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Opened 3 hours ago
#20147 new defect
ChimeraX bug report submission
| Reported by: | 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-13.7.1-x86_64-i386-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
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)
> toolshed reload all
> toolshed install ArtiaX
ChimeraX-ArtiaX (0.6.0) is already installed
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/emd_3947_10Apx_LP60rescale7936box30.mrc
Opened emd_3947_10Apx_LP60rescale7936box30.mrc as #1, grid size 30,30,30,
pixel 7.96, shown at level 0.0295, step 1, values float32
> volume #1 level 0.02622
> volume #1 level 0.02553
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/emd_3947_10Apx_LP60rescale11904box16.mrc
Opened emd_3947_10Apx_LP60rescale11904box16.mrc as #1, grid size 16,16,16,
pixel 11.9, shown at level 0.0327, step 1, values float32
> volume #1 level 0.02656
> volume #1 level 0.02349
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it037_class001.mrc
MRC file is truncated. Failed reading 1 values, type int32
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it037_class001.mrc
Opened run_it037_class001.mrc as #1, grid size 16,16,16, pixel 11.9, shown at
level 1.84, step 1, values float32
> volume #1 level 1.07
> volume #1 level 0.8286
> volume #1 level 0.2798
> volume #1 level 0.6859
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it037_class001job004rescale1984box120.mrc
MRC file is truncated. Failed reading 1 values, type int32
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it037_class001job004rescale1984box120.mrc
Opened run_it037_class001job004rescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 1.45, step 1, values float32
> volume #1 level 0.7824
> volume #1 level 0.2415
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it025_class001job004rescale1984box120.mrc
MRC file is truncated. Failed reading 1 values, type int32
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it025_class001job004rescale1984box120.mrc
Opened run_it025_class001job004rescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 1.57, step 1, values float32
> volume #1 level 1.385
> volume #1 level 1.053
> volume #1 level 0.8067
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it010_class001job004rescale1984box120.mrc
Opened run_it010_class001job004rescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 1.65, step 1, values float32
> volume #1 level 0.9266
> volume #1 level 0.49
> volume #1 level 0.1328
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it020_class001job006rescale1984box120.mrc
Opened run_it020_class001job006rescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 1.48, step 1, values float32
> volume #1 level 0.9774
> volume #1 level 1.007
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it020_class001job006rescale1984box120.mrc
Opened run_it020_class001job006rescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 1.48, step 1, values float32
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it020_class002job006rescale1984box120.mrc
Opened run_it020_class002job006rescale1984box120.mrc as #2, grid size
120,120,120, pixel 1.98, shown at level 1.45, step 1, values float32
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it020_class003job006rescale1984box120.mrc
Opened run_it020_class003job006rescale1984box120.mrc as #3, grid size
120,120,120, pixel 1.98, shown at level 1.48, step 1, values float32
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it020_class004job006rescale1984box120.mrc
Opened run_it020_class004job006rescale1984box120.mrc as #4, grid size
120,120,120, pixel 1.98, shown at level 1.16, step 1, values float32
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it020_class008job006rescale1984box120.mrc
Opened run_it020_class008job006rescale1984box120.mrc as #5, grid size
120,120,120, pixel 1.98, shown at level 1.37, step 1, values float32
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it020_class010job006rescale1984box120.mrc
Opened run_it020_class010job006rescale1984box120.mrc as #6, grid size
120,120,120, pixel 1.98, shown at level 1.41, step 1, values float32
> volume #1 level 1.316
> volume #2 level 1.004
> volume #2 level 0.7377
> volume #3 level 0.6928
> volume #4 level 0.7323
> volume #4 level 0.3477
> volume #5 level 0.8563
> volume #5 level 0.6094
> volume #5 level 0.2652
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it020_class010job006rescale1984box120.mrc
Opened run_it020_class010job006rescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 1.41, step 1, values float32
> volume #1 level 0.7008
> volume #1 level 0.5539
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it020_class005job006rescale1984box120.mrc
Opened run_it020_class005job006rescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 2.68, step 1, values float32
> volume #1 level 2.011
> volume #1 level 2.159
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it020_class006job006rescale1984box120.mrc
Opened run_it020_class006job006rescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 5.75, step 1, values float32
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it020_class007job006rescale1984box120.mrc
Opened run_it020_class007job006rescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 3.31, step 1, values float32
> volume #1 level 2.562
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it020_class009job006rescale1984box120.mrc
Opened run_it020_class009job006rescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 2.69, step 1, values float32
> volume #1 level 2.142
> volume #1 level 2.015
> volume #1 level 2.1
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it035_class001job010rescale1984box120.mrc
Opened run_it035_class001job010rescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 1.33, step 1, values float32
> volume #1 level 0.8092
> volume #1 level 0.7991
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it012_class001job010rescale1984box120.mrc
Opened run_it012_class001job010rescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 1.49, step 1, values float32
> volume #1 level 1.058
> volume #1 level 0.6177
