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Opened 3 days ago
#19263 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Linux-4.18.0-513.24.1.el8_9.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/spuser/Downloads/cryosparc_P12_J680_009_volume_map_sharp.mrc
Opened cryosparc_P12_J680_009_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.0406, step 2, values float32
> set bgColor white
> ui tool show "Hide Dust"
> surface dust #1 size 6.48
> volume #1 level 0.07713
> volume #1 step 1
> volume #1 level 0.1574
> open /home/spuser/Downloads/cryosparc_P12_J668_008_volume_map.mrc
Opened cryosparc_P12_J668_008_volume_map.mrc as #2, grid size 280,280,280,
pixel 1.08, shown at level 0.0135, step 2, values float32
> volume #2 color #729fcf
> volume #2 level 0.07802
> volume #2 step 1
> volume #1 level 0.1835
> volume #2 level 0.05336
> close
> open /home/spuser/Downloads/cryosparc_P12_J564_003_volume_map_sharp(1).mrc
Opened cryosparc_P12_J564_003_volume_map_sharp(1).mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.0158, step 2, values float32
> surface dust #1 size 6.48
> surface dust #1 size 115.75
> volume #1 level 0.0186
> volume gaussian #1 sDev 2
Opened cryosparc_P12_J564_003_volume_map_sharp(1).mrc gaussian as #2, grid
size 280,280,280, pixel 1.08, shown at step 1, values float32
> volume #2 color #729fcf
> volume #2 level 0.004575
> surface dust #2 size 6.48
> surface dust #2 size 124.03
> ui tool show "Segment Map"
Segmenting cryosparc_P12_J564_003_volume_map_sharp(1).mrc gaussian, density
threshold 0.004575
Showing 39 region surfaces
248 watershed regions, grouped to 39 regions
Showing cryosparc_P12_J564_003_volume_map_sharp(1) gaussian.seg - 39 regions,
39 surfaces
> select #3.14
1 model selected
> select add #3.13
2 models selected
> select add #3.24
3 models selected
> select add #3.28
4 models selected
> select add #3.22
5 models selected
> select subtract #3.22
4 models selected
Deleted 4 regions
> select add #3.15
1 model selected
> select add #3.20
2 models selected
> select add #3.17
3 models selected
> select add #3.16
4 models selected
> select add #3.36
5 models selected
> select add #3.29
6 models selected
> select add #3.21
7 models selected
Deleted 7 regions
> select add #3.25
1 model selected
> select add #3.7
2 models selected
Deleted 2 regions
Drag select of 336, 360
Deleted 2 regions
> select #3.32
1 model selected
> select add #3.31
2 models selected
> select add #3.34
3 models selected
> select subtract #3.34
2 models selected
> select add #3.34
3 models selected
> select add #3.19
4 models selected
Deleted 4 regions
> select #3.37
1 model selected
Deleted 1 regions
> select #3.23
1 model selected
Deleted 1 regions
> select #3.1
1 model selected
> select #3.2
1 model selected
> select #3.22
1 model selected
Deleted 1 regions
> select #3.18
1 model selected
> select add #3.26
2 models selected
Deleted 2 regions
> select #3.2
1 model selected
> hide #!2 models
> select #3.30
1 model selected
Deleted 1 regions
> select #3.6
1 model selected
> select #3.4
1 model selected
> select add #3.2
2 models selected
> select add #3.8
3 models selected
> select add #3.5
4 models selected
> select add #3.6
5 models selected
> select subtract #3.8
4 models selected
> select add #3.9
5 models selected
> select add #3.10
6 models selected
> select add #3.11
7 models selected
> select add #3.1
8 models selected
> select add #3.12
9 models selected
> select #3.1
1 model selected
> select #3.1
1 model selected
Ungrouped to 5 regions
> select #3.4
1 model selected
> select add #3.2
2 models selected
Drag select of 366, 362, 26389 of 29000 triangles, 331, 354, 355, 343, 25,
303, 83, 255, 367, 236, 365, 99, 346, 358, 181, 315
> select subtract #3.3
17 models selected
> select subtract #3.13
16 models selected
Saving 16 regions to mrc file...
Opened T2-removal.mrc as #4, grid size 78,115,116, pixel 1.08, shown at step
1, values float32
Wrote T2-removal.mrc
> select #3.3
1 model selected
> select add #3.13
2 models selected
Drag select of 366, 362, 26440 of 29000 triangles, 331, 354, 355, 343, 25,
303, 83, 255, 367, 236, 365, 99, 346, 358, 181, 315, 4 T2-removal.mrc
> select subtract #3.4
19 models selected
> select subtract #3.2
18 models selected
Saving 16 regions to mrc file...
Opened B2-removal as #5, grid size 75,109,119, pixel 1.08, shown at step 1,
values float32
Wrote B2-removal
> volume resample #4 onGrid #1
Opened T2-removal.mrc resampled as #6, grid size 280,280,280, pixel 1.08,
shown at step 1, values float32
> volume resample #5 onGrid #1
Opened B2-removal resampled as #7, grid size 280,280,280, pixel 1.08, shown at
step 1, values float32
> save /home/spuser/J564-T2-rm.mrc models #6
> save /home/spuser/J564-B2-rm.mrc models #7
> open /home/spuser/Downloads/cryosparc_P12_J685_001_volume_map_sharp.mrc
Opened cryosparc_P12_J685_001_volume_map_sharp.mrc as #8, grid size
280,280,280, pixel 1.08, shown at level 0.0257, step 2, values float32
> hide #!7 models
> hide #!8 models
> show #!8 models
> hide #!3 models
> select subtract #4
16 models selected
> surface dust #2 size 131.44
> volume #2 level 0.01037
> volume #8 level 0.09402
> hide #!6 models
> volume #8 level 0.1222
> volume #8 level 0.1297
> close #8
> open /home/spuser/Downloads/cryosparc_P12_J686_002_volume_map_sharp.mrc
Opened cryosparc_P12_J686_002_volume_map_sharp.mrc as #8, grid size
280,280,280, pixel 1.08, shown at level 0.0402, step 2, values float32
> volume #8 level 0.09057
> volume #8 color #729fcf
> volume #8 level 0.122
> volume #8 level 0.09476
> volume #8 step 1
> volume #8 level 0.09698
> surface dust #8 size 6.48
> surface dust #8 size 62.03
> volume #8 level 0.128
> volume #8 level 0.1413
> volume #8 level 0.1258
> close #8
> close #7
> close #6
> close #5
> close #4
> open /home/spuser/Downloads/cryosparc_P12_J689_001_volume_map_sharp.mrc
Opened cryosparc_P12_J689_001_volume_map_sharp.mrc as #4, grid size
280,280,280, pixel 1.08, shown at level 0.0289, step 2, values float32
> surface dust #4 size 6.48
> surface dust #4 size 25.6
> volume #4 level 0.06124
> volume #4 step 1
> volume #4 level 0.1415
> volume #4 level 0.1068
> volume #4 level 0.1451
> volume #4 level 0.125
> close #4
> open /home/spuser/Downloads/cryosparc_P12_J686_003_volume_map_sharp.mrc
Opened cryosparc_P12_J686_003_volume_map_sharp.mrc as #4, grid size
280,280,280, pixel 1.08, shown at level 0.0518, step 2, values float32
> surface dust #4 size 6.48
> volume #4 color #729fcf
> volume #4 step 1
> surface dust #4 size 37.26
> surface dust #4 size 64.57
> volume #4 level 0.1304
> volume #4 level 0.1362
> close #4
> open /home/spuser/Downloads/cryosparc_P12_J694_007_volume_map_sharp.mrc
Opened cryosparc_P12_J694_007_volume_map_sharp.mrc as #4, grid size
280,280,280, pixel 1.08, shown at level 0.169, step 2, values float32
> surface dust #4 size 6.48
> volume #4 step 1
> surface dust #4 size 6.48
> surface dust #4 size 23.93
> volume #4 level 0.231
> volume #4 level 0.3085
> volume #4 level 0.2465
> close #4
> open /home/spuser/Downloads/cryosparc_P12_J689_011_volume_map_sharp.mrc
Opened cryosparc_P12_J689_011_volume_map_sharp.mrc as #4, grid size
280,280,280, pixel 1.08, shown at level 0.1, step 2, values float32
> surface dust #4 size 6.48
> volume #4 color #729fcf
> volume #4 step 1
> surface dust #4 size 51.41
> volume #4 level 0.1898
[Repeated 1 time(s)]
> open /home/spuser/Downloads/cryosparc_P12_J694_007_volume_map_sharp.mrc
Opened cryosparc_P12_J694_007_volume_map_sharp.mrc as #5, grid size
280,280,280, pixel 1.08, shown at level 0.169, step 2, values float32
> close #5
> open /home/spuser/Downloads/cryosparc_P12_J694_007_volume_map_sharp.mrc
Opened cryosparc_P12_J694_007_volume_map_sharp.mrc as #5, grid size
280,280,280, pixel 1.08, shown at level 0.169, step 2, values float32
> surface dust #5 size 6.48
> volume #4 level 0.167
> volume #5 level 0.1558
> close #5
> open /home/spuser/Downloads/cryosparc_P12_J685_003_volume_map_sharp.mrc
Opened cryosparc_P12_J685_003_volume_map_sharp.mrc as #5, grid size
280,280,280, pixel 1.08, shown at level 0.0559, step 2, values float32
> surface dust #5 size 6.48
> surface dust #5 size 21.8
> close #5
> show #!3 models
> hide #!3 models
> open /home/spuser/Downloads/cryosparc_P12_J694_007_volume_map_sharp.mrc
Opened cryosparc_P12_J694_007_volume_map_sharp.mrc as #5, grid size
280,280,280, pixel 1.08, shown at level 0.169, step 2, values float32
> volume #5 step 1
