/Users/jinueki/Library/Application Support/ChimeraX/1.5/site-
packages/jax/interpreters/xla.py", line 78, in  
DeviceArray = device_array.DeviceArray  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-18.8.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16066.0.0,0)
      OS Loader Version: 540.120.3~19

Software:

    System Software Overview:

      System Version: macOS 12.5.1 (21G83)
      Kernel Version: Darwin 21.6.0
      Time since boot: 2 days 4:44

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    absl-py: 1.3.0
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5rc202210312311
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    etils: 0.9.0
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    importlib-resources: 5.10.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jax: 0.3.23
    jaxlib: 0.3.22
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.2
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    opt-einsum: 3.3.0
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.1
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.0
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.10.0

Change History (3)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → partially initialized module 'jax._src.device_array' has no attribute 'DeviceArray

After jax was manually installed via pip

comment:2 by Tom Goddard, 3 years ago

Resolution: → nonchimerax
Status: assigned → closed

This looks like an attempt to fix #7945 where an AlphaFold .pkl file apparently has a jax dependency. And jax needs jaxlib. So the user installed both into ChimeraX successfully. But jax appears to have some problem restoring pickled jax data structures. The error suggests a circular import

AttributeError: partially initialized module 'jax._src.device_array' has no attribute 'DeviceArray' (most likely due to a circular import)

Closing this valiant attempt to get around the bad AlphaFold .pkl file, and will see if I can find how the file was produced and report findings in #7945.

comment:3 by Tom Goddard, 3 years ago

Duplicate of #8032. Work-around was added to ChimeraX 1.5.

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