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Opened 13 months ago
Closed 13 months ago
#16076 closed defect (duplicate)
ArtiaX: arrays used as indices must be of integer (or boolean) type
| Reported by: | Owned by: | Utz Ermel | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/002.cxs
Opened peroxisome_cleaned_half2.mrc as #3, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at level 0.0032, step 1, values int8
Opened peroxisome_cleaned_half1.mrc as #2, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at level 0.0032, step 2, values int8
Opened peroxisome_makeup_final.mrc as #1, grid size 101,101,101, pixel 58.2,
shown at level 0.88, step 1, values float32
Opened peroxisome_makeup_final.mrc copy as #5, grid size 101,101,101, pixel
58.2, shown at level 0.88, step 1, values float32
Log from Sat Oct 5 18:55:48 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/Chlamy_v8a3_002_rec_corrected_model_v10.ckpt_segmented.mrc
> format mrc
Opened Chlamy_v8a3_002_rec_corrected_model_v10.ckpt_segmented.mrc as #1, grid
size 682,960,200, pixel 12.5,12.5,12.5, shown at level 81, step 2, values int8
> volume #1 step 1
> volume #1 level 0.7
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup.mrc
Opened peroxisome_makeup.mrc as #2, grid size 101,101,101, pixel 58.2, shown
at level 1, step 1, values float32
> volume #2 level 0.4381
> volume #2 level 0.7828
> ui tool show "Map Eraser"
> volume erase #1 center 5184.3,6001.7,587.38 radius 3006.8 outside true
Opened Chlamy_v8a3_002_rec_corrected_model_v10.ckpt_segmented.mrc copy as #4,
grid size 682,960,200, pixel 12.5,12.5,12.5, shown at step 1, values int8
> volume erase #4 center 5224.9,6213.1,587.56 radius 1920.1
> volume erase #4 center 2257.3,3985.7,704.28 radius 1920.1
> volume erase #4 center 2012.7,4917.3,1968.3 radius 1553
> volume erase #4 center 1874,7462.5,2517.5 radius 1553
> volume erase #4 center 1517,7906.9,1435.3 radius 1553
> volume erase #4 center 2917.4,4190.6,1936.4 radius 1553
> volume erase #4 center 5036.4,3291.6,3391 radius 1553
> volume erase #4 center 7510.2,3033.5,2283.7 radius 1553
> volume erase #4 center 9053.8,6146.6,2010 radius 1553
> volume erase #4 center 5094.6,6944.7,914.73 radius 1553
> volume #4 level 1.055
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_cleaned.mrc
> models #4
> close #1
> volume #2 color #ffffb299
> volume erase #2 center 5301,6072.8,2250.2 radius 1551.8
Opened peroxisome_makeup.mrc copy as #1, grid size 101,101,101, pixel 58.2,
shown at step 1, values float32
> volume #1 level 0.02491
> close #1
> volume erase #2 center 4861.7,5145.9,1965.5 radius 1551.8
Opened peroxisome_makeup.mrc copy as #1, grid size 101,101,101, pixel 58.2,
shown at step 1, values float32
> close #2
> volume #1 color #ffffb2
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/005/peroxisome_makeup.mrc
Opened peroxisome_makeup.mrc as #2, grid size 102,102,101, pixel
39.2,39.2,39.2, shown at level 1, step 1, values float32
> volume #2 level 0.6044
> volume #2 level 0.5268
> volume #2 color #ffb2b280
> volume #1 color #ffffb280
> close #2
Can only have one displayed volume when erasing
> volume erase #1 center 5260.7,6199.1,-336.13 radius 2824.5
> volume #1 level 0.1508
> volume #1 level 1
> volume #1 color #ffffb2
> volume erase #1 center 5138.1,6542.6,1683.5 radius 1551.8
> volume erase #1 center 6769.2,8011,-684.96 radius 1551.8
> volume #1 color #ffffb2cc
> volume erase #1 center 5998.6,8104.4,914.4 radius 1551.8
> volume erase #1 center 8453.6,6459.8,-604.61 radius 1551.8
> volume erase #1 center 8521.8,5518.3,-911.75 radius 1551.8
> volume erase #1 center 7350.8,4870.3,-2420.4 radius 1551.8
> volume erase #1 center 7139.1,4877.3,-2039.9 radius 1551.8
> volume erase #1 center 4426.2,5874.9,-3080 radius 1551.8
> volume erase #1 center 5541.4,3866.2,-2603.6 radius 1551.8
> volume erase #1 center 4447.1,5232,-1861.6 radius 1551.8
> volume erase #1 center 3782.8,6315.8,-2106.9 radius 1551.8
> volume erase #1 center 4493.1,8481.9,-1954.4 radius 1551.8
> volume erase #1 center 5153.5,7973.7,-1014.8 radius 1551.8
> volume erase #1 center 4473.4,8162.1,603.61 radius 1551.8
> volume erase #1 center 6700.5,6357.3,1152.2 radius 1745.8
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/Chlamy_v8a3_002_rec_corrected_model_v10.ckpt_segmented.mrc
Opened Chlamy_v8a3_002_rec_corrected_model_v10.ckpt_segmented.mrc as #2, grid
size 682,960,200, pixel 12.5,12.5,12.5, shown at level 81, step 2, values int8
> volume #2 level 0.7
> close #2
> volume erase #1 center 3180.4,6969,-483.64 radius 1745.8
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/Chlamy_v8a3_002_rec_corrected_model_v10.ckpt_segmented.mrc
Opened Chlamy_v8a3_002_rec_corrected_model_v10.ckpt_segmented.mrc as #2, grid
size 682,960,200, pixel 12.5,12.5,12.5, shown at level 81, step 2, values int8
> volume #2 level 0.7
> close #1
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/005/peroxisome_makeup.mrc
Opened peroxisome_makeup.mrc as #1, grid size 102,102,101, pixel
39.2,39.2,39.2, shown at level 1, step 1, values float32
> volume #1 level 0.7505
> volume erase #1 center 4760.8,8296.8,1138.3 radius 1745.5
Opened peroxisome_makeup.mrc copy as #5, grid size 102,102,101, pixel
39.2,39.2,39.2, shown at step 1, values float32
> close #1
> close #5
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup.mrc
Opened peroxisome_makeup.mrc as #1, grid size 101,101,101, pixel 58.2, shown
at level 1, step 1, values float32
> volume #1 level 0.5471
> volume #1 color #b2b2b280
Can only have one displayed volume when erasing
> volume erase #1 center 5229.4,6294,-270.19 radius 2533.5
Opened peroxisome_makeup.mrc copy as #5, grid size 101,101,101, pixel 58.2,
shown at step 1, values float32
> close #1
> volume erase #5 center 4128.7,5221.1,-188.48 radius 2527.6
> volume erase #5 center 6355.7,4729.5,-1723.8 radius 2527.6
> volume erase #5 center 4558.1,6835.2,-1530.1 radius 2527.6
> volume erase #5 center 7513.1,6063.1,-2061.4 radius 2527.6
> volume erase #5 center 6069.2,6893.7,-1478.7 radius 2527.6
> volume erase #5 center 4709.6,5878,2478.6 radius 2527.6
> volume erase #5 center 5250,6359.1,-28.719 radius 2527.6
> volume #5 color #e5bf99
> volume erase #5 center 5453.5,8833.3,-2275.4 radius 2527.6
> volume erase #5 center 4413,7934.8,1660.9 radius 596.64
> volume erase #5 center 5166.8,7918,1969.3 radius 596.64
> volume erase #5 center 6026.9,7472.7,1966.5 radius 596.64
> volume erase #5 center 6564.1,6981.6,2193.5 radius 596.64
> close #2
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup_final.mrc
> models #5
> volume erase #5 center 2661.2,7153.1,574.24 radius 649.54
> volume erase #5 center 2690.3,7175.2,275.36 radius 649.54
> volume erase #5 center 2607.8,6873.4,886.72 radius 649.54
> volume erase #5 center 3168.3,7992.7,574.06 radius 649.54
> volume erase #5 center 3124,8013.9,561.1 radius 649.54
> volume erase #5 center 3119.4,7995.2,291.42 radius 649.54
Can only have one displayed volume when erasing
> volume erase #5 center 5858.5,4554.4,1044.9 radius 649.54
> volume erase #5 center 6237.2,4917.8,1283 radius 649.54
> volume erase #5 center 6384.3,5184.5,1316 radius 649.54
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup_final.mrc
> models #5
> volume #5 color #ff40ff
> volume #5 color #ff85ff
> volume #5 color #ff8ad8
> volume #4 color #ff8ad8
> volume #4 color #ff85ff
> volume #4 color #ff8ad8
> volume all surfaceSmoothing true
> volume all smoothingIterations 10
> volume all smoothingFactor 0.5
> volume #5 smoothingFactor 0.8
> volume #5 smoothingIterations 40
> lighting soft
> view orient
> volume #4 level 12.09
> volume #4 level 5.191
> volume #5 level 0.2
> volume #5 level 1
> volume #5 level 0.8
> volume #5 smoothingIterations 20
> ui tool show "Map Eraser"
> volume erase #5 center 6432.1,4310.1,1004.7 radius 1149
> volume erase #5 center 6990.8,6976.6,1147.8 radius 1143.3
> close #5
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup_final.mrc
Opened peroxisome_makeup_final.mrc as #2, grid size 101,101,101, pixel 58.2,