> surface dust #5 size 6.48
[Repeated 1 time(s)]
> surface dust #5 size 22.99
> volume #5 level 0.2482
> volume #5 level 0.2007
> volume #5 color #e9b96e
> volume #5 color #888a85
> volume #5 level 0.1215
> surface dust #5 size 30.08
> volume #5 level 0.2
> volume #5 level 0.12
> volume #4 level 0.13
> volume #4 level 0.075
> volume #5 level 0.075
> surface dust #5 size 44.96
> surface dust #5 size 45.27
> surface dust #5 size 45.59
> volume #5 level 0.09
> volume #5 level 0.08
> surface dust #5 size 63.73
> surface dust #5 size 7
> surface dust #5 size 70
[Repeated 1 time(s)]
> surface dust #5 size 7
> surface dust #5 size 72
> surface dust #5 size 725
> surface dust #5 size 75
> surface dust #5 size 8
> 0
Unknown command: 0
> surface dust #5 size 80
[Repeated 1 time(s)]
> volume #5 step 2
> surface dust #5 size 59.6
> surface dust #5 size 41.5
> volume #5 step 4
> surface dust #5 size 43.19
> volume #5 step 2
> surface dust #5 size 29.28
> surface dust #5 size 20.65
> surface dust #5 size 15.17
[Repeated 2 time(s)]
> surface dust #5 size 15.06
> surface dust #5 size 14.96
> volume #5 step 1
> surface dust #5 size 7
> surface dust #5 size 75
[Repeated 1 time(s)]
> close #4-5
> open /home/spuser/Downloads/cryosparc_P12_J690_013_volume_map.mrc
> /home/spuser/Downloads/cryosparc_P12_J689_012_volume_map.mrc
Opened cryosparc_P12_J690_013_volume_map.mrc as #4.1, grid size 280,280,280,
pixel 1.08, shown at level 0.0254, step 2, values float32
Opened cryosparc_P12_J689_012_volume_map.mrc as #4.2, grid size 280,280,280,
pixel 1.08, shown at level 0.0218, step 2, values float32
> surface dust #4.1 size 6.48
> surface dust #4.2 size 6.48
> volume #4.2 level 0.008879
> volume #4.2 level 0.03482
> volume #4.2 level 0.004556
> volume #4.2 level 0.0132
> volume #4.1 level 0.02536
> surface dust #4.2 size 77.92
> surface dust #4.1 size 26.65
> surface dust #4.1 size 22.99
> surface dust #4.1 size 20.11
> volume #4.2 level 0.0132
> volume #4.2 step 1
> volume #4.1 step 1
> surface dust #4.1 size 28.11
> volume #4.1 color #ad7fa8
> volume #4.2 color #729fcf
> volume #4.2 level 0.04552
> volume #4.2 level 0.04014
> volume #4.2 level 0.0132
> volume #4.2 level 0.01859
> surface dust #4.1 size 12.74
> volume #4.2 level 0.03475
> volume #4.2 level -0.002958
> volume #4.2 level 0.02936
> volume #4.2 level 0.02398
> volume #4.2 level 0.0132
> surface dust #4.1 size 7.25
> volume #4.2 step 2
> volume #4.2 level 0.0132
> surface dust #4.1 size 3.29
> volume #4.2 level 0.01752
> volume #4.2 level -0.004089
> volume #4.2 level 0.004556
> close #1
> close #2
> close #3
> close #4.1
> surface dust #4.2 size 18.8
[Repeated 1 time(s)]
> volume #4.2 level 0.0025
> volume #4.2 level 0.006
> volume #4.2 level 0.0075
> volume #4.2 level 0.0085
> volume #4.2 level 0.0095
> volume #4.2 level 0.0105
> volume #4.2 level 0.05
> volume #4.2 level 0.122
> volume #4.2 step 1
> volume #4.2 level 0.1536
> volume #4.2 level 0.09031
> volume #4.2 level 0.1483
> volume #4.2 level 0.1061
> close
> open /home/spuser/Downloads/cryosparc_P12_J689_012_volume_map_sharp.mrc
Opened cryosparc_P12_J689_012_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.0708, step 2, values float32
> surface dust #1 size 6.48
> surface dust #1 size 9.36
> volume #1 step 1
> volume #1 color #729fcf
> volume #1 level 0.1604
> volume #1 level 0.2201
> volume #1 level 0.1504
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> lighting soft
> lighting full
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> close #1
> open /home/spuser/Downloads/cryosparc_P12_J668_008_volume_map_sharp(1).mrc
> /home/spuser/Downloads/cryosparc_P12_J680_009_volume_map_sharp(1).mrc
Opened cryosparc_P12_J668_008_volume_map_sharp(1).mrc as #1.1, grid size
280,280,280, pixel 1.08, shown at level 0.0766, step 2, values float32
Opened cryosparc_P12_J680_009_volume_map_sharp(1).mrc as #1.2, grid size
280,280,280, pixel 1.08, shown at level 0.0406, step 2, values float32
> surface dust #1.2 size 6.48
> surface dust #1.1 size 6.48
> volume #1.1 color #729fcf
> surface dust #1.1 size 9.49
> volume #1.1 step 1
> surface dust #1.1 size 16.44
> surface dust #1.1 size 24.92
> surface dust #1.1 size 32.59
> volume #1.1 level 0.085
> volume #1.1 level 0.095
> volume #1.1 level 0.105
> volume #1.1 level 0.125
> volume #1.1 level 0.2133
> volume #1.1 level 0.1881
> open /home/spuser/Downloads/B2-For-T157-coot-0(1).pdb
Chain information for B2-For-T157-coot-0(1).pdb #2
---
Chain | Description
A | No description available
> select add #2
3065 atoms, 3161 bonds, 396 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.28651,0.26992,0.91927,3.9725,0.53145,0.84312,-0.081928,-40.586,-0.79717,0.46507,-0.38501,258.07
> view matrix models
> #2,-0.27561,0.64064,0.71667,-16.114,0.61154,0.69208,-0.38347,13.854,-0.74166,0.33258,-0.58252,297.75
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.27561,0.64064,0.71667,-33.424,0.61154,0.69208,-0.38347,49.474,-0.74166,0.33258,-0.58252,300.64
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.069091,0.63906,0.76605,-69.332,0.71207,0.5694,-0.41078,55.912,-0.6987,0.5171,-0.49439,256.9
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.025848,0.63676,0.77063,-82.896,0.74098,0.50525,-0.44234,65.171,-0.67103,0.58245,-0.45877,239.02
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.025848,0.63676,0.77063,-90.162,0.74098,0.50525,-0.44234,67.923,-0.67103,0.58245,-0.45877,232.57
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.025848,0.63676,0.77063,-58.274,0.74098,0.50525,-0.44234,37.126,-0.67103,0.58245,-0.45877,250.19
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.27453,0.74047,0.61347,-82.813,0.58575,0.37717,-0.71739,117.18,-0.76258,0.55628,-0.33018,246.95
> view matrix models
> #2,0.1991,0.81478,0.54451,-71.789,0.52737,0.37924,-0.7603,131.49,-0.82598,0.43854,-0.35418,274.99
> volume #1.1 level 0.09976
> ui tool show "Fit in Map"
> fitmap #2 inMap #1.1
Fit molecule B2-For-T157-coot-0(1).pdb (#2) to map
cryosparc_P12_J668_008_volume_map_sharp(1).mrc (#1.1) using 3065 atoms
average map value = 0.06636, steps = 80
shifted from previous position = 2.12
rotated from previous position = 4.53 degrees
atoms outside contour = 2013, contour level = 0.099758
Position of B2-For-T157-coot-0(1).pdb (#2) relative to
cryosparc_P12_J668_008_volume_map_sharp(1).mrc (#1.1) coordinates:
Matrix rotation and translation
0.21292129 0.79362253 0.56993666 -75.89360319
0.58789197 0.36185029 -0.72349665 120.55624290
-0.78041499 0.48910903 -0.38951868 268.91439269
Axis 0.66388735 0.73930165 -0.11263507
Axis point 26.35975216 0.00000000 179.41104588
Rotation angle (degrees) 114.03995180
Shift along axis 8.45343596
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> view matrix models
> #2,-0.95266,-0.27748,0.12424,295.21,0.272,-0.96046,-0.059422,239.49,0.13582,-0.022815,0.99047,1.2941
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.95266,-0.27748,0.12424,265.34,0.272,-0.96046,-0.059422,270.64,0.13582,-0.022815,0.99047,-38.758
> view matrix models
> #2,-0.95266,-0.27748,0.12424,299.3,0.272,-0.96046,-0.059422,240.74,0.13582,-0.022815,0.99047,-7.7058
> view matrix models
> #2,-0.95266,-0.27748,0.12424,267.61,0.272,-0.96046,-0.059422,269.94,0.13582,-0.022815,0.99047,-35.919
> close #2
> volume #1.1 level 0.2059
> close #1.1-2
> open /home/spuser/Downloads/cryosparc_P12_J694_007_volume_map_sharp.mrc
Opened cryosparc_P12_J694_007_volume_map_sharp.mrc as #2, grid size
280,280,280, pixel 1.08, shown at level 0.169, step 2, values float32
> surface dust #2 size 6.48
> close #2
> open /home/spuser/Downloads/cryosparc_P12_J696_007_volume_map_sharp.mrc
Opened cryosparc_P12_J696_007_volume_map_sharp.mrc as #2, grid size
280,280,280, pixel 1.08, shown at level 0.152, step 2, values float32
> surface dust #2 size 6.48
> volume #2 step 1
> volume #2 color #729fcf
> volume #2 level 0.2015
> volume #2 level -0.04441
> volume #2 level 0.03757
> volume #2 level 0.1031
> volume #2 level 0.1523
> volume #2 level 0.07036
> volume #2 level 0.01
> volume #2 level 0.06
> volume #2 level 0.02
> volume #2 level 0.001
> volume #2 level 0.1
> surface dust #2 size 21.99
> volume #2 level 0.12
> open /home/spuser/Downloads/7_real_space_refined_010-coot-0.pdb
Chain information for 7_real_space_refined_010-coot-0.pdb #3
---
Chain | Description
A | No description available
> select add #3
3065 atoms, 3161 bonds, 396 residues, 1 model selected
