Opened 3 hours ago

#20112 new defect

ChimeraX bug report submission

Reported by: mhvg1994@… Owned by:
Priority: normal Milestone:
Component: Unassigned Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform:
Project:

Description 

The following bug report has been submitted:
Platform:        macOS-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
When i try to load a previous chimerax session from a csx file, i get an error related to some python code.

Log:
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/matthewgraneri/Documents/Postdoc/calculations/others/robert/platinum/isomers/o2o_d/bp86/zora/tddft/o2o_d-
> tddft-bp86-ma-zora-tzvpp.out

> style ball

Changed 4 atom styles  

> size stickRadius 0.09

Changed 1 bond radii  

> size ballScale 0.25

Changed 1 ball scales  

> color byelement

> lighting depthCue false

> lighting intensity 0.5

> style ball

Changed 4 atom styles  

> size stickRadius 0.09

Changed 1 bond radii  

> size ballScale 0.25

Changed 1 ball scales  

> color byelement

> lighting depthCue false

> lighting intensity 0.5

Opened o2o_d-tddft-bp86-ma-zora-tzvpp.out as an ORCA output file  

> style stick

Changed 4 atom styles  

> ui mousemode right bond

> ui mousemode right translate

> ui tool show "Orbital Viewer"

2.332882944  
(27800663, 1888589748)  
Opened MO alpha 41 as #1.2, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin up, -0.81179.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.2

2.332882944  
(27774504, 1888563069)  
Opened MO beta 41 as #1.3, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin down, -0.80119.png" width 4000 height 2357
> supersample 4 transparentBackground true

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin up, -0.78177.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.3

2.332882944  
(27772912, 1888561085)  
Opened MO alpha 43 as #1.4, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin up, -0.77198.png" width 4000 height 2357
> supersample 4 transparentBackground true

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/bp86 zora.cxs"

> show #1.4

> volume #1.4 level -0.100 level 0.100 color #0000ff80 color #00ff0080

> hide #1.4

2.332882944  
(27774336, 1888562149)  
Opened MO beta 42 as #1.5, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin down, -0.75514.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.5

2.332882944  
(27774016, 1888561413)  
Opened MO beta 43 as #1.6, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin down, -0.73894.png" width 4000 height 2357
> supersample 4 transparentBackground true

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin down, -0.73894.png" width 4000 height 2357
> supersample 4 transparentBackground true

> show #1.5

> volume #1.5 level -0.100 level 0.100 color #0000ff80 color #00ff0080

> hide #1.6

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin down, -0.75514.png" width 4000 height 2357
> supersample 4 transparentBackground true

> show #1.4

> volume #1.4 level -0.100 level 0.100 color #0000ff80 color #00ff0080

> hide #1.5

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin up, -0.77198.png" width 4000 height 2357
> supersample 4 transparentBackground true

> show #1.6

> volume #1.6 level -0.100 level 0.100 color #0000ff80 color #00ff0080

> hide #1.4

> hide #1.6

2.332882944  
(27773232, 1749702449)  
Opened MO alpha 44 as #1.7, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin up, -0.69833.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.7

2.332882944  
(27773232, 1638609218)  
Opened MO beta 44 as #1.8, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin down, -0.69811.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.8

2.332882944  
(27773584, 1888560549)  
Opened MO alpha 45 as #1.9, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin up, -0.68710.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.9

2.332882944  
(27773584, 1888560549)  
Opened MO beta 45 as #1.10, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin down, -0.67708.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.10

2.332882944  
(27774656, 1888561637)  
Opened MO beta 46 as #1.11, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin down, -0.66961.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.11

2.332882944  
(27772944, 1888559930)  
Opened MO alpha 46 as #1.12, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin up, -0.66094.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.12

2.332882944  
(27773744, 1666384822)  
Opened MO alpha 47 as #1.13, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin up, -0.60135.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.13

2.332882944  
(27772912, 1610836402)  
Opened MO beta 47 as #1.14, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin down, -0.58644.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.14