shown at level 1, step 1, values float32
> volume #2 level 0.2711
> volume erase #2 center 6533.9,3928.3,1432.2 radius 1137.4
Opened peroxisome_makeup_final.mrc copy as #3, grid size 101,101,101, pixel
58.2, shown at step 1, values float32
> volume erase #3 center 6172.7,3675.7,1256.8 radius 1137.4
> view orient
> close #2
> volume #3 smoothingIterations 20
> volume all smoothingFactor 0.5
> volume #3 smoothingIterations 20
> volume #3 level 0.4219
> volume all smoothingFactor 0.5
> volume #3 smoothingIterations 20
> lighting simple
> volume #3 smoothingIterations 20
> volume all smoothingFactor 0.5
> volume all surfaceSmoothing true
> volume #3 color #ff8ad8
> volume #4 level 0
> volume #4 level 1.034
> lighting soft
> ui mousemode right select
> select #3
2 models selected
> ui mousemode right "translate selected particles"
> mousemode rightMode "translate selected particles"
Invalid "rightMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'
> volume #3 level 1
> select clear
> volume #3 color #ff2f92
> volume #4 color #941751
> volume #3 color #941751
> volume #3 color #ff40ff
> volume #4 color #ff40ff
> ui tool show "Map Eraser"
> volume erase #4 center 6024.8,7267.7,1537.3 radius 806.57
> volume erase #4 center 6577.8,6723.4,1493 radius 800.55
> volume erase #4 center 6726.9,6767.3,1940.2 radius 632.02
> volume #4 color #ff8ad8
> volume #3 color #ff85ff
> volume #3 color #ff8ad8
> volume #4 level 3.217
> close #4
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_cleaned.mrc
Opened peroxisome_cleaned.mrc as #2, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at level 0.0032, step 2, values int8
> volume #2 step 4
> volume all surfaceSmoothing true
> volume all smoothingFactor 0.5
> volume #2 smoothingIterations 10
> volume #2 color #ff8ad8
> volume #2 step 8
> volume #2 step 4
> set bgColor white
> close #3
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup.mrc
Opened peroxisome_makeup.mrc as #3, grid size 101,101,101, pixel 58.2, shown
at level 1, step 1, values float32
> volume #3 level 0.5871
> volume all smoothingFactor 0.5
> volume all surfaceSmoothing true
> volume #3 smoothingIterations 30
> volume #2 step 1
> volume #2 step 4
> volume #2 step 1
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup_2.mrc
Opened peroxisome_makeup_2.mrc as #4, grid size 101,101,101, pixel 58.6, shown
at level 1, step 1, values float32
> volume #4 level 0.09612
> volume all surfaceSmoothing true
> view orient
> close #3
> close #4
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup_2.mrc
Opened peroxisome_makeup_2.mrc as #3, grid size 101,101,101, pixel 60, shown
at level 1, step 1, values float32
> volume #3 level 0.9336
> volume #3 level 0.02513
> volume all surfaceSmoothing true
> volume #3 smoothingIterations 30
> volume #3 color #e5bf9980
> close #3
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup_final.mrc
Opened peroxisome_makeup_final.mrc as #3, grid size 101,101,101, pixel 58.2,
shown at level 1, step 1, values float32
> volume #3 level 0.9246
> volume #2 step 4
> ui mousemode right select
[Repeated 1 time(s)]
> select #3
2 models selected
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-62.919,0,1,0,-12.218,0,0,1,-5.971
> volume all surfaceSmoothing true
> volume all smoothingFactor 0.5
> volume #3 smoothingIterations 30
> volume #3 color #ff8ad8
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> ui mousemode right select
> select #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-95.836,0,1,0,-32.506,0,0,1,-10.972
> view matrix models #3,1,0,0,-135.62,0,1,0,-173.7,0,0,1,145.34
> view matrix models #3,1,0,0,31.684,0,1,0,-26.603,0,0,1,249.05
> view matrix models #3,1,0,0,-111.3,0,1,0,-155.72,0,0,1,199.51
> ui mousemode right select
> select clear
> select #3
2 models selected
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-84.659,0,1,0,-120.14,0,0,1,203.5
> ui mousemode right select
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right select
> select #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-162.14,0,1,0,-175.36,0,0,1,192.03
> close #3
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup_final.mrc
Opened peroxisome_makeup_final.mrc as #3, grid size 101,101,101, pixel 58.2,
shown at level 1, step 1, values float32
> volume #3 level 0.2496
> volume all surfaceSmoothing true
> volume all smoothingFactor 0.5
> volume #3 smoothingIterations 30
> volume #3 color #ff8ad8
> volume #3 level 1
> volume #2 step 1
> volume #2 step 4
> volume #3 smoothingIterations 60
> volume #3 smoothingIterations 80
> volume #3 smoothingIterations 90
> volume #3 smoothingIterations 100
> view orient
> ui tool show "Map Eraser"
> volume erase #2 center 4619.2,8237.9,1854.1 radius 778.83
Opened peroxisome_cleaned.mrc copy as #4, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at step 1, values int8
> close #3
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup_final.mrc
Opened peroxisome_makeup_final.mrc as #3, grid size 101,101,101, pixel 58.2,
shown at level 1, step 1, values float32
> volume #3 level 0.04436
> volume all surfaceSmoothing true
> volume #3 smoothingIterations 100
> volume all smoothingFactor 0.5
> volume #3 color #ff8ad8
> volume #3 step 4
> volume #3 level 0.02033
> volume #3 step 1
> volume #4 step 4
> volume #3 smoothingIterations 120
> volume #3 smoothingIterations 110
> close #2
> volume erase #4 center 6715.9,7458.7,1333.1 radius 1474.7
> volume erase #4 center 6940.7,5843.5,690.71 radius 1474.7
> volume erase #4 center 7107.4,6702.7,551.94 radius 1474.7
> volume erase #4 center 6655.6,7499.6,314.89 radius 1474.7
> volume erase #4 center 5505.1,4241.3,749.99 radius 1474.7
> volume erase #4 center 6125.8,4241.6,1307.1 radius 1474.7
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_cleaned_half1.mrc
> models #4
> volume erase #3 center 6492.2,3753,1085.8 radius 1472.5
Opened peroxisome_makeup_final.mrc copy as #2, grid size 101,101,101, pixel
58.2, shown at step 1, values float32
> close #4
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_cleaned.mrc
Opened peroxisome_cleaned.mrc as #4, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at level 0.0032, step 2, values int8
> volume #4 color #ff8ad8
> volume all surfaceSmoothing true
> volume all smoothingFactor 0.5
> volume #4 smoothingIterations 10
> volume #4 step 4
> close #3
> volume erase #4 center 3801.3,7150.8,1067.4 radius 1649.3
Opened peroxisome_cleaned.mrc copy as #3, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at step 1, values int8
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_cleaned_half2.mrc
> models #3
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup_final.mrc
> models #2
> close #4
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_cleaned_half1.mrc
Opened peroxisome_cleaned_half1.mrc as #4, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at level 0.0032, step 2, values int8
> volume #4 step 4
> volume #4 color #ff8ad8
> ui mousemode right select
> select #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,36.872,0,1,0,-66.505,0,0,1,-14.323
> volume all surfaceSmoothing true
> volume #4 smoothingIterations 10
> volume all smoothingFactor 0.5
> ui mousemode right select
> select clear
> select #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,55.312,0,1,0,-13.535,0,0,1,-18.156
> view matrix models #4,1,0,0,82.378,0,1,0,1.634,0,0,1,-21.902
> ui mousemode right select
> select clear
> select #4
2 models selected
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-3.2393,0,1,0,25.917,0,0,1,-100.85
> view matrix models #4,1,0,0,33.121,0,1,0,-11.266,0,0,1,-96.518
> view matrix models #4,1,0,0,28.129,0,1,0,-9.2218,0,0,1,-116.47
> ui mousemode right select
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,39.63,0,1,0,2.728,0,0,1,-125.01
> volume #4 step 2
> ui mousemode right select
> select clear
> select #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,38.6,0,1,0,-27.787,0,0,1,-122.27
> ui mousemode right select
> select clear