> view matrix models #3,1,0,0,-22.523,0,1,0,45.123,0,0,1,-15.275
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.33117,-0.79483,0.50851,101.25,0.66431,0.57912,0.47256,-55.364,-0.67009,0.18131,0.7198,90.596
> view matrix models
> #3,0.066354,-0.92523,0.37356,172.28,0.62941,0.32932,0.70384,-49.994,-0.77424,0.18842,0.6042,119.54
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.066354,-0.92523,0.37356,207.19,0.62941,0.32932,0.70384,-93.67,-0.77424,0.18842,0.6042,160.95
> view matrix models
> #3,0.066354,-0.92523,0.37356,206.23,0.62941,0.32932,0.70384,-91.916,-0.77424,0.18842,0.6042,161.07
> view matrix models
> #3,0.066354,-0.92523,0.37356,186,0.62941,0.32932,0.70384,-66.209,-0.77424,0.18842,0.6042,138.98
> view matrix models
> #3,0.066354,-0.92523,0.37356,210.71,0.62941,0.32932,0.70384,-89.326,-0.77424,0.18842,0.6042,161.23
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.21913,0.88704,-0.40637,63.484,-0.67307,0.43896,0.59523,88.39,0.70637,0.14308,0.69323,-46.284
> view matrix models
> #3,-0.1017,0.92101,-0.37604,98.617,-0.67753,0.21266,0.70409,103.23,0.72843,0.32638,0.60238,-60.45
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.1017,0.92101,-0.37604,98.228,-0.67753,0.21266,0.70409,101.94,0.72843,0.32638,0.60238,-62.548
> open /home/spuser/Downloads/cryosparc_P12_J564_003_volume_map_sharp.mrc
Opened cryosparc_P12_J564_003_volume_map_sharp.mrc as #4, grid size
280,280,280, pixel 1.08, shown at level 0.0158, step 2, values float32
> volume #4 color #729fcf
> select subtract #3
Nothing selected
> select add #4
2 models selected
> view matrix models #4,1,0,0,-1.5795,0,1,0,-5.7209,0,0,1,-7.3251
> view matrix models #4,1,0,0,-58.722,0,1,0,-25.227,0,0,1,16.641
> surface dust #4 size 6.48
> volume #4 level 0.04485
> view matrix models #4,1,0,0,7.595,0,1,0,-11.081,0,0,1,1.271
> view matrix models #4,1,0,0,-75.858,0,1,0,5.3959,0,0,1,-8.2263
> view matrix models #4,1,0,0,-9.9666,0,1,0,-9.3441,0,0,1,5.571
> view matrix models #4,1,0,0,-81.336,0,1,0,-15.45,0,0,1,9.7988
> select add #3
3065 atoms, 3161 bonds, 396 residues, 3 models selected
> select subtract #4
3065 atoms, 3161 bonds, 396 residues, 1 model selected
> view matrix models
> #3,-0.1017,0.92101,-0.37604,18.125,-0.67753,0.21266,0.70409,97.488,0.72843,0.32638,0.60238,-55.943
> view matrix models
> #3,-0.1017,0.92101,-0.37604,19.336,-0.67753,0.21266,0.70409,101.8,0.72843,0.32638,0.60238,-45.716
> ui tool show "Fit in Map"
> fitmap #3 inMap #2
Fit molecule 7_real_space_refined_010-coot-0.pdb (#3) to map
cryosparc_P12_J696_007_volume_map_sharp.mrc (#2) using 3065 atoms
average map value = 0.00168, steps = 80
shifted from previous position = 2.03
rotated from previous position = 1.21 degrees
atoms outside contour = 3038, contour level = 0.12
Position of 7_real_space_refined_010-coot-0.pdb (#3) relative to
cryosparc_P12_J696_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.11632154 0.92122865 -0.37122376 18.68298714
-0.66547773 0.20516692 0.71766700 98.96087689
0.73729823 0.33052128 0.58919182 -45.33182308
Axis -0.19613091 -0.56158551 -0.80383728
Axis point 60.42980911 57.80093272 0.00000000
Rotation angle (degrees) 99.26386490
Shift along axis -22.79989628
> view matrix models
> #3,-0.11632,0.92123,-0.37122,18.7,-0.66548,0.20517,0.71767,95.85,0.7373,0.33052,0.58919,-48.014
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.46173,0.88101,-0.10308,-91.116,-0.54423,0.37314,0.75139,53.255,0.70044,-0.29084,0.65176,28.167
> fitmap #3 inMap #2
Fit molecule 7_real_space_refined_010-coot-0.pdb (#3) to map
cryosparc_P12_J696_007_volume_map_sharp.mrc (#2) using 3065 atoms
average map value = 0.001147, steps = 76
shifted from previous position = 2.34
rotated from previous position = 3.4 degrees
atoms outside contour = 3047, contour level = 0.12
Position of 7_real_space_refined_010-coot-0.pdb (#3) relative to
cryosparc_P12_J696_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.51308981 0.85264601 -0.09865916 -94.88077268
-0.52153092 0.40098266 0.75313904 47.80869781
0.68172160 -0.33497416 0.65042138 38.38345708
Axis -0.56711446 -0.40672718 -0.71620821
Axis point -15.41829399 97.90216418 0.00000000
Rotation angle (degrees) 73.60564594
Shift along axis 6.87261410
> close #4
> close #3
> close #2
> open /home/spuser/Downloads/cryosparc_P12_J564_003_volume_map_sharp(1).mrc
Opened cryosparc_P12_J564_003_volume_map_sharp(1).mrc as #2, grid size
280,280,280, pixel 1.08, shown at level 0.0158, step 2, values float32
> surface dust #2 size 6.48
> surface dust #2 size 31.48
[Repeated 1 time(s)]
> surface dust #2 size 108.02
> volume gaussian #1 sDev 2
[Repeated 1 time(s)]
> volume gaussian #2 sDev 2
Opened cryosparc_P12_J564_003_volume_map_sharp(1).mrc gaussian as #3, grid
size 280,280,280, pixel 1.08, shown at step 1, values float32
> volume #3 color #729fcf
> volume #3 level 0.00484
> surface dust #3 size 6.48
> surface dust #3 size 94.48
> surface dust #3 size 111.13
> volume #3 level 0.00484
> ui tool show "Segment Map"
Select a density map in the Segment map field
Segmenting cryosparc_P12_J564_003_volume_map_sharp(1).mrc gaussian, density
threshold 0.004840
Showing 39 region surfaces
242 watershed regions, grouped to 39 regions
Showing cryosparc_P12_J564_003_volume_map_sharp(1) gaussian.seg - 39 regions,
39 surfaces
> volume #3 level 0.006442
> hide #1 models
> hide #!3 models
> select #4.22
1 model selected
> select add #4.16
2 models selected
> select add #4.28
3 models selected
> select add #4.24
4 models selected
> select add #4.13
5 models selected
Deleted 5 regions
> select add #4.27
1 model selected
Deleted 1 regions
> select #4.14
1 model selected
Deleted 1 regions
> select #4.15
1 model selected
Deleted 1 regions
> select #4.20
1 model selected
Deleted 1 regions
> select #4.17
1 model selected
Deleted 1 regions
> select #4.7
1 model selected
Drag select of 339, 331, 334, 332, 353, 348
Deleted 6 regions
> select #4.3
1 model selected
> select #4.21
1 model selected
Deleted 1 regions
> select #4.23
1 model selected
Deleted 1 regions
> select #4.38
1 model selected
> select #4.31
1 model selected
Deleted 1 regions
> select #4.2
1 model selected
> select #4.25
1 model selected
Deleted 1 regions
> select #4.2
1 model selected
Ungrouped to 5 regions
> select #4.14
1 model selected
Deleted 1 regions
> select #4.18
1 model selected
Deleted 1 regions
> select #4.1
1 model selected
> select #4.30
1 model selected
Deleted 1 regions
> select #4.1
1 model selected
Ungrouped to 5 regions
> select #4.14
1 model selected
Deleted 1 regions
> select #4.16
1 model selected
Deleted 1 regions
> select #4.19
1 model selected
Deleted 1 regions
> select #4.33
1 model selected
Deleted 1 regions
> select #4.32
1 model selected
Deleted 1 regions
Drag select of 354, 124 of 28896 triangles
> select add #4.20
2 models selected
> select add #4.17
3 models selected
> select add #4.11
4 models selected
> select add #4.12
5 models selected
> select add #4.10
6 models selected
> select add #4.9
7 models selected
> select subtract #4.10
6 models selected
> select add #4.10
7 models selected
Saving 7 regions to mrc file...
Opened J564-B2-full as #5, grid size 59,109,95, pixel 1.08, shown at step 1,
values float32
Wrote J564-B2-full
> hide #!5 models
Drag select of 323, 347, 326, 16448 of 17392 triangles, 330, 65, 15, 349, 18
Saving 8 regions to mrc file...
Opened J564-B2-full-rem as #6, grid size 76,107,78, pixel 1.08, shown at step
1, values float32
Wrote J564-B2-full-rem
Showing 19 region surfaces
> select #4.3
1 model selected
> select add #4.20
2 models selected
Drag select of 350, 186 of 45532 triangles
> select add #4.17
2 models selected
> select clear
> select #4.4
1 model selected
> select #4.13
1 model selected
Saving 1 regions to mrc file...
Opened J564-T2-full as #7, grid size 47,49,58, pixel 1.08, shown at step 1,
values float32
Wrote J564-T2-full
> hide #!6 models
> hide #!4 models
> volume #7 level 0.04243
> close #7
> show #!4 models
> select #4.4
1 model selected
> select add #4.13
2 models selected
Saving 2 regions to mrc file...
Opened J564-T2-full as #7, grid size 52,73,74, pixel 1.08, shown at step 1,
values float32
Wrote J564-T2-full
> hide #!7 models
Drag select of 354, 347, 326, 330, 25, 319, 79, 258, 346, 230, 65, 15, 18,
106, 97, 182, 350
> select subtract #4.15
16 models selected
> select subtract #4.7
15 models selected
> select subtract #4.39
14 models selected
> select subtract #4.38
13 models selected
Saving 13 regions to mrc file...