2.332882944  
(27773520, 1888560122)  
Opened MO alpha 48 as #1.15, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin up, -0.58324.png" width 4000 height 2357
> supersample 4 transparentBackground true

> show #1.12

> volume #1.12 level -0.100 level 0.100 color #0000ff80 color #00ff0080

> hide #1.15

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin up, -0.66094.png" width 4000 height 2357
> supersample 4 transparentBackground true

> show #1.13

> volume #1.13 level -0.100 level 0.100 color #0000ff80 color #00ff0080

> hide #1.12

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin up, -0.60135.png" width 4000 height 2357
> supersample 4 transparentBackground true

> show #1.11

> volume #1.11 level -0.100 level 0.100 color #0000ff80 color #00ff0080

> hide #1.13

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin down, -0.66961.png" width 4000 height 2357
> supersample 4 transparentBackground true

> show #1.15

> volume #1.15 level -0.100 level 0.100 color #0000ff80 color #00ff0080

> hide #1.11

> hide #1.15

2.332882944  
(27774320, 1638610263)  
Opened MO alpha 49 as #1.16, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin up, -0.57913.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.16

2.332882944  
(27773360, 1888560186)  
Opened MO beta 48 as #1.17, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin down, -0.57803.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.17

2.332882944  
(27773808, 1888560650)  
Opened MO beta 49 as #1.18, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin down, -0.57535.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.18

2.332882944  
(27773232, 1638609319)  
Opened MO alpha 50 as #1.19, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin up, -0.54759.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.19

2.332882944  
(27773488, 1888560298)  
Opened MO alpha 51 as #1.20, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin up, -0.53481.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.20

2.332882944  
(27775200, 1888561954)  
Opened MO beta 50 as #1.21, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/spin down, -0.53094.png" width 4000 height 2357
> supersample 4 transparentBackground true

> hide #1.21

2.332882944  
(27772976, 1749697782)  
Opened MO beta 51 as #1.22, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/unocc, spin down, -0.51207.png" width 4000 height
> 2357 supersample 4 transparentBackground true

> hide #1.22

2.332882944  
(27773200, 1888559970)  
Opened MO alpha 52 as #1.23, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/unocc, spin up, -0.49947.png" width 4000 height
> 2357 supersample 4 transparentBackground true

> hide #1.23

2.332882944  
(27773296, 1610836526)  
Opened MO beta 52 as #1.24, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/unocc, spin down, -0.48241.png" width 4000 height
> 2357 supersample 4 transparentBackground true

> show #1.24

> volume #1.24 level -0.100 level 0.100 color #0000ff80 color #00ff0080

> hide #1.24

2.332882944  
(27773776, 1499747350)  
Opened MO alpha 53 as #1.25, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/unocc, spin up, -0.45016.png" width 4000 height
> 2357 supersample 4 transparentBackground true

> hide #1.25

2.332882944  
(27774336, 1555292210)  
Opened MO beta 53 as #1.26, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/unocc, spin down, -0.44446.png" width 4000 height
> 2357 supersample 4 transparentBackground true

> hide #1.26

2.332882944  
(27773264, 1638609271)  
Opened MO alpha 54 as #1.27, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/unocc, spin up, -0.26366.png" width 4000 height
> 2357 supersample 4 transparentBackground true

> hide #1.27

2.332882944  
(27773808, 1888560498)  
Opened MO alpha 55 as #1.28, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/unocc, spin up, -0.25464.png" width 4000 height
> 2357 supersample 4 transparentBackground true

> hide #1.28

2.332882944  
(27773264, 1833018750)  
Opened MO beta 55 as #1.29, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/unocc, spin down, -0.24588.png" width 4000 height
> 2357 supersample 4 transparentBackground true

> hide #1.29

2.332882944  
(27773232, 1749697687)  
Opened MO beta 54 as #1.30, grid size 192,147,123, pixel 0.0502,0.05,0.0501,
shown at level -0.1,0.1, step 1, values float64  