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it010_class001job010rescale1984box120.mrc
Opened run_it010_class001job010rescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 1.51, step 1, values float32
> volume #1 level 0.9483
> volume #1 level 0.688
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_class001.mrc
Opened run_class001.mrc as #1, grid size 16,16,16, pixel 11.9, shown at level
1.71, step 1, values float32
> volume #1 level 1.093
> volume #1 level 0.7028
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_class001job011refinerescale1984box120.mrc
Opened run_class001job011refinerescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 1.54, step 1, values float32
> volume #1 level 1.237
> volume #1 level 1.087
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx7048particlesData.Boxes/emd3947_10Apx_LP60_rescale1984box120.mrc
Opened emd3947_10Apx_LP60_rescale1984box120.mrc as #2, grid size 120,120,120,
pixel 1.98, shown at level 0.0295, step 1, values float32
> volume #1 level 1.034
> volume #1 level 1.132
> volume #2 level 0.02265
> volume #2 level 0.02195
> volume #2 level 0.02578
> volume #1 level 1.447
> volume #1 level 1.087
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx7048particlesData.Boxes/run_it028_class006job010rescale1984box120.mrc
Opened run_it028_class006job010rescale1984box120.mrc as #3, grid size
120,120,120, pixel 1.98, shown at level 1.38, step 1, values float32
> volume #3 level 1.05
> volume #3 level 0.6545
> volume #3 level 0.7835
> volume #3 level 0.8437
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx7048particlesData.Boxes/run_it028_class010job010rescale1984box120.mrc
Opened run_it028_class010job010rescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 1.49, step 1, values float32
> volume #1 level 1.029
> volume #1 level 0.5542
> volume #1 level 1.468
> volume #1 level 0.8354
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx7048particlesData.Boxes/run_it028_class010job010rescale1984box120.mrc
> format mrc
Opened run_it028_class010job010rescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 1.49, step 1, values float32
> volume #1 level 1.152
> volume #1 level 0.6684
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx7048particlesData.Boxes/emd3947_10Apx_LP60_rescale1984box120.mrc
Opened emd3947_10Apx_LP60_rescale1984box120.mrc as #2, grid size 120,120,120,
pixel 1.98, shown at level 0.0295, step 1, values float32
> volume #2 level 0.02459
> volume #2 level 0.02682
> close session
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it025_class001job015refinerescale1984box120.mrc
Opened run_it025_class001job015refinerescale1984box120.mrc as #1, grid size
120,120,120, pixel 1.98, shown at level 1.32, step 1, values float32
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it025_class002job015refinerescale1984box120.mrc
Opened run_it025_class002job015refinerescale1984box120.mrc as #2, grid size
120,120,120, pixel 1.98, shown at level 1.43, step 1, values float32
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it025_class003job015refinerescale1984box120.mrc
Opened run_it025_class003job015refinerescale1984box120.mrc as #3, grid size
120,120,120, pixel 1.98, shown at level 1.41, step 1, values float32
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it025_class004job015refinerescale1984box120.mrc
Opened run_it025_class004job015refinerescale1984box120.mrc as #4, grid size
120,120,120, pixel 1.98, shown at level 1.37, step 1, values float32
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it025_class005job015refinerescale1984box120.mrc
Opened run_it025_class005job015refinerescale1984box120.mrc as #5, grid size
120,120,120, pixel 1.98, shown at level 1.36, step 1, values float32
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/10Apx5degrees/1A2810Apx2521particlesLP60Data.Boxes/run_it025_class006job015refinerescale1984box120.mrc
Opened run_it025_class006job015refinerescale1984box120.mrc as #6, grid size
120,120,120, pixel 1.98, shown at level 1.29, step 1, values float32
> volume #1 level 1.078
> volume #1 level 0.7977
> volume #2 level 0.931
> volume #2 level 0.6383
> volume #3 level 0.8705
> volume #3 level 0.6759
> volume #3 level 0.7296
> volume #4 level 0.7106
> volume #5 level 0.7005
> volume #5 level 0.6926
> volume #6 level 0.4013
> close session
> preset artiax "artiax default"
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> artiax start
[Repeated 1 time(s)]Opened 1A28blackcontrastdeconvinverted.mrc as #1.1.1, grid
size 792,1128,496, pixel 1, shown at level -33.3, step 1, values float32
> artiax clip off
> artiax tomo #1.1.1 sliceDirection 0,0,1
> artiax view xy
> artiax tomo #1.1.1 contrastCenter -33.51344859
> artiax tomo #1.1.1 contrastWidth 1.88774538
> artiax tomo #1.1.1 contrastCenter -33.74941664
> artiax tomo #1.1.1 contrastWidth 1.17984124
> artiax tomo #1.1.1 slice 267
> artiax tomo #1.1.1 slice 202
> artiax tomo #1.1.1 slice 173
> artiax tomo #1.1.1 sliceDirection 0,0,1
> artiax view xy
> mousemode rightMode "move planes"
> artiax tomo #1.1.1 sliceDirection 0,1,0
> artiax view xz
> mousemode rightMode "move planes"
> artiax tomo #1.1.1 sliceDirection 1,0,0
> artiax view yz
> mousemode rightMode "move planes"
> artiax tomo #1.1.1 sliceDirection 0,0,1
> artiax view xy
> mousemode rightMode "move planes"
> artiax tomo #1.1.1 contrastWidth 0.94387319
> artiax tomo #1.1.1 contrastCenter -33.74941664
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/Denoise/10Apxdenoisewhitecontrast.rec/isonet2/job7/particles.star
> format star
Summary of feedback from opening
/Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/Denoise/10Apxdenoisewhitecontrast.rec/isonet2/job7/particles.star
---
notes | Processed as relion
Processed as relion
Traceback (most recent call last):
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 216, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__
super().__init__(
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__
self.read_file()
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type
TypeError: Cannot interpret '' as a data type
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
See log for complete Python traceback.