Opened J564-T2-full-rem as #8, grid size 75,109,119, pixel 1.08, shown at step
1, values float32
Wrote J564-T2-full-rem
> hide #!4 models
> show #!5 models
> hide #!8 models
> volume #5 level 0.003905
> hide #!5 models
> show #!6 models
> volume #6 level 0.006115
> hide #!6 models
> show #!7 models
> volume #7 level 0.00905
> hide #!7 models
> show #!8 models
> volume #8 level 0.01014
> volume resample #5 onGrid #1
[Repeated 2 time(s)]
> volume resample #5 onGrid #2
Opened J564-B2-full resampled as #9, grid size 280,280,280, pixel 1.08, shown
at step 1, values float32
> volume resample #6 onGrid #2
Opened J564-B2-full-rem resampled as #10, grid size 280,280,280, pixel 1.08,
shown at step 1, values float32
> volume resample #7 onGrid #2
Opened J564-T2-full resampled as #11, grid size 280,280,280, pixel 1.08, shown
at step 1, values float32
> volume resample #8 onGrid #2
Opened J564-T2-full-rem resampled as #12, grid size 280,280,280, pixel 1.08,
shown at step 1, values float32
> save /home/spuser/Downloads/J564-B2-full.mrc models #9
> save /home/spuser/Downloads/J564-B2-full-rem.mrc models #10
> save /home/spuser/Downloads/J564-T2-full.mrc models #11
> save /home/spuser/Downloads/J564-T2-full-rem.mrc models #12
> close
> open /home/spuser/Downloads/cryosparc_P12_J721_004_volume_map_sharp.mrc
Opened cryosparc_P12_J721_004_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.161, step 2, values float32
> surface dust #1 size 6.48
> volume #1 step 1
> volume #1 color #729fcf
> surface dust #1 size 13.2
> volume #1 level 0.1997
[Repeated 1 time(s)]
> volume #1 step 2
> volume #1 level 0.06433
> volume #1 level 0.09965
> volume #1 level 0.1526
> volume #1 step 1
> surface dust #1 size 25.27
> volume #1 level 0.19
> volume #1 level 0.25
> volume #1 level 0.2175
> volume #1 style mesh
> volume #1 level 0.1915
> volume #1 style surface
> close #1
> open /home/spuser/Downloads/cryosparc_P12_J721_006_volume_map_sharp.mrc
Opened cryosparc_P12_J721_006_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.214, step 2, values float32
> surface dust #1 size 6.48
> volume #1 step 1
> volume #1 color #729fcf
> surface dust #1 size 15.97
> volume #1 level 0.2
> volume #1 level 0.25
> volume #1 style mesh
> volume #1 style surface
> lighting simple
> lighting soft
> lighting full
> lighting soft
> close #1
> open /home/spuser/Downloads/cryosparc_P12_J728_002_volume_map_sharp.mrc
Opened cryosparc_P12_J728_002_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.0522, step 2, values float32
> lighting simple
> lighting shadows true
> lighting shadows false
> surface dust #1 size 6.48
> surface dust #1 size 6.53
> volume #1 level 0.09753
> volume #1 step 1
> volume #1 level 0.1216
> volume #1 color #729fcf
> volume #1 level 0.1628
> volume #1 level 0.1147
> open /home/spuser/Downloads/fold_4_B2_only_573.pdb
Chain information for fold_4_B2_only_573.pdb #2
---
Chain | Description
A | No description available
> select add #2
3065 atoms, 3154 bonds, 396 residues, 1 model selected
> view matrix models
> #2,-0.98805,0.097848,0.11911,235.1,0.09965,0.99498,0.0092521,-14.011,-0.11761,0.021011,-0.99284,306.41
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.98805,0.097848,0.11911,247.13,0.09965,0.99498,0.0092521,-21.769,-0.11761,0.021011,-0.99284,320.02
> view matrix models
> #2,-0.98805,0.097848,0.11911,223.76,0.09965,0.99498,0.0092521,-0.89026,-0.11761,0.021011,-0.99284,296.51
> view matrix models
> #2,-0.98805,0.097848,0.11911,244.55,0.09965,0.99498,0.0092521,-18.556,-0.11761,0.021011,-0.99284,322.07
> view matrix models
> #2,-0.98805,0.097848,0.11911,244.54,0.09965,0.99498,0.0092521,-19.754,-0.11761,0.021011,-0.99284,321.31
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.88993,-0.32232,-0.3227,118.97,0.29729,-0.12664,0.94635,-20.204,-0.3459,-0.93812,-0.016872,348.54
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.88993,-0.32232,-0.3227,120.91,0.29729,-0.12664,0.94635,-22.522,-0.3459,-0.93812,-0.016872,350.52
> volume #1
[Repeated 1 time(s)]
> volume list
Expected a density maps specifier or a keyword
> open list
'list' has no suffix
> volume #1 info
Expected a keyword
> volume settings #1
Settings for map cryosparc_P12_J728_002_volume_map_sharp.mrc
grid size = 280 280 280
region = 0 0 0 to 279 279 279
step = 1 1 1
voxel size = 1.08 1.08 1.08
origin = 0 0 0
origin index = 0 0 0
surface levels = 0.1147
surface colors = #729fcf
image levels =
image colors =
image brightness factor = 1
image transparency depth = 0.5
backingColor = None
blendOnGpu = False
btCorrection = False
capFaces = True
colorMode = auto8
colormapOnGpu = False
colormapSize = 2048
dimTransparency = True
dimTransparentVoxels = True
flipNormals = False
imageMode = full region
limitVoxelCount = True
lineThickness = 1.0
linearInterpolation = True
maximumIntensityProjection = False
meshLighting = True
minimalTextureMemory = False
orthoplanePositions = (0, 0, 0)
orthoplanesShown = (False, False, False)
outlineBoxLinewidth = 1.0
outlineBoxRgb = (100.0, 100.0, 100.0)
planeSpacing = min
projectionMode = auto
showOutlineBox = False
smoothLines = False
smoothingFactor = 0.3
smoothingIterations = 2
squareMesh = True
subdivideSurface = False
subdivisionLevels = 1
surfaceSmoothing = False
tiltedSlabAxis = (0, 0, 1)
tiltedSlabOffset = 0
tiltedSlabPlaneCount = 1
tiltedSlabSpacing = 1
twoSidedLighting = True
voxelLimit = 21.1444091796875
> fitmap #2 #1 search 1000
Missing required "in_map" argument
> fitmap #2 inMap #1 search 1000
Found 494 unique fits from 1000 random placements having fraction of points
inside contour >= 0.100 (509 of 1000).
Average map values and times found:
0.06297 (1), 0.06006 (1), 0.06005 (1), 0.05974 (1), 0.05965 (1), 0.05908 (2),
0.05895 (1), 0.05785 (2), 0.05784 (1), 0.05695 (1), 0.05674 (1), 0.05648 (1),
0.05643 (1), 0.05611 (1), 0.056 (1), 0.05585 (1), 0.05582 (1), 0.05525 (1),
0.05495 (1), 0.05469 (1), 0.05462 (1), 0.05453 (1), 0.05447 (1), 0.05428 (3),
0.05427 (1), 0.05422 (1), 0.05419 (1), 0.05414 (1), 0.05406 (5), 0.05397 (2),
0.05392 (1), 0.05386 (1), 0.05375 (1), 0.05373 (1), 0.05367 (1), 0.05367 (1),
0.05359 (1), 0.05339 (1), 0.05322 (1), 0.05314 (1), 0.05306 (1), 0.05305 (1),
0.05295 (1), 0.05293 (1), 0.0529 (1), 0.05269 (1), 0.05252 (1), 0.05235 (1),
0.05213 (1), 0.05199 (1), 0.05177 (2), 0.05169 (1), 0.05168 (1), 0.05168 (1),
0.05165 (1), 0.05161 (1), 0.05156 (1), 0.05132 (1), 0.0512 (1), 0.05116 (1),
