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Opened 28 hours ago
#19237 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: Linux-6.8.0-85-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
Opened rec_L04_2_ts_003_crop.mrc as #1.1.1, grid size 680,849,200, pixel 10,
shown at level 0.325, step 2, values float32
> artiax clip off
> artiax tomo #1.1.1 sliceDirection 0,0,1
> artiax view xy
> open
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/pyTOM/templateMatch/rec_L04_2_ts_003_crop_particles.star
> format star
Summary of feedback from opening
/home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/pyTOM/templateMatch/rec_L04_2_ts_003_crop_particles.star
---
notes | Processed as relion
> artiax clip off
Opened Particle list rec_L04_2_ts_003_crop_particles.star with 1000 particles.
> artiax particles #1.2.1 originScaleFactor 10.0
> artiax view xy
> artiax particles #1.2.1 transScaleFactor 1.0
> artiax view xy
> artiax hide axes
minimum: 15.0, maximum: 664.0
1000 atoms, 1000 residues, atom rlnCoordinateX range 15 to 664
[Repeated 1 time(s)]
> artiax colormap #1.2.1.3 rlnCoordinateX palette redgreen minValue 15.0
> maxValue 664.0 transparency 0.0
minimum: 0.344379, maximum: 0.482966
1000 atoms, 1000 residues, atom rlnLCCmax range 0.344 to 0.483
[Repeated 1 time(s)]
> artiax colormap #1.2.1.3 rlnLCCmax palette redgreen minValue 0.344379
> maxValue 0.482966 transparency 0.0
> artiax view xy
> artiax tomo #1.1.1 slice 187
> artiax tomo #1.1.1 slice 163
> artiax tomo #1.1.1 slice 146
> artiax tomo #1.1.1 slice 118
> artiax tomo #1.1.1 slice 173
> artiax tomo #1.1.1 slice 144
> artiax tomo #1.1.1 slice 85
> artiax tomo #1.1.1 slice 123
> artiax tomo #1.1.1 slice 148
> artiax tomo #1.1.1 slice 135
> artiax tomo #1.1.1 slice 120
> artiax tomo #1.1.1 contrastWidth 1.18749845
> artiax tomo #1.1.1 contrastWidth 1.15871063
> artiax tomo #1.1.1 slice 141
> open
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6945869.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6949002.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6949081.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6951289.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6951722.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6951763.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952458.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952468.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952470.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952471.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952476.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952486.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952487.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952488.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952492.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952497.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952499.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952504.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/cellmem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952510.mrc
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6945869.mrc
as #2.1, grid size 20,8,23, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6949002.mrc
as #2.2, grid size 24,10,18, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6949081.mrc
as #2.3, grid size 22,13,23, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6951289.mrc
as #2.4, grid size 24,13,14, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6951722.mrc
as #2.5, grid size 32,12,16, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6951763.mrc
as #2.6, grid size 20,17,18, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952458.mrc
as #2.7, grid size 39,18,35, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952468.mrc
as #2.8, grid size 304,101,173, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952470.mrc
as #2.9, grid size 406,96,171, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952471.mrc
as #2.10, grid size 235,89,183, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952476.mrc
as #2.11, grid size 177,52,151, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952486.mrc
as #2.12, grid size 60,22,41, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952487.mrc
as #2.13, grid size 51,33,52, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952488.mrc
as #2.14, grid size 38,19,28, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952492.mrc
as #2.15, grid size 35,28,24, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952497.mrc
as #2.16, grid size 31,20,31, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952499.mrc
as #2.17, grid size 42,24,29, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952504.mrc
as #2.18, grid size 39,23,29, pixel 10, shown at level 20, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952510.mrc