> volume #4 step 1
> volume #4 step 4
> select #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,70.961,0,1,0,36.531,0,0,1,-116.2
> ui mousemode right select
> select clear
> ui mousemode right select
> select #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,83.539,0,1,0,26.115,0,0,1,-118.99
> ui mousemode right select
> select clear
Drag select of eraser sphere, 12 of 1000 triangles
> ui tool show "Map Eraser"
> volume erase #2 center 3096.4,7707.5,1137.7 radius 650.58
> ui mousemode right select
> select #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,18.858,0,1,0,-0.85756,0,0,1,1.1696
> ui mousemode right select
> select clear
> ui mousemode right select
> select #2
2 models selected
> close #4
> close #3
> close #2
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_cleaned_half1.mrc
Opened peroxisome_cleaned_half1.mrc as #1, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at level 0.0032, step 2, values int8
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_cleaned_half2.mrc
Opened peroxisome_cleaned_half2.mrc as #2, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at level 0.0032, step 2, values int8
> volume #2 color #ff8ad8
> volume #1 color #ff8ad8
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup_final.mrc
Opened peroxisome_makeup_final.mrc as #3, grid size 101,101,101, pixel 58.2,
shown at level 1, step 1, values float32
> volume #3 level 0.8636
> volume #3 color #ff8ad8
> ui mousemode right "translate selected models"
> ui mousemode right select
> select #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-139.93,0,1,0,-100.12,0,0,1,172
> volume all surfaceSmoothing true
> volume all smoothingFactor 0.5
> volume all smoothingIterations 10
> ui mousemode right select
> select clear
> close #3
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup_final.mrc
Opened peroxisome_makeup_final.mrc as #3, grid size 101,101,101, pixel 58.2,
shown at level 1, step 1, values float32
> volume #2 step 4
> volume #1 step 4
> volume #3 level 0.5225
> volume #3 color #ff8ad8
> volume all smoothingIterations 10
> volume all surfaceSmoothing true
> volume a#3 smoothingFactor 0.8
Expected a density maps specifier or a keyword
> volume #3 smoothingFactor 0.8
> volume #3 smoothingIterations 10
> volume #3 smoothingIterations 100
> volume #3 smoothingIterations 80
> volume #3 smoothingIterations 90
> rotate #2 z 80
Unknown command: rotate #2 z 80
> turn #2 z 80
Expected an axis vector or a keyword
> ui tool show "Map Eraser"
> close #3
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup.mrc
Opened peroxisome_makeup.mrc as #3, grid size 101,101,101, pixel 58.2, shown
at level 1, step 1, values float32
> volume #3 level 0.9834
> volume #3 level 0.03142
> volume erase #3 center 5094.8,6049.1,-44.9 radius 2589.3
Opened peroxisome_makeup.mrc copy as #5, grid size 101,101,101, pixel 58.2,
shown at step 1, values float32
> volume #5 color #ff8ad8
> volume #5 color #ff8ad899
> volume erase #5 center 3395.4,4421.8,26.37 radius 2589.3
> volume erase #5 center 6224.5,5138.2,-1483.8 radius 2589.3
> volume erase #5 center 5977.2,6559.6,-1289.6 radius 2589.3
> volume all surfaceSmoothing true
> volume #5 smoothingFactor 0.8
> volume #5 smoothingIterations 90
> volume #5 smoothingIterations 30
> volume #5 color #ff8ad8
> volume erase #5 center 3528.3,6899.5,-2018.3 radius 2589.3
> volume erase #5 center 5231.7,6005.5,1964.7 radius 1604.7
> volume #5 smoothingIterations 20
> volume #1 step 1
> volume #1 step 2
> volume #1 step 4
> volume #5 smoothingIterations 10
> volume erase #5 center 3883.7,6238.5,1463.4 radius 1604.7
> volume erase #5 center 3106.5,6698.3,645.19 radius 1604.7
> close #3
> volume erase #5 center 4446.5,7763.2,1492.9 radius 725.96
> volume erase #5 center 5627.3,4210,1752.5 radius 720.08
> volume erase #5 center 6442.5,4722,1663.7 radius 781.8
> volume erase #5 center 6773.1,5412.9,2334.4 radius 429.11
> volume erase #5 center 6791,5886.4,1993.9 radius 429.11
> volume erase #5 center 6657.8,6388.5,1960.4 radius 429.11
> volume #5 smoothingIterations 30
> volume #5 smoothingIterations 5
> close #5
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup.mrc
Opened peroxisome_makeup.mrc as #3, grid size 101,101,101, pixel 58.2, shown
at level 1, step 1, values float32
> volume #3 level 0.1498
> volume #2 step 1
> volume #1 step 1
> volume all surfaceSmoothing true
> volume #3 smoothingIterations 10
> volume #3 smoothingFactor 0.8
> volume #3 color #ff8ad8
> volume erase #3 center 5230.2,6164.1,-255.72 radius 2745.1
Opened peroxisome_makeup.mrc copy as #5, grid size 101,101,101, pixel 58.2,
shown at step 1, values float32
> close #3
> volume #5 color #ff8ad8b3
> volume erase #5 center 5508.6,6625.9,-1147.4 radius 2745.1
Can only have one displayed volume when erasing
> volume erase #5 center 2559.7,4672.8,-1768.8 radius 2745.1
> volume erase #5 center 3954.1,7257.7,-2160.4 radius 2745.1
> volume erase #5 center 3591,4857.8,860.89 radius 1246.2
> volume erase #5 center 5610.7,6304,2016.7 radius 1246.2
> volume erase #5 center 4835.6,5667.3,1658.3 radius 1246.2
> volume erase #5 center 4570.9,6393.3,1415.1 radius 1246.2
> volume erase #5 center 4640.8,6837.3,1392.5 radius 1246.2
> volume erase #5 center 4371.9,6330.8,1443.4 radius 1246.2
> volume erase #5 center 3225.7,5244.9,766.84 radius 1246.2
> volume erase #5 center 3202.2,5971.2,260.65 radius 1111
> volume erase #5 center 2865.9,7076.7,-465.43 radius 1111
> volume erase #5 center 5269.8,7183.4,2549.4 radius 1111
> volume erase #5 center 6080.9,6198.4,1438.1 radius 1111
> volume #1 step 4
> volume #2 step 4
> volume #3 smoothingIterations 40
No volumes specified
> volume #5 smoothingIterations 40
> volume #5 color #ff8ad8
> volume erase #5 center 5859.1,3648.1,-914.52 radius 1404.9
> volume erase #5 center 4860.1,3428.7,-98.082 radius 1404.9
> volume erase #5 center 7366,4338.4,-1228.5 radius 1404.9
> volume erase #5 center 5399,4355.4,1691.7 radius 1404.9
> volume erase #5 center 6249.9,4478.7,1566.2 radius 1404.9
> volume erase #5 center 7409.6,4010.3,131.21 radius 1404.9
> volume erase #5 center 8439.2,4495.1,-298.99 radius 1404.9
> volume erase #5 center 8376.3,6675.6,-875.71 radius 1404.9
> volume #1 step 1
> volume #1 step 4
> volume erase #2 center 6254,6981.9,3078.2 radius 1402.5
Opened peroxisome_cleaned_half2.mrc copy as #3, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at step 1, values int8
> close #3
> volume erase #2 center 6576.2,7948,2138 radius 589.9
Opened peroxisome_cleaned_half2.mrc copy as #3, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at step 1, values int8
> close #3
> volume erase #2 center 6353,7675.4,1688.3 radius 583.86
Opened peroxisome_cleaned_half2.mrc copy as #3, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at step 1, values int8
> volume erase #3 center 6940.7,7195.1,2429.6 radius 583.9
> volume erase #3 center 6862,6336,2319.4 radius 583.9
> volume erase #3 center 6500,6503.8,1648.8 radius 577.84
> volume erase #5 center 6957.6,6140.4,2066.4 radius 243.95
> volume erase #3 center 6893.5,6446.6,1688.4 radius 240.77
> close #2
> volume erase #5 center 3968.9,7948.4,1485.2 radius 232.19
> volume erase #5 center 3773.4,7920.3,1114.6 radius 232.19
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup_final.mrc
> models #5
> volume erase #5 center 2626.4,6879.4,727.69 radius 226.31
> volume erase #5 center 4144.1,8126.9,1311.5 radius 226.31
> volume erase #5 center 4303.5,8026.5,1648.5 radius 226.31
> volume erase #1 center 4215.5,8386.3,1256.3 radius 222.71
Opened peroxisome_cleaned_half1.mrc copy as #2, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at step 1, values int8
> volume erase #5 center 3880.4,8247.7,1028.1 radius 214.55
> volume erase #5 center 4252.8,8398.8,1225.1 radius 208.68
> close #2
> volume erase #5 center 4771.7,8277.4,1517.6 radius 467.32
> volume erase #5 center 5386.8,8027.2,1614.4 radius 467.32
> volume erase #5 center 5923.7,7804.9,1714.6 radius 467.32
> close #5