> transparency 20 surfaces

> save "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/unocc, spin down, -0.25450.png" width 4000 height
> 2357 supersample 4 transparentBackground true

> close

> open
> /Users/matthewgraneri/Documents/Postdoc/calculations/others/robert/platinum/isomers/o2o_q/bp86/zora/tddft/o2o_q-
> tddft-bp86-ma-zora-tzvpp.out

> style ball

Changed 4 atom styles  

> size stickRadius 0.09

Changed 1 bond radii  

> size ballScale 0.25

Changed 1 ball scales  

> color byelement

> lighting depthCue false

> lighting intensity 0.5

> style ball

Changed 4 atom styles  

> size stickRadius 0.09

Changed 1 bond radii  

> size ballScale 0.25

Changed 1 ball scales  

> color byelement

> lighting depthCue false

> lighting intensity 0.5

Opened o2o_q-tddft-bp86-ma-zora-tzvpp.out as an ORCA output file  

> style stick

Changed 4 atom styles  

> ui mousemode right bond

> close

> open "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/bp86 zora.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/Chimera/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/matthewgraneri/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/SEQCROW/__init__.py", line 293,
in restore_snapshot  
return Orbitals(data)  
^^^^^^^^^^^^^^  
File "/Users/matthewgraneri/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/orbitals.py", line
71, in __init__  
self._load_orca_out_data(filereader)  
File "/Users/matthewgraneri/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/orbitals.py", line
1204, in _load_orca_out_data  
if "beta_nrgs" not in filereader or not filereader["beta_nrgs"]:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  

> view name session-start

opened ChimeraX session  

> open "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/bp86 zora.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/Chimera/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/matthewgraneri/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/SEQCROW/__init__.py", line 293,
in restore_snapshot  
return Orbitals(data)  
^^^^^^^^^^^^^^  
File "/Users/matthewgraneri/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/orbitals.py", line
71, in __init__  
self._load_orca_out_data(filereader)  
File "/Users/matthewgraneri/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/orbitals.py", line
1204, in _load_orca_out_data  
if "beta_nrgs" not in filereader or not filereader["beta_nrgs"]:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  

> view name session-start

opened ChimeraX session  

> open "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/bp86 zora.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/Chimera/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/matthewgraneri/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/SEQCROW/__init__.py", line 293,
in restore_snapshot  
return Orbitals(data)  
^^^^^^^^^^^^^^  
File "/Users/matthewgraneri/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/orbitals.py", line
71, in __init__  
self._load_orca_out_data(filereader)  
File "/Users/matthewgraneri/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/orbitals.py", line
1204, in _load_orca_out_data  
if "beta_nrgs" not in filereader or not filereader["beta_nrgs"]:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  

> view name session-start

opened ChimeraX session  

> open "/Users/matthewgraneri/Documents/Postdoc/Platinum/Orbital
> Pictures/o2o_d/BP86(ZORA)/bp86 zora.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/Chimera/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/matthewgraneri/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/SEQCROW/__init__.py", line 293,
in restore_snapshot  
return Orbitals(data)  
^^^^^^^^^^^^^^  
File "/Users/matthewgraneri/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/orbitals.py", line
71, in __init__  
self._load_orca_out_data(filereader)  
File "/Users/matthewgraneri/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/orbitals.py", line
1204, in _load_orca_out_data  
if "beta_nrgs" not in filereader or not filereader["beta_nrgs"]:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  

> view name session-start

opened ChimeraX session  

Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable  

[Repeated 2 time(s)]




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

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

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: Z14X000EVX/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 Performance and 2 Efficiency)
      Memory: 64 GB
      System Firmware Version: 13822.81.10
      OS Loader Version: 13822.81.10

Software:

    System Software Overview:

      System Version: macOS 26.3.1 (25D2128)
      Kernel Version: Darwin 25.3.0
      Time since boot: 4 hours, 13 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        HP E243:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          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-OpenCommands: 1.2
    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
    Send2Trash: 1.8.3
    SEQCROW: 1.9.7
    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

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