0.05113 (1), 0.0511 (1), 0.05087 (1), 0.05083 (2), 0.05081 (1), 0.05078 (1),
0.05078 (1), 0.05069 (1), 0.05068 (1), 0.05062 (3), 0.05053 (1), 0.05043 (1),
0.05043 (1), 0.05043 (1), 0.05043 (1), 0.05042 (1), 0.05026 (1), 0.05026 (1),
0.05021 (1), 0.05017 (1), 0.05002 (1), 0.05 (1), 0.04997 (1), 0.04995 (1),
0.04986 (2), 0.04986 (1), 0.0496 (1), 0.0496 (1), 0.04951 (1), 0.04945 (2),
0.04941 (1), 0.04941 (1), 0.04933 (1), 0.04917 (1), 0.04915 (1), 0.0491 (1),
0.04907 (1), 0.04899 (1), 0.04888 (1), 0.04881 (1), 0.04871 (1), 0.04869 (1),
0.04863 (1), 0.04835 (1), 0.04831 (1), 0.04828 (1), 0.04818 (1), 0.04817 (1),
0.04814 (1), 0.04813 (1), 0.04805 (1), 0.04792 (1), 0.04792 (1), 0.04783 (1),
0.04778 (1), 0.04777 (1), 0.04774 (1), 0.04772 (1), 0.04767 (1), 0.04766 (1),
0.04764 (1), 0.04761 (1), 0.04758 (1), 0.04758 (1), 0.04755 (1), 0.04751 (1),
0.0475 (1), 0.04747 (1), 0.04741 (1), 0.04728 (1), 0.04714 (1), 0.04704 (1),
0.04695 (1), 0.04691 (1), 0.04685 (1), 0.04679 (1), 0.04669 (1), 0.04665 (1),
0.04662 (1), 0.04657 (1), 0.04657 (1), 0.04656 (1), 0.04652 (1), 0.04643 (1),
0.04641 (1), 0.04641 (1), 0.04638 (1), 0.04638 (1), 0.04634 (1), 0.04627 (1),
0.04625 (1), 0.04621 (1), 0.04618 (1), 0.04617 (1), 0.04613 (1), 0.04608 (1),
0.04606 (1), 0.04605 (1), 0.04597 (1), 0.04588 (1), 0.04587 (1), 0.0457 (1),
0.04567 (1), 0.04566 (1), 0.04566 (1), 0.04556 (1), 0.04553 (1), 0.04548 (1),
0.04534 (1), 0.04532 (1), 0.04532 (1), 0.04532 (1), 0.04526 (1), 0.04525 (1),
0.04523 (1), 0.0452 (1), 0.04511 (1), 0.04505 (1), 0.04483 (1), 0.04475 (1),
0.04475 (1), 0.04466 (1), 0.0446 (1), 0.04459 (1), 0.04458 (1), 0.04438 (1),
0.04433 (1), 0.04427 (1), 0.04424 (1), 0.04418 (1), 0.04414 (1), 0.04401 (1),
0.04399 (1), 0.04393 (1), 0.04391 (1), 0.0439 (1), 0.04389 (1), 0.04375 (1),
0.0437 (1), 0.04357 (1), 0.04355 (1), 0.04353 (1), 0.04353 (1), 0.04325 (1),
0.04317 (1), 0.04316 (1), 0.043 (1), 0.04296 (1), 0.04296 (1), 0.04285 (1),
0.04284 (1), 0.04284 (1), 0.04283 (1), 0.0428 (1), 0.04272 (1), 0.04271 (1),
0.04271 (1), 0.04263 (1), 0.04262 (1), 0.04255 (1), 0.04253 (1), 0.04251 (1),
0.04251 (1), 0.04247 (1), 0.04235 (1), 0.04231 (1), 0.0423 (1), 0.04205 (1),
0.04202 (1), 0.04198 (1), 0.04196 (1), 0.0419 (1), 0.04186 (1), 0.04184 (1),
0.04184 (1), 0.0418 (1), 0.04149 (1), 0.0411 (1), 0.04108 (1), 0.04107 (1),
0.04092 (1), 0.04091 (1), 0.04088 (1), 0.04087 (1), 0.04085 (1), 0.04078 (1),
0.04077 (1), 0.04074 (1), 0.0407 (1), 0.04063 (1), 0.04043 (1), 0.04042 (1),
0.0403 (1), 0.04019 (1), 0.04002 (1), 0.03997 (1), 0.03996 (1), 0.03977 (1),
0.03975 (1), 0.03946 (1), 0.03942 (1), 0.03934 (1), 0.03924 (1), 0.03898 (1),
0.0389 (1), 0.03881 (1), 0.03855 (1), 0.03851 (1), 0.03848 (1), 0.03844 (1),
0.03842 (1), 0.03841 (1), 0.0384 (1), 0.03839 (1), 0.03838 (1), 0.03835 (1),
0.03826 (1), 0.0382 (1), 0.03817 (1), 0.03808 (1), 0.03799 (1), 0.03796 (1),
0.03792 (1), 0.03791 (1), 0.03783 (1), 0.03773 (1), 0.03772 (1), 0.03764 (1),
0.03755 (1), 0.03747 (1), 0.03743 (1), 0.03743 (1), 0.03741 (1), 0.0373 (1),
0.03727 (1), 0.03726 (1), 0.03695 (1), 0.03693 (1), 0.03693 (1), 0.03687 (1),
0.03685 (1), 0.03683 (1), 0.03678 (1), 0.03663 (1), 0.03663 (1), 0.0366 (1),
0.0365 (1), 0.03631 (1), 0.03619 (1), 0.03612 (1), 0.03601 (1), 0.03598 (1),
0.03563 (1), 0.0356 (1), 0.03543 (1), 0.03539 (1), 0.03535 (1), 0.03532 (1),
0.0353 (1), 0.03525 (1), 0.03522 (1), 0.03516 (1), 0.03499 (1), 0.03491 (1),
0.03487 (1), 0.03486 (1), 0.03475 (1), 0.03473 (1), 0.03473 (1), 0.03471 (1),
0.03469 (1), 0.03455 (1), 0.03448 (1), 0.03447 (1), 0.0344 (1), 0.03436 (1),
0.03416 (1), 0.03402 (1), 0.034 (1), 0.03386 (1), 0.03381 (1), 0.03377 (1),
0.03374 (1), 0.03373 (1), 0.03371 (1), 0.0337 (1), 0.03369 (1), 0.03366 (1),
0.03358 (1), 0.03357 (1), 0.03354 (1), 0.03353 (1), 0.03331 (1), 0.03326 (1),
0.03314 (1), 0.03314 (1), 0.03312 (1), 0.03301 (1), 0.03297 (1), 0.0329 (1),
0.03287 (1), 0.03269 (1), 0.03255 (1), 0.03255 (1), 0.03253 (1), 0.03238 (1),
0.03237 (1), 0.03219 (1), 0.03215 (1), 0.03211 (1), 0.03207 (1), 0.03204 (1),
0.03202 (1), 0.03196 (1), 0.03193 (1), 0.03192 (1), 0.03192 (1), 0.03181 (1),
0.03156 (1), 0.03152 (1), 0.03143 (1), 0.03136 (1), 0.03132 (1), 0.0313 (1),
0.03129 (1), 0.03126 (1), 0.03116 (1), 0.03114 (1), 0.03096 (1), 0.0309 (1),
0.03085 (1), 0.03069 (1), 0.03048 (1), 0.03048 (1), 0.03047 (1), 0.03043 (1),
0.03039 (1), 0.03037 (1), 0.03023 (1), 0.03014 (1), 0.03005 (1), 0.02986 (1),
0.02986 (1), 0.02977 (1), 0.02968 (1), 0.02948 (1), 0.02939 (1), 0.02933 (1),
0.02922 (1), 0.02919 (1), 0.02918 (1), 0.02913 (1), 0.02902 (1), 0.02898 (1),
0.02886 (1), 0.02885 (1), 0.02877 (1), 0.02876 (1), 0.02875 (1), 0.02869 (1),
0.02868 (1), 0.02867 (1), 0.02862 (1), 0.02859 (1), 0.0285 (1), 0.02848 (1),
0.02841 (1), 0.02836 (1), 0.02819 (1), 0.02818 (1), 0.02811 (1), 0.0281 (1),
0.02803 (1), 0.028 (1), 0.02799 (1), 0.02775 (1), 0.02762 (1), 0.02744 (1),
0.02744 (1), 0.02739 (1), 0.02735 (1), 0.02717 (1), 0.02716 (1), 0.02696 (1),
0.02692 (1), 0.02678 (1), 0.02678 (1), 0.02675 (1), 0.02672 (1), 0.02672 (1),
0.02664 (1), 0.02654 (1), 0.02645 (1), 0.02637 (1), 0.02635 (1), 0.02633 (1),
0.02632 (1), 0.02625 (1), 0.02622 (1), 0.02613 (1), 0.02611 (1), 0.02608 (1),
0.02592 (1), 0.02543 (1), 0.02533 (1), 0.0253 (1), 0.02516 (1), 0.02514 (1),
0.02508 (1), 0.02487 (1), 0.02464 (1), 0.02446 (1), 0.02419 (1), 0.02382 (1),
0.02375 (1), 0.02369 (1), 0.02359 (1), 0.02354 (1), 0.02342 (1), 0.02337 (1),
0.02333 (1), 0.02322 (1), 0.02275 (1), 0.02272 (1), 0.0222 (1), 0.02192 (1),
0.02183 (1), 0.02142 (1), 0.02137 (1), 0.02086 (1), 0.02063 (1), 0.02011 (1),
0.0194 (1), 0.01743 (1)
Best fit found:
Fit molecule fold_4_B2_only_573.pdb (#2) to map
cryosparc_P12_J728_002_volume_map_sharp.mrc (#1) using 3065 atoms
average map value = 0.06297, steps = 324
shifted from previous position = 16.9
rotated from previous position = 25.1 degrees
atoms outside contour = 2347, contour level = 0.1147
Position of fold_4_B2_only_573.pdb (#2) relative to
cryosparc_P12_J728_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.73983034 -0.43209220 -0.51570085 386.37778514
-0.55020384 0.82970689 0.09413913 72.66971086
0.38720379 0.35338760 -0.85158115 173.68816957
Axis 0.27382054 -0.95365592 -0.12475056
Axis point 180.45753844 0.00000000 132.54179245
Rotation angle (degrees) 151.74534711
Shift along axis 14.82857860
Found 494 fits.