as #2.19, grid size 39,18,21, pixel 10, shown at level 20, step 1, values
float32
> color #2 #26a269ff models
> vop #2 level 0.5
> artiax tomo #1.1.1 slice 75
> color #2 #77767bff models
> color #2 #dedddaff models
> open
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/innermem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952478.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/innermem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952479.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/innermem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952481.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/innermem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952482.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/innermem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952484.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/innermem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952489.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/innermem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952493.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/innermem/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952495.mrc
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952478.mrc
as #3.1, grid size 159,68,179, pixel 10, shown at level 29, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952479.mrc
as #3.2, grid size 100,40,135, pixel 10, shown at level 44, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952481.mrc
as #3.3, grid size 123,51,145, pixel 10, shown at level 32, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952482.mrc
as #3.4, grid size 64,27,87, pixel 10, shown at level 46, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952484.mrc
as #3.5, grid size 75,31,117, pixel 10, shown at level 45, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952489.mrc
as #3.6, grid size 51,12,69, pixel 10, shown at level 33, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952493.mrc
as #3.7, grid size 46,16,46, pixel 10, shown at level 44, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952495.mrc
as #3.8, grid size 33,12,63, pixel 10, shown at level 44, step 1, values
float32
> color #3 #cdab8fff models
> color #3 #cccc99ff models
> vop #3 level 0.5
> open
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6949079.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6951728.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6951754.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952037.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952039.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952211.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952472.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952473.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952474.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952480.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952483.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952485.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952496.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952498.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952500.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/mitochondria/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952502.mrc
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6949079.mrc
as #4.1, grid size 12,23,17, pixel 10, shown at level 16, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6951728.mrc
as #4.2, grid size 18,17,19, pixel 10, shown at level 16, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6951754.mrc
as #4.3, grid size 15,15,18, pixel 10, shown at level 16, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952037.mrc
as #4.4, grid size 22,9,46, pixel 10, shown at level 4, step 1, values float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952039.mrc
as #4.5, grid size 25,14,30, pixel 10, shown at level 4, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952211.mrc
as #4.6, grid size 18,18,24, pixel 10, shown at level 4, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952472.mrc
as #4.7, grid size 105,167,162, pixel 10, shown at level 16, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952473.mrc
as #4.8, grid size 171,218,197, pixel 10, shown at level 4, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952474.mrc
as #4.9, grid size 158,85,161, pixel 10, shown at level 4, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952480.mrc
as #4.10, grid size 167,167,169, pixel 10, shown at level 4, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952483.mrc
as #4.11, grid size 79,37,107, pixel 10, shown at level 12, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952485.mrc
as #4.12, grid size 54,20,83, pixel 10, shown at level 12, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952496.mrc