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup_final.mrc
Opened peroxisome_makeup_final.mrc as #2, grid size 101,101,101, pixel 58.2,
shown at level 1, step 1, values float32
> volume #2 level 0.9391
> volume all surfaceSmoothing true
> volume #2 color #ff8ad8
> volume #2 smoothingIterations 40
> volume erase #2 center 2426.2,6692.8,782.64 radius 461.44
Opened peroxisome_makeup_final.mrc copy as #5, grid size 101,101,101, pixel
58.2, shown at step 1, values float32
> volume #3 step 4
> volume #3 step 1
> volume #1 step 1
> volume erase #5 center 4382.8,7964.4,1406.2 radius 461.44
> volume erase #5 center 4021.7,7791.5,1424.5 radius 461.44
> volume erase #5 center 4731.8,7866.3,2061.2 radius 461.44
> volume erase #5 center 4710.1,7924.8,2014.2 radius 461.44
> volume erase #1 center 6900.6,5496.3,1948.1 radius 457.46
Opened peroxisome_cleaned_half1.mrc copy as #6, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at step 1, values int8
> close #1
Can only have one displayed volume when erasing
> volume erase #2 center 4215.2,7922.4,1674.7 radius 288.03
Opened peroxisome_makeup_final.mrc copy as #1, grid size 101,101,101, pixel
58.2, shown at step 1, values float32
> close #2
> volume #2 smoothingIterations 20
No volumes specified
> volume #5 smoothingIterations 20
> volume #5 smoothingIterations 10
> close #6
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_cleaned_half1.mrc
Opened peroxisome_cleaned_half1.mrc as #2, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at level 0.0032, step 2, values int8
> volume #2 step 1
> volume #2 color #ff8ad8
> volume all surfaceSmoothing true
> volume #2 smoothingFactor 0.5
> volume #2 smoothingIterations 10
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_cleaned_half2.mrc
> models #3
> view orient
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_cleaned_half1.mrc
Opened peroxisome_cleaned_half1.mrc as #6, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at level 0.0032, step 2, values int8
> volume #6 step 1
> volume all surfaceSmoothing true
> volume #6 smoothingFactor 0.5
> volume #6 color #ff8ad8
> volume #6 smoothingIterations 10
> ui mousemode right select
> select #2
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,129.6,0,1,0,75.177,0,0,1,-5.9119
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.96944,0.2377,-0.060716,-1195.6,-0.23697,0.97133,0.019056,1432.4,0.063504,-0.0040856,0.99797,-296.48
> view matrix models
> #2,0.96299,0.19091,0.1903,-1165,-0.22116,0.96318,0.15289,1242,-0.1541,-0.18932,0.96975,2044.4
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.96299,0.19091,0.1903,-1071.7,-0.22116,0.96318,0.15289,1280.2,-0.1541,-0.18932,0.96975,2039
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.952,0.17137,0.25364,-966.36,-0.22249,0.95647,0.18885,1286.7,-0.21023,-0.23622,0.94869,2654
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.952,0.17137,0.25364,-1026.3,-0.22249,0.95647,0.18885,1282.8,-0.21023,-0.23622,0.94869,2658.9
> view matrix models
> #2,0.952,0.17137,0.25364,-1043.7,-0.22249,0.95647,0.18885,1302.4,-0.21023,-0.23622,0.94869,2645.3
> view matrix models
> #2,0.952,0.17137,0.25364,-1034.2,-0.22249,0.95647,0.18885,1265.2,-0.21023,-0.23622,0.94869,2628.9
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.94813,0.1682,0.26972,-1013.8,-0.21749,0.96209,0.16456,1233.1,-0.23182,-0.21469,0.94877,2596.8
> ui mousemode right select
> select #1
2 models selected
> select clear
> select #2
2 models selected
> select #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.94813,0.1682,0.26972,-1122.2,-0.21749,0.96209,0.16456,1101.1,-0.23182,-0.21469,0.94877,2611.7
> ui mousemode right select
> select clear
> select #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.94813,0.1682,0.26972,-883.63,-0.21749,0.96209,0.16456,1191.5,-0.23182,-0.21469,0.94877,2547.2
> ui mousemode right select
> select clear
> select #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.94813,0.1682,0.26972,-620.63,-0.21749,0.96209,0.16456,1299.2,-0.23182,-0.21469,0.94877,2467.2
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.94376,0.31051,0.11357,-1337.3,-0.31415,0.73503,0.60087,2735,0.1031,-0.60275,0.79124,3510.2
> view matrix models
> #2,0.7302,0.48544,0.48078,-1855.4,-0.61483,0.77377,0.15252,4545.4,-0.29797,-0.40697,0.86347,4161.6
> view matrix models
> #2,0.65849,0.57845,0.48144,-2103,-0.70863,0.69199,0.1378,5570.2,-0.25344,-0.4319,0.86558,4097.7
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.65849,0.57845,0.48144,-2713.1,-0.70863,0.69199,0.1378,5648.5,-0.25344,-0.4319,0.86558,4367.8
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.36126,0.90211,-0.23598,-2452.4,-0.92514,0.37841,0.0303,8919.9,0.11663,0.20737,0.97128,-1803.2
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.36126,0.90211,-0.23598,-3035.2,-0.92514,0.37841,0.0303,8571.2,0.11663,0.20737,0.97128,-1715.8
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.71479,0.35762,-0.60099,-809.22,-0.48362,0.87352,-0.055412,3217.3,0.50516,0.33026,0.79734,-4262
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.71479,0.35762,-0.60099,-713.98,-0.48362,0.87352,-0.055412,3055.5,0.50516,0.33026,0.79734,-4364.4
> view matrix models
> #2,0.71479,0.35762,-0.60099,-696.41,-0.48362,0.87352,-0.055412,3163.7,0.50516,0.33026,0.79734,-4383
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.71479,0.35762,-0.60099,-611.66,-0.48362,0.87352,-0.055412,2953,0.50516,0.33026,0.79734,-4151.6
> view matrix models
> #2,0.71479,0.35762,-0.60099,-777.97,-0.48362,0.87352,-0.055412,3070.7,0.50516,0.33026,0.79734,-4176.2
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.75196,0.65439,-0.079535,-3543.9,-0.64808,0.71181,-0.27077,5219.7,-0.12058,0.25516,0.95935,-733.34
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.75196,0.65439,-0.079535,-3549.6,-0.64808,0.71181,-0.27077,4920.8,-0.12058,0.25516,0.95935,-1088.1
> view matrix models
> #2,0.75196,0.65439,-0.079535,-3486,-0.64808,0.71181,-0.27077,5005.3,-0.12058,0.25516,0.95935,-1041.8
> ui mousemode right select
> select clear
Drag select of 8 peroxisome_cleaned_half1.mrc
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.75196,0.65439,-0.079535,-3624,-0.64808,0.71181,-0.27077,6311.4,-0.12058,0.25516,0.95935,-166.74,#6,1,0,0,-137.97,0,1,0,1306,0,0,1,875.09
> undo
> ui mousemode right select
> select #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.75196,0.65439,-0.079535,-888.83,-0.64808,0.71181,-0.27077,6979.4,-0.12058,0.25516,0.95935,-503.42
> close #2
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_cleaned_half1.mrc
Opened peroxisome_cleaned_half1.mrc as #2, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at level 0.0032, step 2, values int8
> volume #2 color #ff8ad8
> volume #2 step 1
> volume all surfaceSmoothing true
> volume #6 smoothingIterations 10
> volume #6 smoothingFactor 0.5
> volume #2 smoothingFactor 0.5
> volume #2 smoothingIterations 10
> ui mousemode right select
> select #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,483.85,0,1,0,-359.4,0,0,1,17.308
> undo
> view matrix models #6,1,0,0,0.37864,0,1,0,2.4894,0,0,1,0.23218
> ui mousemode right select
> select #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,917.68,0,1,0,-715.84,0,0,1,-298.21
> view matrix models #6,1,0,0,142.54,0,1,0,672.52,0,0,1,-307.83
> view matrix models #6,1,0,0,228.46,0,1,0,566.45,0,0,1,-311.34
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.96128,0.052314,0.27056,-250.15,-0.19125,0.83353,0.51832,1982,-0.19841,-0.54999,0.81126,4513.6
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.96128,0.052314,0.27056,204.37,-0.19125,0.83353,0.51832,2312.1,-0.19841,-0.54999,0.81126,4409.8
> view matrix models
> #6,0.96128,0.052314,0.27056,97.755,-0.19125,0.83353,0.51832,2224.3,-0.19841,-0.54999,0.81126,4435.2
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.93851,0.20419,0.27839,-789.82,-0.31884,0.82193,0.47199,2999.3,-0.13244,-0.53173,0.8365,3952.7
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.93851,0.20419,0.27839,-812.94,-0.31884,0.82193,0.47199,3011.5,-0.13244,-0.53173,0.8365,3955.2