> scalebar #2 0.5
Expected a number or a keyword
> scalebar #2 0.5
Expected a number or a keyword
> scalebar #2 factor 0.5
Expected a number or a keyword
> transform scale 0.5 models #2
Unknown command: transform scale 0.5 models #2
> surface scale #2 s 0.5
Expected an atoms specifier or a keyword
> transform scale 0.5 models #2
Unknown command: transform scale 0.5 models #2
> transform #2 matrix scale 0.5
Unknown command: transform #2 matrix scale 0.5
> transform #2 matrix scale 0.5,0.5,0.5
Unknown command: transform #2 matrix scale 0.5,0.5,0.5
> version
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> hide #2 models
> close #1
> open /home/spuser/Downloads/cryosparc_P12_J728_008_volume_map_sharp.mrc
Opened cryosparc_P12_J728_008_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.138, step 2, values float32
> surface dust #1 size 6.48
> volume #1 level 0.1234
> volume #1 step 1
> volume #1 color #729fcf
> surface dust #1 size 23.2
> volume #1 level 0.1876
> volume #1 level 0.2334
> show #2 models
> transform #2 matrix scale 0.5
Unknown command: transform #2 matrix scale 0.5
> matrix scale #2 0.5
Unknown command: matrix scale #2 0.5
> help matrix
No help found for 'matrix'
> help transform
No help found for 'transform'
> bounds #2
Unknown command: measure bounds #2
> open /home/spuser/Downloads/cryosparc_P12_J564_003_volume_map_sharp.mrc
Opened cryosparc_P12_J564_003_volume_map_sharp.mrc as #3, grid size
280,280,280, pixel 1.08, shown at level 0.0158, step 2, values float32
> hide #2 models
> volume #3 color #888a85
> surface dust #3 size 6.48
> surface dust #3 size 119.98
> select add #3
3065 atoms, 3154 bonds, 396 residues, 3 models selected
> select subtract #2
2 models selected
> view matrix models #3,1,0,0,-49.365,0,1,0,28.033,0,0,1,-28.853
> view matrix models #3,1,0,0,-1.5981,0,1,0,-2.5085,0,0,1,-3.1982
> view matrix models #3,1,0,0,-0.35778,0,1,0,-7.1825,0,0,1,-2.7206
> volume #3 level 0.02406
> surface dust #3 size 21.9
> volume #3 level 0.06536
> view matrix models #3,1,0,0,-13.933,0,1,0,16.043,0,0,1,-20.313
> view matrix models #3,1,0,0,-3.8514,0,1,0,0.59016,0,0,1,0.79719
> show #2 models
> view matrix models #3,1,0,0,-3.7416,0,1,0,-0.19145,0,0,1,0.84661
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #2
3065 atoms, 3154 bonds, 396 residues, 3 models selected
> select subtract #3
3065 atoms, 3154 bonds, 396 residues, 1 model selected
> view matrix models
> #2,-0.73983,-0.43209,-0.5157,413.06,-0.5502,0.82971,0.094139,29.293,0.3872,0.35339,-0.85158,228.82
> volume #3 level 0.02878
> view matrix models
> #2,-0.73983,-0.43209,-0.5157,408,-0.5502,0.82971,0.094139,40.988,0.3872,0.35339,-0.85158,219.38
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.92747,-0.21238,-0.30773,370.38,-0.21767,0.97587,-0.017463,-8.6174,0.30401,0.050786,-0.95131,289.55
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.92747,-0.21238,-0.30773,376.98,-0.21767,0.97587,-0.017463,-9.0348,0.30401,0.050786,-0.95131,306.23
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume #1 level 0.2151
> show #!3 models
> view matrix models
> #2,-0.92747,-0.21238,-0.30773,339.38,-0.21767,0.97587,-0.017463,33.651,0.30401,0.050786,-0.95131,258.82
> view matrix models
> #2,-0.92747,-0.21238,-0.30773,374.84,-0.21767,0.97587,-0.017463,-7.6607,0.30401,0.050786,-0.95131,303.04
> hide #!3 models
> select subtract #2
Nothing selected
> hide #2 models
> show #!3 models
> select add #3
2 models selected
> view matrix models #3,1,0,0,-40.977,0,1,0,46.256,0,0,1,-44.202
> volume #3 level 0.07657
> volume #1 level 0.1417
> volume #1 level 0.105
> view matrix models #3,1,0,0,-39.671,0,1,0,33.615,0,0,1,-28.255
> view matrix models #3,1,0,0,-39.603,0,1,0,32.839,0,0,1,-27.363
> view matrix models #3,1,0,0,-37.258,0,1,0,6.1323,0,0,1,3.3098
> view matrix models #3,1,0,0,-0.2495,0,1,0,7.8653,0,0,1,-5.9619
> view matrix models #3,1,0,0,-0.7956,0,1,0,2.1188,0,0,1,-0.37175
> view matrix models #3,1,0,0,-0.81164,0,1,0,1.9501,0,0,1,-0.20765
> view matrix models #3,1,0,0,-0.97671,0,1,0,1.1271,0,0,1,-0.071581
> view matrix models #3,1,0,0,-0.68558,0,1,0,2.1218,0,0,1,0.89187
> volume #3 level 0.07775
> view matrix models #3,1,0,0,8.7583,0,1,0,39.422,0,0,1,-24.189
> hide #!3 models
> close #3
> close #1
> open /home/spuser/Downloads/cryosparc_P12_J728_011_volume_map_sharp.mrc
Opened cryosparc_P12_J728_011_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.0948, step 2, values float32
> surface dust #1 size 6.48
> volume #1 color #729fcf
> volume #1 level 0.0781
> volume #1
> volume #1 style mesh
> volume #1 style surface
> volume #1 step 1
> surface dust #1 size 6.48
> surface dust #1 size 27.28
> close #1
> open /home/spuser/Downloads/cryosparc_P12_J731_005_volume_map_sharp.mrc
Opened cryosparc_P12_J731_005_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.0599, step 2, values float32
> surface dust #1 size 6.48
> surface dust #1 size 14.38
> volume #1 level 0.1474
> volume #1 step 1
> volume #1 level 0.1474
> volume #1 level 0.1597
> volume #1 level 0.2332
> show #2 models
> select add #2
3065 atoms, 3154 bonds, 396 residues, 1 model selected
> view matrix models
> #2,-0.92747,-0.21238,-0.30773,335.37,-0.21767,0.97587,-0.017463,21.433,0.30401,0.050786,-0.95131,258.37
> view matrix models
> #2,-0.92747,-0.21238,-0.30773,347.38,-0.21767,0.97587,-0.017463,21.142,0.30401,0.050786,-0.95131,251.69
> view matrix models
> #2,-0.92747,-0.21238,-0.30773,346.51,-0.21767,0.97587,-0.017463,21.239,0.30401,0.050786,-0.95131,250.22
> view matrix models
> #2,-0.92747,-0.21238,-0.30773,316.78,-0.21767,0.97587,-0.017463,12.226,0.30401,0.050786,-0.95131,266.36
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.60204,-0.58025,-0.5485,362.42,0.53748,-0.80251,0.25902,130.41,-0.59047,-0.13887,0.79502,156.87
> view matrix models
> #2,-0.38874,-0.7681,-0.50882,355.43,0.6649,-0.61618,0.42218,61.978,-0.6378,-0.17419,0.75025,175
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.38874,-0.7681,-0.50882,378.71,0.6649,-0.61618,0.42218,77.664,-0.6378,-0.17419,0.75025,161.24
> view matrix models
> #2,-0.38874,-0.7681,-0.50882,379.83,0.6649,-0.61618,0.42218,76.111,-0.6378,-0.17419,0.75025,162.26
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.59112,-0.76403,-0.25851,210.76,0.28322,-0.10349,0.95346,-25.985,-0.75523,-0.63682,0.15521,333.45
> view matrix models
> #2,0.65756,-0.68882,-0.30519,197.7,0.33016,-0.10065,0.93854,-30.506,-0.67721,-0.71791,0.16124,333.96
> view matrix models
> #2,0.93635,-0.34668,-0.055399,73.366,0.044645,-0.038935,0.99824,-9.9976,-0.34823,-0.93717,-0.020979,348.73
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.93635,-0.34668,-0.055399,73.331,0.044645,-0.038935,0.99824,-8.8723,-0.34823,-0.93717,-0.020979,349.13
> view matrix models
> #2,0.93635,-0.34668,-0.055399,77.615,0.044645,-0.038935,0.99824,-9.461,-0.34823,-0.93717,-0.020979,346.55
> view matrix models
> #2,0.93635,-0.34668,-0.055399,77.384,0.044645,-0.038935,0.99824,-6.8677,-0.34823,-0.93717,-0.020979,347.18
> view matrix models
> #2,0.93635,-0.34668,-0.055399,77.083,0.044645,-0.038935,0.99824,-6.0448,-0.34823,-0.93717,-0.020979,347.1
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.86699,-0.33417,0.36967,254.78,0.24743,-0.9326,-0.26274,283.39,0.43256,-0.13632,0.89124,-9.4302
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.86699,-0.33417,0.36967,256.05,0.24743,-0.9326,-0.26274,282.54,0.43256,-0.13632,0.89124,-8.1912
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.91562,-0.35657,-0.18576,101.8,0.15673,-0.10892,0.98162,-9.2495,-0.37024,-0.9279,-0.043846,353.31
> volume #1 level 0.06772
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.91562,-0.35657,-0.18576,105.16,0.15673,-0.10892,0.98162,-10.069,-0.37024,-0.9279,-0.043846,353.51
> view matrix models
> #2,0.91562,-0.35657,-0.18576,104.65,0.15673,-0.10892,0.98162,-13.509,-0.37024,-0.9279,-0.043846,356.48
> view matrix models
> #2,0.91562,-0.35657,-0.18576,106.68,0.15673,-0.10892,0.98162,-13.653,-0.37024,-0.9279,-0.043846,354.35
> volume #1 level 0.09224
> close #2
> close #1
> open /home/spuser/Downloads/cryosparc_P12_J728_011_volume_map.mrc
Opened cryosparc_P12_J728_011_volume_map.mrc as #1, grid size 280,280,280,
pixel 1.08, shown at level 0.0227, step 2, values float32
> surface dust #1 size 6.48
> volume #1 step 1
> surface dust #1 size 21.28
> surface dust #1 size 38.86
> volume #1 level 0.05298
> volume #1 level 0.01266
> volume #1 level 0.0681
> volume #1 color #729fcf
> volume #1 level 0.1639
> close
> open /home/spuser/Downloads/cryosparc_P12_J564_003_volume_map_sharp.mrc
Opened cryosparc_P12_J564_003_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.0158, step 2, values float32
> surface dust #1 size 6.48
> surface dust #1 size 110.06
> volume gaussian #1 sDev 2
Opened cryosparc_P12_J564_003_volume_map_sharp.mrc gaussian as #2, grid size
280,280,280, pixel 1.08, shown at step 1, values float32
> volume #2 color #729fcf
> surface dust #2 size 6.48
> surface dust #2 size 79.55
> ui tool show "Segment Map"
Segmenting cryosparc_P12_J564_003_volume_map_sharp.mrc gaussian, density
threshold 0.002081
Only showing 60 of 326 regions.