as #4.13, grid size 39,15,48, pixel 10, shown at level 8, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952498.mrc
as #4.14, grid size 26,8,53, pixel 10, shown at level 9, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952500.mrc
as #4.15, grid size 40,24,25, pixel 10, shown at level 16, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952502.mrc
as #4.16, grid size 14,27,21, pixel 10, shown at level 16, step 1, values
float32
> vop #4 level 0.5
> color #3 #8ff0a4ff models
> color #3 #cccc99ff models
> color #4 #8ff0a4ff models
> color #4 #ffb2ffff models
> color #4 #f66151ff models
> open
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/vacuole/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6951755.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/vacuole/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952209.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/vacuole/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952469.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/vacuole/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952475.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/vacuole/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952477.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/vacuole/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952501.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/vacuole/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952507.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/vacuole/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952508.mrc
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6951755.mrc
as #5.1, grid size 21,16,17, pixel 10, shown at level 1, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952209.mrc
as #5.2, grid size 30,17,16, pixel 10, shown at level 1, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952469.mrc
as #5.3, grid size 273,262,168, pixel 10, shown at level 1, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952475.mrc
as #5.4, grid size 235,214,171, pixel 10, shown at level 1, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952477.mrc
as #5.5, grid size 215,185,152, pixel 10, shown at level 1, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952501.mrc
as #5.6, grid size 42,28,32, pixel 10, shown at level 1, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952507.mrc
as #5.7, grid size 44,26,26, pixel 10, shown at level 1, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952508.mrc
as #5.8, grid size 26,19,22, pixel 10, shown at level 1, step 1, values
float32
> vop #5 level 0.5
> color #5 #99c1f1ff models
> color #5 #b2ffffff models
> color #4 #804040ff models
> color #4 #ff4040ff models
> color #4 #ffaaaaff models
> open
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/vesicle/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952490.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/vesicle/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952491.mrc
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/predictions_v10alpha/L04_2_ts_003_60seg/vesicle/rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952505.mrc
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952490.mrc
as #6.1, grid size 35,21,30, pixel 10, shown at level 47, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952491.mrc
as #6.2, grid size 53,48,26, pixel 10, shown at level 43, step 1, values
float32
Opened
rec_L04_2_ts_003_crop_sp_MemBrain_seg_v10_alpha.ckpt_segmented_region_6952505.mrc
as #6.3, grid size 24,12,24, pixel 10, shown at level 48, step 1, values
float32
> vop #6 level 0.5
> color #6 #99c1f1ff models
> color #6 #62a0eaff models
> color #6 #99c1f1ff models
> color #6 #62a0eaff models
> color #6 #bf4840ff models
> color #6 #40bfb5ff models
> color #6 #bf5240ff models
> color #6 #40bf86ff models
> color #6 #4096bfff models
> color #6 #4079bfff models
> color #6 #407fbfff models
> color #6 #40b2bfff models
> color #6 #40b0bfff models
> color #6 #aaaaffff models
> color #6 #aaffffff models
> color #6 #b2ffffff models
> color #6 #8ac5c5ff models
> color #6 #9cdfdfff models
> color #6 #9cffdfff models
> color #6 blue models
> color #6 lime models
> color #6 #aaaaffff models
> color #6 #aa99ffff models
> color #6 #5555ffff models
> color #6 #bbbbffff models
> color #6 #99bbffff models
> color #6 #99ffffff models
> color #6 cyan models
> color #6 #62a0eaff models
> ui tool show "Color Actions"
> color gainsboro
> select #2
39 models selected
> color sel gainsboro
[Repeated 2 time(s)]
> select #3
17 models selected
> color sel navajo white
[Repeated 1 time(s)]
> color sel bisque
[Repeated 1 time(s)]
> color sel moccasin
[Repeated 1 time(s)]
> color sel peach puff
[Repeated 1 time(s)]
> color sel pink
[Repeated 1 time(s)]
> color sel khaki
[Repeated 1 time(s)]
> color sel pale goldenrod
[Repeated 2 time(s)]
> color sel light goldenrod yellow
[Repeated 1 time(s)]
> color sel beige