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/Denoise/10Apxdenoisewhitecontrast.rec/isonet2/job7/particles.star
> format star
Summary of feedback from opening
/Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/Denoise/10Apxdenoisewhitecontrast.rec/isonet2/job7/particles.star
---
notes | Processed as relion
Processed as relion
Traceback (most recent call last):
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 216, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__
super().__init__(
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__
self.read_file()
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type
TypeError: Cannot interpret '' as a data type
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
See log for complete Python traceback.
> artiax clip off
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/Denoise/10Apxdenoisewhitecontrast.rec/isonet2/job7/particles.star
> format star
Summary of feedback from opening
/Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/Denoise/10Apxdenoisewhitecontrast.rec/isonet2/job7/particles.star
---
notes | Processed as relion
Processed as relion
Traceback (most recent call last):
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 216, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__
super().__init__(
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__
self.read_file()
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type
TypeError: Cannot interpret '' as a data type
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
See log for complete Python traceback.
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/Denoise/10Apxdenoisewhitecontrast.rec/isonet2/job7/particles.star
> format star
Summary of feedback from opening
/Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/Denoise/10Apxdenoisewhitecontrast.rec/isonet2/job7/particles.star
---
notes | Processed as relion
Processed as relion
Traceback (most recent call last):
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 216, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__
super().__init__(
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__
self.read_file()
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type
TypeError: Cannot interpret '' as a data type
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
See log for complete Python traceback.
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/Denoise/10Apxdenoisewhitecontrast.rec/isonet2/job7/particlesmodify.star
> format star
Summary of feedback from opening
/Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/Denoise/10Apxdenoisewhitecontrast.rec/isonet2/job7/particlesmodify.star
---
notes | Processed as relion
Processed as relion
Traceback (most recent call last):
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 216, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__
super().__init__(
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__
self.read_file()
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type
Window position QRect(-251,347 600x300) outside any known screen, using
primary screen
TypeError: Cannot interpret '' as a data type
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
See log for complete Python traceback.
> select add #1
7 models selected
> select add #1
7 models selected
> select subtract #1.2
6 models selected
> select add #1.2
7 models selected
> select subtract #1.3
6 models selected
> select add #1.3
7 models selected
> select subtract #1.2
6 models selected
> volume #1.1.1 level -34.22,0 level -33.82,0.4538 level -33.28,1
> hide #!1.1.1 models
> show #!1.1.1 models
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/Denoise/10Apxdenoisewhitecontrast.rec/isonet2/job7/particles.star
> format star
Summary of feedback from opening
/Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/Denoise/10Apxdenoisewhitecontrast.rec/isonet2/job7/particles.star
---
notes | Processed as relion
Processed as relion
Traceback (most recent call last):
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 216, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__
super().__init__(
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__
self.read_file()
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type
TypeError: Cannot interpret '' as a data type
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
See log for complete Python traceback.
> open
> /Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/Denoise/10Apxdenoisewhitecontrast.rec/isonet2/job7/particles.star
> format star
Summary of feedback from opening
/Users/pliu1/Desktop/Tomodataprocessing/20251021TMwithDynamo/Denoise/10Apxdenoisewhitecontrast.rec/isonet2/job7/particles.star
---
notes | Processed as relion
Processed as relion
Traceback (most recent call last):
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 216, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__
super().__init__(
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__
self.read_file()
File "/Users/pliu1/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type
TypeError: Cannot interpret '' as a data type
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac18,3
Processor Name: Quad-Core Intel Core i7
Processor Speed: 4,2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 64 GB
System Firmware Version: 529.140.2.0.0
OS Loader Version: 577.140.2~30
SMC Version (system): 2.41f2
Software:
System Software Overview:
System Version: macOS 13.7.1 (22H221)
Kernel Version: Darwin 22.6.0
Time since boot: 20 days, 3 hours, 43 minutes
Graphics/Displays:
Radeon Pro 580:
Chipset Model: Radeon Pro 580
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c0
ROM Revision: 113-D000AA-931
VBIOS Version: 113-D0001A1X-025
EFI Driver Version: 01.00.931
Metal Support: Metal 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.6.0
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
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: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
geomdl: 5.4.0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
pandas: 3.0.2
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pyarrow: 23.0.1
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starfile: 0.5.13
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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