Showing 60 of 326 region surfaces
1263 watershed regions, grouped to 326 regions
Showing cryosparc_P12_J564_003_volume_map_sharp gaussian.seg - 326 regions, 60
surfaces
> select #3.14
1 model selected
> select add #3.13
2 models selected
> select add #3.28
3 models selected
> select add #3.27
4 models selected
> select add #3.31
5 models selected
> select add #3.26
6 models selected
> select add #3.19
7 models selected
> select add #3.2
8 models selected
> select add #3.22
9 models selected
> select add #3.44
10 models selected
> select add #3.52
11 models selected
> hide #!2 models
> select subtract #3.2
10 models selected
Deleted 10 regions
Drag select of 1772, 2382 of 3280 triangles, 1770, 1730, 859 of 1880
triangles, 1789
Deleted 4 regions
Drag select of 1764, 1595
Deleted 2 regions
Drag select of 1760
Deleted 1 regions
Drag select of 1781
Deleted 1 regions
Drag select of 1605, 51 of 12252 triangles, 1661, 597 of 11400 triangles,
1649, 103 of 6104 triangles, 1817, 38 of 7428 triangles
Drag select of 1605, 8914 of 12252 triangles, 1661, 8567 of 11400 triangles,
1649, 5879 of 6104 triangles, 1817, 6064 of 7428 triangles, 1822, 1377 of 3916
triangles, 1798, 1323 of 4516 triangles, 1752, 1526, 28 of 1244 triangles,
1796, 1799
Deleted 10 regions
Drag select of 1765
Deleted 1 regions
Drag select of 1745, 599 of 1344 triangles, 1759, 768 of 1612 triangles
Deleted 2 regions
Drag select of 1739, 2052 of 3468 triangles, 1755, 236 of 2528 triangles
Deleted 2 regions
> select #3.1
1 model selected
> select #3.1
1 model selected
> select #3.1
1 model selected
Ungrouped to 11 regions
> select #3.27
1 model selected
Deleted 1 regions
> select #3.19
1 model selected
Deleted 1 regions
> select #3.23
1 model selected
> select #3.15
1 model selected
> select #3.17
1 model selected
> select #3.20
1 model selected
> select add #3.23
2 models selected
> select add #3.15
3 models selected
> select add #3.17
4 models selected
Deleted 4 regions
> select #3.11
1 model selected
Deleted 1 regions
> select #3.21
1 model selected
Deleted 1 regions
Drag select of 1625, 1465 of 1588 triangles
Deleted 1 regions
Drag select of 1766, 6 of 3696 triangles, 1800, 2041 of 3604 triangles, 1756,
348 of 1404 triangles
Deleted 3 regions
> select #3.41
1 model selected
Deleted 1 regions
> select #3.24
1 model selected
Deleted 1 regions
> select #3.3
1 model selected
Ungrouped to 2 regions
> select #3.1
1 model selected
Ungrouped to 3 regions
> select #3.15
1 model selected
Deleted 1 regions
> select #3.14
1 model selected
Deleted 1 regions
> select #3.30
1 model selected
Deleted 1 regions
> select clear
> select #3.39
1 model selected
Deleted 1 regions
> select #3.2
1 model selected
Ungrouped to 7 regions
> select #3.21
1 model selected
> select #3.15
1 model selected
Deleted 1 regions
> select #3.21
1 model selected
Deleted 1 regions
> select #3.43
1 model selected
Deleted 1 regions
> select #3.19
1 model selected
Deleted 1 regions
> select #3.14
1 model selected
Ungrouped to 4 regions
> select #3.21
1 model selected
> select #3.23
1 model selected
> select #3.20
1 model selected
> select add #3.15
2 models selected
Deleted 2 regions
Drag select of 1674, 309 of 468 triangles
Deleted 1 regions
> select #3.25
1 model selected
Deleted 1 regions
> select #3.18
1 model selected
> select add #3.26
2 models selected
> select add #3.22
3 models selected
> select subtract #3.22
2 models selected
> select add #3.5
3 models selected
> select subtract #3.5
2 models selected
Deleted 2 regions
> select #3.5
1 model selected
> select add #3.6
2 models selected
> select add #3.8
3 models selected
Drag select of 1725, 2689 of 18944 triangles, 1622, 4483 of 16476 triangles,
1366, 902 of 1104 triangles, 1487, 6467 of 22568 triangles, 1367, 4882 of
32120 triangles
> select #3.4
1 model selected
> select add #3.21
2 models selected
> select add #3.19
3 models selected
> select add #3.8
4 models selected
> select add #3.6
5 models selected
> select add #3.5
6 models selected
Drag select of 1438, 13801 of 18144 triangles, 1683, 7821 of 18788 triangles,
1725, 16668 of 18944 triangles, 1622, 1767, 242, 1366, 240, 1487, 1367, 25125
of 32120 triangles
Drag select of 1438, 17787 of 18144 triangles, 1683, 14593 of 18788 triangles,
1725, 1622, 275, 1740 of 10676 triangles, 1767, 242, 1366, 240, 1487, 1367,
28943 of 32120 triangles
Saving 11 regions to mrc file...
Opened J564-T2-removal as #4, grid size 80,122,78, pixel 1.08, shown at step
1, values float32
Wrote J564-T2-removal
> hide #!4 models
Drag select of 1382, 516, 1270, 456, 596, 1632, 1042, 1054, 1455, 1117
> select #3.22
1 model selected
Ungrouped to 3 regions
> select #3.14
1 model selected
Ungrouped to 10 regions
> select #3.25
1 model selected
> select #3.15
1 model selected
> select add #3.30
2 models selected
Deleted 2 regions
> select #3.25
1 model selected
> select add #3.32
2 models selected
> select add #3.7
3 models selected
Deleted 3 regions
> select #3.28
1 model selected
Deleted 1 regions
> select #3.29
1 model selected
Deleted 1 regions
> select #3.17
1 model selected
Deleted 1 regions
> select #3.3
1 model selected
Drag select of 1382, 516, 1270, 596, 1054, 1455, 946, 1301, 1312, 1320, 791,
826, 734
Saving 13 regions to mrc file...
Opened J564-B2-full-final as #5, grid size 59,102,92, pixel 1.08, shown at
step 1, values float32
Wrote J564-B2-full-final
> hide #!5 models
> volume resample #4 onGrid #1
Opened J564-T2-removal resampled as #6, grid size 280,280,280, pixel 1.08,
shown at step 1, values float32
> volume resample #5 onGrid #1
Opened J564-B2-full-final resampled as #7, grid size 280,280,280, pixel 1.08,
shown at step 1, values float32
> save /home/spuser/Downloads/J564-T2-removal.mrc models #6
> save /home/spuser/Downloads/J564-B2-full-final.mrc models #7
> close
> open /home/spuser/Downloads/cryosparc_P12_J731_013_volume_map.mrc
Opened cryosparc_P12_J731_013_volume_map.mrc as #1, grid size 280,280,280,
pixel 1.08, shown at level 0.0137, step 2, values float32
> surface dust #1 size 6.48
> surface dust #1 size 16.92
> volume #1 step 1
> surface dust #1 size 22.12
> volume #1 step 2
> volume #1 color #729fcf
> volume #1 level 0.02703
> volume #1 level 0.06691
> volume #1 level 0.1334
> volume #1 level 0.05805
> volume #1 level 0.03589
> open /home/spuser/Downloads/fold_4_B2_only_573.pdb
Chain information for fold_4_B2_only_573.pdb #2
---
Chain | Description
A | No description available
> ui mousemode right "rotate selected models"
> select add #2
3065 atoms, 3154 bonds, 396 residues, 1 model selected
> view matrix models
> #2,0.98833,-0.15035,0.024352,19.989,-0.060059,-0.23778,0.96946,46.392,-0.13997,-0.95961,-0.24403,342.62
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.98833,-0.15035,0.024352,25.906,-0.060059,-0.23778,0.96946,32.391,-0.13997,-0.95961,-0.24403,361.36
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.94302,0.2924,0.15877,200.64,0.28337,0.95589,-0.077364,-34.194,-0.17439,-0.027965,-0.98428,338.69
> view matrix models
> #2,0.94439,0.13189,0.30122,-50.315,-0.26859,-0.21907,0.93801,62.293,0.1897,-0.96675,-0.17147,307.44
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.94439,0.13189,0.30122,-51.177,-0.26859,-0.21907,0.93801,63.069,0.1897,-0.96675,-0.17147,306.38
> view matrix models
> #2,0.94439,0.13189,0.30122,-41.917,-0.26859,-0.21907,0.93801,61.535,0.1897,-0.96675,-0.17147,306.55
> view matrix models
> #2,0.94439,0.13189,0.30122,-73.33,-0.26859,-0.21907,0.93801,93.09,0.1897,-0.96675,-0.17147,269.4
> volume #1 level 0.09793
> volume #1 level 0.06248
> view matrix models
> #2,0.94439,0.13189,0.30122,-42.056,-0.26859,-0.21907,0.93801,70.092,0.1897,-0.96675,-0.17147,307.06
> view matrix models
> #2,0.94439,0.13189,0.30122,-38.345,-0.26859,-0.21907,0.93801,70.26,0.1897,-0.96675,-0.17147,307.2
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.82996,-0.4339,-0.35057,155.91,0.33537,-0.11407,0.93516,-25.796,-0.44576,-0.89371,0.05084,349.08
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.82996,-0.4339,-0.35057,149.84,0.33537,-0.11407,0.93516,-21.157,-0.44576,-0.89371,0.05084,346.03
> view matrix models
> #2,0.82996,-0.4339,-0.35057,174.66,0.33537,-0.11407,0.93516,-34.425,-0.44576,-0.89371,0.05084,360.23
> view matrix models
> #2,0.82996,-0.4339,-0.35057,175.05,0.33537,-0.11407,0.93516,-25.321,-0.44576,-0.89371,0.05084,365.46
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.91287,0.080736,0.40019,223.11,-0.079626,-0.99664,0.019432,294.56,0.40041,-0.014126,0.91623,-4.4765
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.91287,0.080736,0.40019,234.22,-0.079626,-0.99664,0.019432,293.33,0.40041,-0.014126,0.91623,3.191