> view matrix models
> #6,0.93851,0.20419,0.27839,-930.8,-0.31884,0.82193,0.47199,2658.3,-0.13244,-0.53173,0.8365,4133.6
> view matrix models
> #6,0.93851,0.20419,0.27839,-941.55,-0.31884,0.82193,0.47199,2593,-0.13244,-0.53173,0.8365,4143.4
> view matrix models
> #6,0.93851,0.20419,0.27839,-1392.8,-0.31884,0.82193,0.47199,2023.5,-0.13244,-0.53173,0.8365,4344.6
> view matrix models
> #6,0.93851,0.20419,0.27839,-1860.8,-0.31884,0.82193,0.47199,1713,-0.13244,-0.53173,0.8365,4526.7
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.50193,0.70662,-0.49876,-1993.5,-0.86295,0.44792,-0.23384,7762.3,0.058171,0.54777,0.8346,-3485.9
> view matrix models
> #6,0.8443,0.52987,-0.07991,-3075.8,-0.53461,0.8431,-0.058033,3310.8,0.036622,0.091718,0.99511,-593.59
> view matrix models
> #6,0.95299,0.083061,-0.29141,-443.54,-0.0042247,0.96525,0.26131,-549.55,0.30299,-0.24779,0.92022,375.95
> view matrix models
> #6,0.41705,0.88288,0.21588,-3594.1,-0.90796,0.41541,0.055153,7847.1,-0.040984,-0.21901,0.97486,1852.8
> ui mousemode right select
> select clear
> select #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.41705,0.88288,0.21588,-5084.6,-0.90796,0.41541,0.055153,8611.3,-0.040984,-0.21901,0.97486,1774.1
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.90837,0.25885,-0.32841,-2812.9,-0.18164,0.95166,0.24767,1213.4,0.37665,-0.16533,0.91148,-601.9
> ui mousemode right select
Drag select of 6 peroxisome_cleaned_half1.mrc
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.90837,0.25885,-0.32841,-753.12,-0.18164,0.95166,0.24767,1091.8,0.37665,-0.16533,0.91148,-119
> view matrix models
> #6,0.90837,0.25885,-0.32841,-793.28,-0.18164,0.95166,0.24767,1123.5,0.37665,-0.16533,0.91148,-116.58
> view matrix models
> #6,0.90837,0.25885,-0.32841,-800.09,-0.18164,0.95166,0.24767,1082.9,0.37665,-0.16533,0.91148,-129.17
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.94962,0.221,-0.22223,-890.54,-0.19241,0.9708,0.14324,1140,0.24739,-0.093266,0.96442,-14.194
> view matrix models
> #6,0.9496,0.22664,-0.21654,-934.31,-0.1805,0.96015,0.2134,1063.7,0.25628,-0.16356,0.95266,414.92
> view matrix models
> #6,0.94983,0.23201,-0.20975,-978.86,-0.17683,0.9515,0.25174,1054.7,0.25798,-0.20202,0.94479,667.33
> ui mousemode right select
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right select
> select #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.94983,0.23201,-0.20975,-927.95,-0.17683,0.9515,0.25174,979.15,0.25798,-0.20202,0.94479,664.26
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.98413,0.082447,0.15716,-572.92,-0.12974,0.93846,0.32009,743.48,-0.1211,-0.33539,0.93426,3457.6
> view matrix models
> #6,0.98507,0.086412,0.14893,-593.48,-0.13288,0.93158,0.33838,781.86,-0.1095,-0.35311,0.92915,3521.2
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.98507,0.086412,0.14893,-226.56,-0.13288,0.93158,0.33838,947.1,-0.1095,-0.35311,0.92915,3528.6
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.97254,0.023516,0.23155,146.3,-0.083797,0.96354,0.2541,594.41,-0.21713,-0.26653,0.93905,3492.5
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.97254,0.023516,0.23155,243.44,-0.083797,0.96354,0.2541,506.55,-0.21713,-0.26653,0.93905,3373.5
> view matrix models
> #6,0.97254,0.023516,0.23155,235.44,-0.083797,0.96354,0.2541,525.21,-0.21713,-0.26653,0.93905,3374
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.91794,0.099072,0.38414,-170.52,-0.15033,0.98297,0.10572,915.14,-0.36712,-0.15479,0.9172,3425.7
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.91794,0.099072,0.38414,-71.484,-0.15033,0.98297,0.10572,689.2,-0.36712,-0.15479,0.9172,3403.9
> view matrix models
> #6,0.91794,0.099072,0.38414,-234.8,-0.15033,0.98297,0.10572,764.91,-0.36712,-0.15479,0.9172,2927.3
> view matrix models
> #6,0.91794,0.099072,0.38414,-247.23,-0.15033,0.98297,0.10572,739.99,-0.36712,-0.15479,0.9172,2937
> ui mousemode right select
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right select
> select #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.91794,0.099072,0.38414,-336.92,-0.15033,0.98297,0.10572,760.42,-0.36712,-0.15479,0.9172,2990.1
> view matrix models
> #6,0.91794,0.099072,0.38414,-313.56,-0.15033,0.98297,0.10572,791.86,-0.36712,-0.15479,0.9172,2979
> view matrix models
> #6,0.91794,0.099072,0.38414,-301.72,-0.15033,0.98297,0.10572,787.08,-0.36712,-0.15479,0.9172,2967.8
> view matrix models
> #6,0.91794,0.099072,0.38414,-292.68,-0.15033,0.98297,0.10572,784.41,-0.36712,-0.15479,0.9172,2961.5
> ui mousemode right select
> select clear
> ui mousemode right select
> select #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.91794,0.099072,0.38414,-248.62,-0.15033,0.98297,0.10572,710.46,-0.36712,-0.15479,0.9172,2926.1
> ui mousemode right select
> select clear
> ui mousemode right select
> select #6
2 models selected
> close #6
> ui mousemode right select
> select #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,3.1302,0,1,0,-73.19,0,0,1,-25.3
> view matrix models #2,1,0,0,-17.905,0,1,0,-82.097,0,0,1,-24.606
> ui mousemode right select
> select clear
> view orient
> close #5
> view orient
> select #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-9.7986,0,1,0,-102.62,0,0,1,-24.606
> ui mousemode right select
> select clear
> undo
[Repeated 1 time(s)]
> select clear
> undo
[Repeated 2 time(s)]
> select clear
> select #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,4.1127,0,1,0,-12.338,0,0,1,0
> undo
> ui mousemode right select
> select #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-13.793,0,1,0,-90.323,0,0,1,-24.606
> ui mousemode right select
> select clear
> volume #2 step 4
> volume #2 step 2
> ui tool show "Map Filter"
> ui tool show "Map Eraser"
Can only have one displayed volume when erasing
> volume erase #1 center 2870.7,6617.9,290.2 radius 896.43
> volume erase #1 center 2724.4,6903.8,542.09 radius 896.43
> volume erase #1 center 3261.8,7280.4,373.6 radius 890.55
> view orient
[Repeated 1 time(s)]
> close #1
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/peroxisome_makeup_final.mrc
Opened peroxisome_makeup_final.mrc as #1, grid size 101,101,101, pixel 58.2,
shown at level 1, step 1, values float32
> volume #1 level 0.8798
> volume all surfaceSmoothing true
> volume #2 smoothingIterations 10
> volume #2 smoothingFactor 0.5
> volume #1 smoothingFactor 0.5
> volume #1 smoothingIterations 10
> volume #1 color #ff8ad8
> volume #1 smoothingIterations 30
> view orient
> ui tool show "Map Eraser"
> volume erase #1 center 2840.9,6142.9,392.61 radius 896.43
Opened peroxisome_makeup_final.mrc copy as #5, grid size 101,101,101, pixel
58.2, shown at step 1, values float32
> volume erase #5 center 4150.4,7882,1721.8 radius 199.86
> view orient
[Repeated 1 time(s)]
> volume #2 step 4
> volume #2 step 1
> volume #2 step 2
> view orient
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/002.cxs
\u2014\u2014\u2014 End of log from Sat Oct 5 18:55:48 2024 \u2014\u2014\u2014
opened ChimeraX session
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/cargo_loaded_1.mrc
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/CE.mrc
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/ER_and_vesicle.mrc
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/thylakoids.mrc
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/vacuole.mrc
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/vacuole2_makeup.mrc
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/vacuole2.mrc
Opened cargo_loaded_1.mrc as #4.1, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at level 0.0016, step 2, values int8
Opened CE.mrc as #4.2, grid size 682,960,200, pixel 12.5,12.5,12.5, shown at
level 0.0015, step 2, values int8
Opened ER_and_vesicle.mrc as #4.3, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at level 32, step 2, values int8
Opened thylakoids.mrc as #4.4, grid size 682,960,200, pixel 12.5,12.5,12.5,
shown at level 54, step 2, values int8
Opened vacuole.mrc as #4.5, grid size 682,960,200, pixel 12.5,12.5,12.5, shown
