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Opened 6 hours ago
Last modified 2 hours ago
#20112 assigned defect
SEQCROW session restore: testing numpy array as boolean
| Reported by: | Owned by: | Tony Schaefer | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
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
Change History (1)
comment:1 by , 2 hours ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → SEQCROW session restore: testing numpy array as boolean |
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Reported by Matthew