[Repeated 1 time(s)]
> color sel pale goldenrod
[Repeated 1 time(s)]
> select #3
17 models selected
> select #4
33 models selected
> color sel plum
[Repeated 1 time(s)]
> color sel light pink
[Repeated 1 time(s)]
> color sel light salmon
[Repeated 1 time(s)]
> color sel salmon
[Repeated 1 time(s)]
> color sel light salmon
[Repeated 1 time(s)]
> color sel peach puff
[Repeated 1 time(s)]
> color sel pink
[Repeated 1 time(s)]
> color sel light pink
[Repeated 1 time(s)]
> color sel light salmon
[Repeated 1 time(s)]
> select #5
17 models selected
> color sel sky blue
[Repeated 1 time(s)]
> color sel pale turquoise
[Repeated 1 time(s)]
> color sel powder blue
[Repeated 1 time(s)]
> color sel light cyan
[Repeated 1 time(s)]
> color sel dark turquoise
[Repeated 1 time(s)]
> color sel powder blue
[Repeated 1 time(s)]
> color sel pale turquoise
[Repeated 1 time(s)]
> color sel light blue
[Repeated 1 time(s)]
> color sel light sky blue
[Repeated 1 time(s)]
> color sel light blue
[Repeated 1 time(s)]
> select #6
7 models selected
> color sel sky blue
[Repeated 1 time(s)]
> color sel light sky blue
[Repeated 3 time(s)]
> color sel royal blue
[Repeated 1 time(s)]
> color sel cornflower blue
[Repeated 1 time(s)]
> color sel dodger blue
[Repeated 1 time(s)]
> color sel cornflower blue
[Repeated 1 time(s)]
> color sel deep sky blue
[Repeated 1 time(s)]
> color sel cornflower blue
[Repeated 1 time(s)]
> color sel light sky blue
[Repeated 1 time(s)]
> color sel sky blue
[Repeated 1 time(s)]
> color sel light steel blue
[Repeated 1 time(s)]
> color sel cornflower blue
[Repeated 1 time(s)]
> artiax clip off
> select clear
> save session movie.cxs
Cannot determine format for 'session'
> save movie.cxs session
Expected a keyword
> save movie.cxs session
Expected a keyword
> save movie.cxs session
Expected a keyword
> ui windowfill toggle
> save movie.cxs session
Expected a keyword
> ui windowfill toggle
> savesession
Unknown command: savesession
> savesession
Unknown command: savesession
> save session
Cannot determine format for 'session'
> save session test.cxs
Cannot determine format for 'session'
> save session test.cxs
Cannot determine format for 'session'
> open help:user/artiax_index.html
Opened help:user/artiax_index.html
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/options_window.py", line 213, in
_update_partlist_options
self._show_tab("partlist")
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/options_window.py", line 248, in _show_tab
self._update_partlist_ui()
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/options_window.py", line 1647, in _update_partlist_ui
self.color_selection.set_partlist(pl)
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/widgets/ColorRangeWidget.py", line 301, in
set_partlist
curr_min = max(self.partlist.color_settings['minimum'], self.minimum)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'list' object is not callable
Error processing trigger "options partlist changed":
TypeError: 'list' object is not callable
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/widgets/ColorRangeWidget.py", line 301, in
set_partlist
curr_min = max(self.partlist.color_settings['minimum'], self.minimum)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> artiax particles #1.2.1 color 94,64,100,100
minimum: 0.0, maximum: 1.0
1000 atoms, 1000 residues, atom rlnLCCmax range 0.344 to 0.483
[Repeated 1 time(s)]
> artiax colormap #1.2.1.3 rlnLCCmax palette redgreen minValue 0.0 maxValue
> 1.0 transparency 0.0
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/options_window.py", line 213, in
_update_partlist_options
self._show_tab("partlist")
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/options_window.py", line 248, in _show_tab
self._update_partlist_ui()
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/options_window.py", line 1647, in _update_partlist_ui
self.color_selection.set_partlist(pl)
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/widgets/ColorRangeWidget.py", line 301, in
set_partlist
curr_min = max(self.partlist.color_settings['minimum'], self.minimum)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'list' object is not callable
Error processing trigger "options partlist changed":
TypeError: 'list' object is not callable
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/widgets/ColorRangeWidget.py", line 301, in
set_partlist
curr_min = max(self.partlist.color_settings['minimum'], self.minimum)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> open
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/pyTOM/templateMatch/rec_L04_2_ts_003_crop_particles.star
> format star
Summary of feedback from opening
/home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/pyTOM/templateMatch/rec_L04_2_ts_003_crop_particles.star
---
notes | Processed as relion
> artiax clip off
Opened Particle list rec_L04_2_ts_003_crop_particles.star with 1000 particles.