at level 0.0003, step 2, values int8
Opened vacuole2_makeup.mrc as #4.6, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at level 0.0001, step 2, values int8
Opened vacuole2.mrc as #4.7, grid size 682,960,200, pixel 12.5,12.5,12.5,
shown at level 0.0019, step 2, values int8
> lighting simple
> view orient
> volume #4.1 step 1
> volume #4.2 step 1
> volume #4.5 step 1
> volume #4.6 step 1
> volume #4.4 step 1
> volume #4.4 level 14.5
> volume #4.7 step 1
> volume #4.3 step 1
> volume #4.3 level 0.7
> ui mousemode right select
Drag select of 4.1 cargo_loaded_1.mrc , 4.3 ER_and_vesicle.mrc
[Repeated 1 time(s)]
> select clear
> select #4.1
2 models selected
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/isonet_denoised_tomos/Chlamy_v8a3_002_rec_corrected.mrc
Opened Chlamy_v8a3_002_rec_corrected.mrc as #6, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at level 0.115, step 2, values float32
> volume #6 step 1
> volume #6 style image region 0,0,99,681,959,99 step 1 showOutlineBox true
> volume #6 level -0.8714,0 level 0.1536,0.8 level 0.6769,1
[Repeated 1 time(s)]
> volume #6 color #ffd4aa color white color #ffd4aa
> volume #6 color white color white color #ffd4aa
[Repeated 1 time(s)]
> view orient
> volume #6 transparency 0
> volume #6 level -2.034,0 level 0.1536,0.8 level 0.6769,1
> ui mousemode right "translate selected models"
> volume #6 level -2.034,0 level 0.1536,0.8 level 0.6769,1
> volume #6 color white color white color white
> view matrix models #4.1,1,0,0,1378.5,0,1,0,-467.8,0,0,1,0
> view matrix models #4.1,1,0,0,1409.9,0,1,0,-544.19,0,0,1,506.87
> view matrix models #4.1,1,0,0,1608.2,0,1,0,-302.37,0,0,1,549.36
> ui mousemode right "rotate selected models"
> view matrix models
> #4.1,0.60367,0.55241,-0.57483,-2454.3,0.23472,0.56592,0.79034,2605.6,0.7619,-0.61203,0.21197,6246.3
> view matrix models
> #4.1,0.44677,0.77844,-0.44094,-4643.1,0.83525,-0.18633,0.51734,9459,0.32055,-0.59943,-0.73344,8505.8
> view matrix models
> #4.1,0.50712,0.79539,-0.33194,-5120.9,0.86176,-0.47439,0.17982,12904,-0.014439,-0.37724,-0.926,7246.3
> ui mousemode right "translate selected models"
> view matrix models
> #4.1,0.50712,0.79539,-0.33194,-5113.2,0.86176,-0.47439,0.17982,12889,-0.014439,-0.37724,-0.926,7141.7
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/cargo_loaded_1.mrc
Opened cargo_loaded_1.mrc as #7, grid size 682,960,200, pixel 12.5,12.5,12.5,
shown at level 0.0016, step 2, values int8
> volume #7 step 1
> volume #7 color #c0bfe5
> volume #7 color #c0c0e5
> volume #7 color silver
> ui mousemode right select
> select #7
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,-345.71,0,1,0,-2746.2,0,0,1,4.1733
> view matrix models #7,1,0,0,-55.522,0,1,0,-4007.2,0,0,1,426.73
> view matrix models #7,1,0,0,527.56,0,1,0,-3141.1,0,0,1,678.32
> view matrix models #7,1,0,0,538.17,0,1,0,-3148,0,0,1,508.07
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.95849,-0.033456,0.28317,598.31,0.088135,0.97922,-0.18263,-2889.5,-0.27118,0.20001,0.94152,-859.66
> view orient
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/002.cxs
> volume #4.3 color #c0ffff
> volume #4.3 color #c0c0ff
> volume #4.3 color silver
> volume all surfaceSmoothing true
> close #1
> volume all smoothingIterations 10
> volume all smoothingFactor 0.8
> lighting soft
> volume all smoothingFactor 0.5
> volume #5 smoothingFactor 0.8
> volume #5 smoothingIterations 30
> volume #5 smoothingIterations 40
> volume #2 step 4
> volume #5 smoothingIterations 30
> view orient
> ui mousemode right select
> select clear
> volume #4.2 color #42ffb2
> volume #4.2 color #4242b2
> volume #4.2 color #424242
> volume #4.4 color #00b200
> volume #4.4 color #008f00
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/002.cxs
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> set bgColor white
> volume #4.5 color #ff40ff
> volume #4.5 color #00fdff
> volume #4.5 color #ff40ff
> volume #4.5 color #9437ff
> volume #4.5 color #d783ff
> volume #4.5 color #7a81ff
> volume #4.7 color #7a81ff
> volume #4.6 color #7a81ff
> select #4.6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4.6,1,0,0,983.35,0,1,0,252.63,0,0,1,0
> lighting simple
> ui mousemode right "rotate selected models"
> view matrix models
> #4.6,0.69687,0.70553,0.12886,-291.34,-0.71067,0.70347,-0.0083249,1846,-0.096525,-0.085778,0.99163,323.3
> ui mousemode right "translate selected models"
> view matrix models
> #4.6,0.69687,0.70553,0.12886,-326.8,-0.71067,0.70347,-0.0083249,2055,-0.096525,-0.085778,0.99163,323.3
> view matrix models
> #4.6,0.69687,0.70553,0.12886,-303.01,-0.71067,0.70347,-0.0083249,2005.7,-0.096525,-0.085778,0.99163,353.65
> ui mousemode right "rotate selected models"
> view matrix models
> #4.6,0.49406,0.84673,0.19737,-447.47,-0.84756,0.51965,-0.10769,2762.8,-0.19375,-0.11408,0.97439,578.32
> ui mousemode right "translate selected models"
> view matrix models
> #4.6,0.49406,0.84673,0.19737,-429.79,-0.84756,0.51965,-0.10769,2677.8,-0.19375,-0.11408,0.97439,467.92
> view matrix models
> #4.6,0.49406,0.84673,0.19737,-395.34,-0.84756,0.51965,-0.10769,2717.7,-0.19375,-0.11408,0.97439,448.56
> ui mousemode right "rotate selected models"
> view matrix models
> #4.6,0.49148,0.83008,0.26347,-487.88,-0.83755,0.53342,-0.11822,2696.6,-0.23867,-0.16256,0.9574,642.21
> ui mousemode right select
> select clear
> lighting soft
> lighting simple
> select #4.6
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4.6,0.51223,0.82413,0.24172,-461.42,-0.83881,0.54049,-0.065266,2579.8,-0.18444,-0.16933,0.96815,560.57
> volume #4.6 step 4
> ui mousemode right select
> select clear
> volume #4.6 step 2
> volume #4.7 step 2
> volume #4.7 step 1
> volume #4.7 step 2
> volume #4.7 step 4
> volume #4.7 step 2
> volume #4.7 step 1
> volume #4.6 step 4
> ui mousemode right select
> select #4.6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #4.6,0.51223,0.82413,0.24172,-477.22,-0.83881,0.54049,-0.065266,2572.3,-0.18444,-0.16933,0.96815,568.01
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> ui mousemode right select
> select clear
> view orient
> lighting soft
> volume #4.6 step 1
> select #4.6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #4.6,0.51223,0.82413,0.24172,-473.12,-0.83881,0.54049,-0.065266,2605.5,-0.18444,-0.16933,0.96815,556.62
> view matrix models
> #4.6,0.51223,0.82413,0.24172,-475.17,-0.83881,0.54049,-0.065266,2585.9,-0.18444,-0.16933,0.96815,563.31
> ui mousemode right "rotate selected models"
> view matrix models
> #4.6,0.50627,0.8228,0.25823,-496.77,-0.8438,0.53445,-0.048623,2572.3,-0.17802,-0.19328,0.96486,609.75
> lighting simple
> view matrix models
> #4.6,0.53296,0.81942,0.21097,-433.49,-0.83329,0.55158,-0.037249,2500.7,-0.14689,-0.15595,0.97678,467.66
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #4.6,0.53296,0.81942,0.21097,-419.24,-0.83329,0.55158,-0.037249,2504,-0.14689,-0.15595,0.97678,464.73
> ui mousemode right "rotate selected models"
> view matrix models
> #4.6,0.56746,0.8145,0.12076,-279.08,-0.81344,0.57728,-0.071237,2491.3,-0.12774,-0.057809,0.99012,212.47
> view orient
> ui mousemode right select
> select clear
> lighting soft
> ui tool show "Map Eraser"
> lighting simple
Can only have one displayed volume when erasing
> volume erase #4.7 center 2730.9,2195.2,2116.1 radius 270.86
Opened vacuole2.mrc copy as #9, grid size 682,960,200, pixel 12.5,12.5,12.5,
shown at step 1, values int8
> volume erase #4.6 center 3103.7,2402.8,1497.8 radius 270.86
Opened vacuole2_makeup.mrc copy as #10, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at step 1, values int8
> close #4.6
> close #4.7
> view orient
No map chosen to save
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/vacuole2.mrc
> models #9
> view orient
[Repeated 1 time(s)]
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/002.cxs
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/ribosomes/ribosome/Chlamy_v8a3_002_1_bin6.em
> format motl
> artiax clip off
Opened Particle list Chlamy_v8a3_002_1_bin6.em with 600 particles.
> artiax particles #1.2.1 originScaleFactor 12.54
> artiax view xy
> artiax hide axes
> ui mousemode right "delete picked particle"
> view orient
> open
> /Users/zhenhou/Desktop/projects/2023/Thylakoid/segmentation_thylakoid/80S/run_class001\u2014\u201480S.mrc
Opened run_class001\u2014\u201480S.mrc as #8, grid size 96,96,96, pixel 3.88, shown at
level 76.3, step 1, values float32
> artiax attach #8 toParticleList #1.2.1
Opened run_class001\u2014\u201480S.mrc as #1.2.1.1.1, grid size 96,96,96, pixel 3.88,
shown at level 76.3, step 1, values float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
> artiax particles #1.2.1 color 0,46,86,100
> artiax particles #1.2.1 surfaceLevel 29.82896354
> artiax hide markers
> artiax particles #1.2.1 surfaceLevel 45.4092802
> view orient
> artiax show markers
> artiax hide surfaces
> artiax particles #1.2.1 radius 140.33992248
> ui mousemode right "delete picked particle"
> view orient
> artiax hide markers
> artiax show surfaces
> lighting soft
> lighting simple
> artiax particles #1.2.1 surfaceLevel 32.3218142
> lighting soft
> view orient
> lighting simple
> hide #!1.2.1 models
> lighting soft
> ui tool show "Map Eraser"
> volume erase #10 center 2193.6,2174.8,1381.3 radius 463.48
> volume erase #10 center 2428.3,1943,1606.9 radius 463.48
> view orient
> volume erase #10 center 1806,2288.9,2222.4 radius 198.63
> view orient
> volume #10 step 2
> volume erase #10 center 3063.5,2128.3,1973.4 radius 192.61
> volume erase #10 center 3107.5,2171.7,1964.7 radius 192.61
> volume erase #10 center 3090.1,2145.3,1969.1 radius 192.61
> volume erase #10 center 3081.8,2151.1,1969.3 radius 192.61
> volume erase #10 center 3047.4,2159.2,1946 radius 192.61
> lighting simple
> view orient
> show #!1.2.1 models
> artiax clip off
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/original_tomograms/Chlamy_v8a3_002_rec.mrc
Opened Chlamy_v8a3_002_rec.mrc as #8, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at level 31.9, step 2, values float32
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.1 models
> volume #8 step 1
> volume #8 level -95.05
> volume #8 level -78.71
> volume #8 level -29.3
> volume #8 step 2
> volume #8 level 10.57
> volume #8 level 41.62
> volume #8 level 0.7
> volume #8 level 10
> ui tool show "Map Eraser"
> volume erase #8 center 6006.7,4263.6,-12.54 radius 493.01 outside true
Opened Chlamy_v8a3_002_rec.mrc copy as #12, grid size 682,960,200, pixel
12.5,12.5,12.5, shown at step 1, values float32
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/ROS2.mrc
> models #12
> close #12
> close #8
> view orient
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/ROS2.mrc
Opened ROS2.mrc as #8, grid size 682,960,200, pixel 12.5,12.5,12.5, shown at
level 0.0121, step 2, values float32
> artiax attach #8 toParticleList #1.2.2
Opened ROS2.mrc as #1.2.2.1.1, grid size 682,960,200, pixel 12.5,12.5,12.5,
shown at level 0.0121, step 2, values float32
> volume #1.2.2.1.1 capFaces false
> artiax show #1.2.2 surfaces
> ui mousemode right "mark plane"
> marker #1.2.2.3 position 4469,7184,601.9 color #f0a3ff radius 12.54
> artiax particles #1.2.2 surfaceLevel -9.87216645
> marker #1.2.2.3 position 4820,6570,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 3947,6655,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5272,7264,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4247,7700,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 3810,7393,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 3431,6337,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4183,5839,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4815,5772,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5520,6370,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5822,7203,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5100,7735,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5755,8308,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4908,8380,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 6538,7765,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 6569,6974,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 6174,6228,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 6865,6160,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 7242,7152,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 6002,5486,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5379,5274,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 6041,4593,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4691,4882,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 3999,5124,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5472,5812,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5169,4183,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4437,4155,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5333,4691,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 6526,5022,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 6571,5615,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 6092,6708,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4233,6548,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 3442,5620,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5838,3923,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5780,4046,601.9 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4605,6198,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4521,6761,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 3941,7017,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 3759,6562,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 3839,5596,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4517,7268,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4150,7825,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4981,7727,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5719,7586,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5222,6958,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5341,6098,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4690,5162,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4606,5722,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4650,4962,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 4854,4381,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5440,3827,1053 color #f0a3ff radius 12.54
> marker #1.2.2.3 position 5650,4154,1053 color #f0a3ff radius 12.54
> marker #1.2.1.3 position 4556,7304,865.3 color #f0a3ff radius 12.54
> ui mousemode right "mark plane"
> marker #1.2.1.3 position 4982,7069,865.3 color #f0a3ff radius 12.54
> artiax show axes
Traceback (most recent call last):
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/tool.py", line 496, in _close_partlist
artia.close_partlist(artia.selected_partlist)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/ArtiaX.py", line 461, in close_partlist
self.partlists.get(identifier).delete()
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/ParticleList.py", line 1128, in delete
Model.delete(self)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 112, in delete
models.close([self]) # Remove from open models list.
^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 987, in close
m.delete()
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/ParticleList.py", line 1123, in delete
self.collection_model.delete()
^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/ParticleList.py", line 179, in
collection_model
self._collection_model.colors = self.particle_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 297, in
scm_set_colors
Drawing.set_color(self, rgba[0, :])
~~~~^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 297, in
scm_set_colors
Drawing.set_color(self, rgba[0, :])
~~~~^^^^^^
See log for complete Python traceback.