> artiax particles #1.2.1 originScaleFactor 10.0
> artiax view xy
> artiax particles #1.2.1 transScaleFactor 1.0
> artiax view xy
> artiax hide axes
minimum: 15.0, maximum: 664.0
1000 atoms, 1000 residues, atom rlnCoordinateX range 15 to 664
[Repeated 1 time(s)]
> artiax colormap #1.2.1.3 rlnCoordinateX palette redgreen minValue 15.0
> maxValue 664.0 transparency 0.0
minimum: 0.344379, maximum: 0.482966
1000 atoms, 1000 residues, atom rlnLCCmax range 0.344 to 0.483
[Repeated 1 time(s)]
> artiax colormap #1.2.1.3 rlnLCCmax palette redgreen minValue 0.344379
> maxValue 0.482966 transparency 0.0
> open
> /home/takahiro/DATA/250528_BY4502_Glycerol_trueMirror/MembrainSeg/pyTOM/relion_locres_filtered_FlipY_Low20A_b64.mrc
Opened relion_locres_filtered_FlipY_Low20A_b64.mrc as #7, grid size 64,64,64,
pixel 10, shown at level 0.104, step 1, values float32
> artiax attach #7 toParticleList #1.2.1
Opened relion_locres_filtered_FlipY_Low20A_b64.mrc as #1.2.1.1.1, grid size
64,64,64, pixel 10, shown at level 0.104, step 1, values float32
> volume #1.2.1.1.1 capFaces false
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/options_window.py", line 1681, in _partlist_changed
self._update_partlist_ui()
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/options_window.py", line 1647, in _update_partlist_ui
self.color_selection.set_partlist(pl)
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/widgets/ColorRangeWidget.py", line 301, in
set_partlist
curr_min = max(self.partlist.color_settings['minimum'], self.minimum)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'list' object is not callable
Error processing trigger "partlist changed":
TypeError: 'list' object is not callable
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/widgets/ColorRangeWidget.py", line 301, in
set_partlist
curr_min = max(self.partlist.color_settings['minimum'], self.minimum)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> artiax show #1.2.1 surfaces
Traceback (most recent call last):
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/options_window.py", line 1846, in
_browse_display_volume
self._attach_display_model(file[0])
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/options_window.py", line 1825, in
_attach_display_model
self._update_partlist_ui()
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/options_window.py", line 1647, in _update_partlist_ui
self.color_selection.set_partlist(pl)
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/widgets/ColorRangeWidget.py", line 301, in
set_partlist
curr_min = max(self.partlist.color_settings['minimum'], self.minimum)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'list' object is not callable
TypeError: 'list' object is not callable
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/widgets/ColorRangeWidget.py", line 301, in
set_partlist
curr_min = max(self.partlist.color_settings['minimum'], self.minimum)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> ui tool show "Side View"
> artiax tomo #1.1.1 slice 0
> artiax tomo #1.1.1 slice 199
> artiax tomo #1.1.1 slice 195
> artiax tomo #1.1.1 slice 194
> artiax tomo #1.1.1 slice 189
> artiax tomo #1.1.1 slice 185
> artiax tomo #1.1.1 slice 180
> artiax tomo #1.1.1 slice 170
> ui mousemode right "delete picked particle"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/options_window.py", line 1681, in _partlist_changed
self._update_partlist_ui()
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/options_window.py", line 1647, in _update_partlist_ui
self.color_selection.set_partlist(pl)
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/widgets/ColorRangeWidget.py", line 301, in
set_partlist
curr_min = max(self.partlist.color_settings['minimum'], self.minimum)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'list' object is not callable
Error processing trigger "partlist changed":
TypeError: 'list' object is not callable
File "/home/takahiro/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/artiax/widgets/ColorRangeWidget.py", line 301, in
set_partlist
curr_min = max(self.partlist.color_settings['minimum'], self.minimum)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.5 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.3
OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits)
OpenGL vendor: Mesa
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: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:21
Manufacturer:
Model:
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD EPYC 7543 32-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 251Gi 4.4Gi 243Gi 225Mi 3.9Gi 245Gi
Swap: 7.6Gi 0B 7.6Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102GL [RTX A5000] [10de:2231] (rev a1)
Subsystem: NVIDIA Corporation GA102GL [RTX A5000] [10de:147e]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 1.0.0
annotated-types: 0.7.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2025.7.14
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-ArtiaX: 0.6.0
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
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: 1.10.1
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: 2.5.1
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-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
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: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
geomdl: 5.4.0
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: 4.3.2
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
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
pandas: 2.3.2
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
pyarrow: 21.0.0
pycollada: 0.8
pydantic: 2.11.9
pydantic_core: 2.33.2
pydicom: 2.4.4
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: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
starfile: 0.5.13
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-inspection: 0.4.1
typing_extensions: 4.14.1
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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