> artiax clip off
> artiax particles #1.2.2 radius 0.1
> open
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/ROS2.mrc
Opened ROS2.mrc as #8, grid size 682,960,200, pixel 12.5,12.5,12.5, shown at
level 0.0121, step 2, values float32
> artiax attach #8 toParticleList #1.2.2
Opened ROS2.mrc as #1.2.2.1.1, grid size 682,960,200, pixel 12.5,12.5,12.5,
shown at level 0.0121, step 2, values float32
> volume #1.2.2.1.1 capFaces false
> artiax show #1.2.2 surfaces
> marker #1.2.2.3 position 4464,7063,865.3 color #f0a3ff radius 4
> artiax particles #1.2.2 surfaceLevel -12.90794778
> marker #1.2.2.3 position 3801,6532,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 3843,7222,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 4422,8046,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 5335,7710,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 5139,8352,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 5143,8239,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 6132,7914,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 6558,7459,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 7100,7039,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 6354,6450,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 5853,7038,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 4846,6313,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 5397,6556,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 5159,7191,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 5703,5930,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 5204,5568,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 4602,5381,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 4893,4521,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 6114,5173,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 5679,5069,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 4205,5795,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 4077,4917,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 5312,4124,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 6110,4401,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 6983,5873,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 6417,5843,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 6674,5088,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 7333,6472,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 7423,5314,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 3620,5632,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 4245,4202,865.3 color #f0a3ff radius 4
> marker #1.2.2.3 position 5134,6170,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 5337,4541,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 4632,5032,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 4475,5876,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 4298,6721,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 5285,7404,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 4806,7638,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 4272,7508,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 5627,6978,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 5128,6754,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 5948,6289,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 6336,6905,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 5922,7705,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 6901,6258,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 6202,5607,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 5484,5523,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 6199,4717,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 4201,5349,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 3808,6272,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 4671,4447,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 5288,3934,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 3778,4744,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 4077,4183,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 4610,3854,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 3482,5433,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 5828,4313,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 6025,5687,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 4788,5703,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 4736,7094,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 3692,6922,1317 color #f0a3ff radius 4
> marker #1.2.2.3 position 5194,7800,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 5303,7671,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 6068,7207,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 5763,5884,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 5492,6407,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 4576,6215,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 5119,6619,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 4754,7199,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 3992,6902,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 3895,5805,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 4780,5138,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 5116,5679,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 5841,5012,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 6702,5908,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 6545,6459,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 6591,5757,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 6459,5135,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 6314,5309,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 6073,6729,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 5491,7182,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 3991,6389,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 4189,5303,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 4347,4743,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 5069,4488,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 5399,5317,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 5591,4521,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 3938,5373,1743 color #f0a3ff radius 4
> marker #1.2.2.3 position 3431,5135,288.4 color #f0a3ff radius 4
> marker #1.2.2.3 position 3184,5868,288.4 color #f0a3ff radius 4
> marker #1.2.2.3 position 3853,7718,288.4 color #f0a3ff radius 4
> artiax particles #1.2.2 color 94,64,100,100
> artiax particles #1.2.2 color 100,80,60,100
> ui mousemode right select
> select clear
Drag select of axes, 1 of 87 instances, surfaces, 1 of 87 instances, 3
peroxisome_cleaned_half2.mrc , 1 atoms
Drag select of 3 peroxisome_cleaned_half2.mrc
> select clear
Drag select of axes, 1 of 87 instances, surfaces, 1 of 87 instances, 5
peroxisome_makeup_final.mrc copy , 1 atoms
> select #1.2.2.2
1 model selected
Drag select of axes, 1 of 87 instances, surfaces, 1 of 87 instances, 1 atoms
> select clear
Drag select of axes, 1 of 86 instances, surfaces, 1 of 86 instances, 1 atoms
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select clear
Drag select of axes, 1 of 85 instances, surfaces, 1 of 85 instances, 1 atoms
> ui mousemode right "translate selected particles"
> view orient
> ui mousemode right "rotate selected particles"
> ui mousemode right select
Drag select of axes, 1 of 85 instances, surfaces, 1 of 85 instances, 1 atoms
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select clear
[Repeated 1 time(s)]Drag select of axes, 1 of 85 instances, surfaces, 1 of 85
instances, 1 atoms
> ui mousemode right "rotate selected particles"
> ui mousemode right select
Drag select of axes, 3 of 85 instances, surfaces, 3 of 85 instances, 3 atoms
> ui mousemode right "rotate selected particles"
> ui mousemode right select
Drag select of axes, 1 of 85 instances, surfaces, 1 of 85 instances, 1 atoms
> ui mousemode right "rotate selected particles"
> ui mousemode right select
Drag select of 5 peroxisome_makeup_final.mrc copy
Drag select of axes, 1 of 85 instances, surfaces, 1 of 85 instances, 1 atoms
[Repeated 1 time(s)]
> ui mousemode right "rotate selected particles"
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select clear
Drag select of axes, 1 of 85 instances, surfaces, 1 of 85 instances, 1 atoms
Drag select of axes, 2 of 85 instances, surfaces, 2 of 85 instances, 2 atoms
> ui mousemode right "rotate selected particles"
> ui mousemode right select
Drag select of axes, 1 of 85 instances, surfaces, 1 of 85 instances, 1 atoms
> ui mousemode right "rotate selected particles"
> ui mousemode right select
Drag select of axes, 1 of 85 instances, surfaces, 1 of 85 instances, 1 atoms
Drag select of axes, 4 of 85 instances, surfaces, 4 of 85 instances, 5
peroxisome_makeup_final.mrc copy , 4 atoms
Drag select of axes, 5 of 85 instances, surfaces, 5 of 85 instances, 5 atoms
> ui mousemode right "rotate selected particles"
> ui mousemode right select
Drag select of axes, 1 of 85 instances, surfaces, 1 of 85 instances, 1 atoms
[Repeated 3 time(s)]
> ui mousemode right "rotate selected particles"
> ui mousemode right select
Drag select of axes, 1 of 85 instances, surfaces, 1 of 85 instances, 1 atoms
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select clear
Drag select of axes, 1 of 85 instances, surfaces, 1 of 85 instances, 1 atoms
> ui mousemode right "rotate selected particles"
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select clear
Drag select of axes, 2 of 85 instances, surfaces, 2 of 85 instances, 2 atoms
> ui mousemode right "translate selected particles"
> ui mousemode right "mark point"
> marker #1.2.2.3 position 4598,5276,-203.1 color #ffcc99 radius 0.1
> ui mousemode right "translate selected particles"
> ui mousemode right select
Drag select of 4.2 CE.mrc , 4.4 thylakoids.mrc , axes, 2 of 86 instances,
surfaces, 2 of 86 instances, 5 peroxisome_makeup_final.mrc copy , 2 atoms
Drag select of axes, 1 of 86 instances, surfaces, 1 of 86 instances, 1 atoms
[Repeated 1 time(s)]
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> ui mousemode right select
Drag select of 4.3 ER_and_vesicle.mrc , axes, 1 of 86 instances, surfaces, 1
of 86 instances, 1 atoms, 10 vacuole2_makeup.mrc copy
Drag select of 10 vacuole2_makeup.mrc copy
> select clear
[Repeated 1 time(s)]Drag select of axes, 1 of 86 instances, surfaces, 1 of 86
instances, 1 atoms
> ui mousemode right "translate selected particles"
> view orient
> ui mousemode right select
> select clear
[Repeated 1 time(s)]Drag select of axes, 1 of 86 instances, surfaces, 1 of 86
instances, 1 atoms
[Repeated 1 time(s)]
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select clear
> view orient
> artiax particles #1.2.2 color 100,64,2,100
> lighting soft
> ui mousemode right "mark plane"
> lighting simple
> marker #1.2.2.3 position 4766,5751,1831 color #ffa405 radius 0.1
> marker #1.2.2.3 position 5112,5682,1831 color #ffa405 radius 0.1
> marker #1.2.2.3 position 4839,5084,1831 color #ffa405 radius 0.1
> ui mousemode right select
> select clear
> lighting soft
> view orient
> artiax particles #1.2.2 color 100,80,60,100
> artiax particles #1.2.2 color 100,100,50,100
[Repeated 1 time(s)]
> artiax particles #1.2.2 color 98,85,54,100
[Repeated 1 time(s)]
> show #!1.2.1 models
> artiax hide axes
> artiax hide markers
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/ROS2.em
> partlist #1.2.2
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/Ribosomes.em
> partlist #1.2.1
> lighting simple
> ui mousemode right "mark plane"
> marker #1.2.1.3 position 3106,4793,1693 color #0075dc radius 140.3
> marker #1.2.1.3 position 3807,4243,1693 color #0075dc radius 140.3
> marker #1.2.1.3 position 3070,3853,1693 color #0075dc radius 140.3
> marker #1.2.1.3 position 3467,3653,1693 color #0075dc radius 140.3
> marker #1.2.1.3 position 5629,3896,1693 color #0075dc radius 140.3
> marker #1.2.1.3 position 3392,4657,1517 color #0075dc radius 140.3
> marker #1.2.1.3 position 3338,4937,1517 color #0075dc radius 140.3
> marker #1.2.1.3 position 2956,4516,1517 color #0075dc radius 140.3
> ui mousemode right "rotate selected particles"
> ui mousemode right select
Drag select of surfaces, 1 of 521 instances
> ui mousemode right "rotate selected particles"
> ui mousemode right select
Drag select of surfaces, 1 of 521 instances
> ui mousemode right "rotate selected particles"
> ui mousemode right select
Drag select of surfaces, 1 of 521 instances
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #6
3 models selected
> view orient
> ui mousemode right "mark plane"
> marker #1.2.1.3 position 2839,4695,526.7 color #0075dc radius 140.3
> ui mousemode right "rotate selected particles"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 42, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/mouse.py", line 86, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 620, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
^^^^^^^^^^^^^^^^^^
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 402, in
masked_bounds
spos = self.child_positions.masked(mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 739, in masked
p = Places(place_array=self.array()[mask])
~~~~~~~~~~~~^^^^^^
See log for complete Python traceback.
> ui mousemode right select
Drag select of surfaces, 1 of 522 instances
[Repeated 1 time(s)]
> view orient
Drag select of surfaces, 1 of 522 instances
> ui mousemode right "rotate selected particles"
> ui mousemode right select
Drag select of surfaces, 1 of 522 instances
> ui mousemode right "rotate selected particles"
> view orient
> ui mousemode right select
> select clear
> lighting soft
> lighting simple
> view orient
> lighting soft
> save /Users/zhenhou/Desktop/image1.png supersample 3
> lighting simple
> lighting soft
> save /Users/zhenhou/Desktop/image2.png supersample 3
> lighting simple
> view orient
> save
> /Users/zhenhou/Desktop/projects/2024/autophagy/segmentation/segmented_volumes/002/002.cxs
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac
Model Identifier: Mac14,7
Model Number: Z16S000PAB/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6 (23G80)
Kernel Version: Darwin 23.6.0
Time since boot: 67 days, 5 hours, 23 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
annotated-types: 0.7.0
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.4.5
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
geomdl: 5.3.1
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
pandas: 2.2.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pyarrow: 15.0.0
pycollada: 0.7.2
pydantic: 2.8.2
pydantic-core: 2.20.1
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
starfile: 0.5.6
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 13 months ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ArtiaX: arrays used as indices must be of integer (or boolean) type |
comment:2 by , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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