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.97917,-0.18956,0.072761,330.95,-0.19191,0.98105,-0.026813,25.701,-0.066299,-0.040219,-0.99699,351.65
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.97917,-0.18956,0.072761,311.53,-0.19191,0.98105,-0.026813,24.575,-0.066299,-0.040219,-0.99699,315.17
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.93959,-0.21616,0.26542,281.72,-0.21556,0.97597,0.031761,19.861,-0.26591,-0.027373,-0.96361,335.17
> view matrix models
> #2,-0.88615,-0.228,-0.40343,374.85,-0.34071,0.91065,0.23372,16.464,0.31409,0.34456,-0.88466,191.2
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.88615,-0.228,-0.40343,371.23,-0.34071,0.91065,0.23372,22.774,0.31409,0.34456,-0.88466,186.79
> view matrix models
> #2,-0.88615,-0.228,-0.40343,364.24,-0.34071,0.91065,0.23372,17.458,0.31409,0.34456,-0.88466,193.63
> view matrix models
> #2,-0.88615,-0.228,-0.40343,313.15,-0.34071,0.91065,0.23372,50.942,0.31409,0.34456,-0.88466,170.16
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.78476,0.42286,0.45315,78.018,-0.55595,-0.80345,-0.21304,396.62,0.274,-0.41911,0.8656,29.4
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.78476,0.42286,0.45315,83.107,-0.55595,-0.80345,-0.21304,404.18,0.274,-0.41911,0.8656,44.073
> view matrix models
> #2,-0.78476,0.42286,0.45315,97.895,-0.55595,-0.80345,-0.21304,417.27,0.274,-0.41911,0.8656,28.02
> view matrix models
> #2,-0.78476,0.42286,0.45315,99.349,-0.55595,-0.80345,-0.21304,412.21,0.274,-0.41911,0.8656,28.596
> view matrix models
> #2,-0.78476,0.42286,0.45315,109.34,-0.55595,-0.80345,-0.21304,416.96,0.274,-0.41911,0.8656,23.281
> view matrix models
> #2,-0.78476,0.42286,0.45315,145.66,-0.55595,-0.80345,-0.21304,377.24,0.274,-0.41911,0.8656,46.425
> view matrix models
> #2,-0.78476,0.42286,0.45315,145.43,-0.55595,-0.80345,-0.21304,374.71,0.274,-0.41911,0.8656,43.854
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.78476,0.42286,0.45315,130.17,-0.55595,-0.80345,-0.21304,370.44,0.274,-0.41911,0.8656,49.331
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.39326,0.031661,0.91888,66.222,-0.53026,-0.82426,-0.19854,367.9,0.75111,-0.56533,0.34093,83.987
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.39326,0.031661,0.91888,57.214,-0.53026,-0.82426,-0.19854,359.15,0.75111,-0.56533,0.34093,91.781
> view matrix models
> #2,-0.39326,0.031661,0.91888,57.264,-0.53026,-0.82426,-0.19854,361.02,0.75111,-0.56533,0.34093,93.256
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.63814,0.11225,0.76169,101.52,-0.29723,-0.94854,-0.10923,334.76,0.71023,-0.2961,0.63867,15.454
> view matrix models
> #2,-0.64936,0.094635,0.75457,106.65,-0.3223,-0.93296,-0.16036,343.38,0.6888,-0.34733,0.63633,26.176
> view matrix models
> #2,-0.412,0.055746,0.90948,57.642,-0.37263,-0.92115,-0.11235,341.34,0.8315,-0.38519,0.40029,47.342
> view matrix models
> #2,-0.39687,0.25766,0.88097,30.252,-0.51307,-0.85812,0.019838,331.49,0.76109,-0.44413,0.47276,54.746
> volume #1 level 0.01373
> view matrix models
> #2,0.79525,-0.39532,-0.45968,163.33,0.36772,-0.28832,0.88411,2.4191,-0.48204,-0.87212,-0.083917,366.38
> view matrix models
> #2,0.68822,-0.44454,-0.57336,201.67,0.49718,-0.28656,0.81896,-5.6222,-0.52836,-0.84868,0.023808,353.3
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.68822,-0.44454,-0.57336,206.01,0.49718,-0.28656,0.81896,-9.6866,-0.52836,-0.84868,0.023808,355.74
> close #1
> open /home/spuser/Downloads/cryosparc_P12_J734_002_volume_map.mrc
Opened cryosparc_P12_J734_002_volume_map.mrc as #1, grid size 280,280,280,
pixel 1.08, shown at level 0.0041, step 2, values float32
> volume #1 level 0.01542
> view matrix models
> #2,0.68822,-0.44454,-0.57336,215.48,0.49718,-0.28656,0.81896,-41.806,-0.52836,-0.84868,0.023808,386.19
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99834,-0.018105,-0.054729,34.971,0.048679,-0.24376,0.96861,-9.8975,-0.030878,-0.96967,-0.24247,376.33
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99834,-0.018105,-0.054729,25.81,0.048679,-0.24376,0.96861,25.122,-0.030878,-0.96967,-0.24247,348.37
> ui mousemode right "rotate selected models"
[Repeated 2 time(s)]
> view matrix models
> #2,0.93284,-0.24242,-0.26653,98.658,0.19331,-0.2875,0.93807,16.605,-0.30403,-0.92659,-0.22133,375.63
> view matrix models
> #2,0.97365,-0.18202,-0.13738,65.302,0.08273,-0.27945,0.95659,27.546,-0.21251,-0.94275,-0.25702,370.97
> view matrix models
> #2,0.98791,-0.11436,-0.10465,48.657,0.079212,-0.20787,0.97494,14.835,-0.13324,-0.97145,-0.1963,355.57
> view matrix models
> #2,0.9768,-0.0049453,0.2141,-12.843,-0.20944,-0.23068,0.95022,60.582,0.04469,-0.97302,-0.22637,336.34
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.9768,-0.0049453,0.2141,-13.169,-0.20944,-0.23068,0.95022,60.235,0.04469,-0.97302,-0.22637,335.05
> volume #1 style mesh
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.75003,-0.48164,-0.45328,185.43,0.34049,-0.30637,0.88893,6.4964,-0.56702,-0.82107,-0.06579,371.29
> view matrix models
> #2,0.70959,-0.47598,-0.51954,199.79,0.42953,-0.29228,0.85444,-2.4404,-0.55855,-0.82947,-0.0029494,362.12
> view matrix models
> #2,0.68401,-0.49785,-0.53317,208.44,0.44889,-0.28886,0.84561,-4.2386,-0.575,-0.81774,0.025898,358.36
> view matrix models
> #2,0.83855,-0.44401,-0.31574,147.76,0.23843,-0.222,0.94544,-0.47699,-0.48988,-0.86808,-0.080292,369.95
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule fold_4_B2_only_573.pdb (#2) to map
cryosparc_P12_J734_002_volume_map.mrc (#1) using 3065 atoms
average map value = 0.05624, steps = 480
shifted from previous position = 8.05
rotated from previous position = 18.7 degrees
atoms outside contour = 1451, contour level = 0.015421
Position of fold_4_B2_only_573.pdb (#2) relative to
cryosparc_P12_J734_002_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.78639572 -0.45725299 -0.41533290 172.15346104
0.14923278 -0.51181661 0.84603386 70.12895918
-0.59942581 -0.72729871 -0.33425326 408.59318328
Axis -0.92756375 0.10853262 0.35755582
Axis point 0.00000000 167.87574651 216.32664503
Rotation angle (degrees) 121.99444797
Shift along axis -5.97715849
> volume #1 level 0.02862
> volume #1 level 0.007877
> volume #1 level 0.00882
> volume #1 level 0.03145
> volume #1 level 0.005047
> fitmap #2 inMap #1
Fit molecule fold_4_B2_only_573.pdb (#2) to map
cryosparc_P12_J734_002_volume_map.mrc (#1) using 3065 atoms
average map value = 0.05624, steps = 480
shifted from previous position = 8.05
rotated from previous position = 18.7 degrees
atoms outside contour = 1240, contour level = 0.0050473
Position of fold_4_B2_only_573.pdb (#2) relative to
cryosparc_P12_J734_002_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.78639572 -0.45725299 -0.41533290 172.15346104
0.14923278 -0.51181661 0.84603386 70.12895918
-0.59942581 -0.72729871 -0.33425326 408.59318328
Axis -0.92756375 0.10853262 0.35755582
Axis point 0.00000000 167.87574651 216.32664503
Rotation angle (degrees) 121.99444797
Shift along axis -5.97715849
> open /home/spuser/Downloads/J564-B2-full-final.mrc
Opened J564-B2-full-final.mrc as #3, grid size 280,280,280, pixel 1.08, shown
at level 1.01e-05, step 2, values float32
> volume #3 style mesh
> hide #!1 models
> fitmap #2 inMap #1
Fit molecule fold_4_B2_only_573.pdb (#2) to map
cryosparc_P12_J734_002_volume_map.mrc (#1) using 3065 atoms
average map value = 0.05624, steps = 480
shifted from previous position = 8.05
rotated from previous position = 18.7 degrees
atoms outside contour = 1240, contour level = 0.0050473
Position of fold_4_B2_only_573.pdb (#2) relative to
cryosparc_P12_J734_002_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.78639572 -0.45725299 -0.41533290 172.15346104
0.14923278 -0.51181661 0.84603386 70.12895918
-0.59942581 -0.72729871 -0.33425326 408.59318328
Axis -0.92756375 0.10853262 0.35755582
Axis point 0.00000000 167.87574651 216.32664503
Rotation angle (degrees) 121.99444797
Shift along axis -5.97715849
> volume #3 level 0.009431
> volume #3 style surface
> volume #3 color #729fcf
> volume #3 style mesh
> select add #3
3065 atoms, 3154 bonds, 396 residues, 3 models selected
> select subtract #3
3065 atoms, 3154 bonds, 396 residues, 1 model selected
> volume #3 level 0.02643
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #2 models
> show #2 models
> hide #!3 models
> surface dust #1 size 8.34
> surface dust #1 size 86.72
> surface dust #1 size 48.88
> volume #1 level 0.01071
> volume #1 level 0.01542
> volume #1 level 0.006933
> open /home/spuser/Downloads/cryosparc_P12_J734_006_volume_map.mrc
Opened cryosparc_P12_J734_006_volume_map.mrc as #4, grid size 280,280,280,
pixel 1.08, shown at level 0.00558, step 2, values float32
> hide #2 models
> hide #!1 models
> color #4 #888a85ff models
> surface dust #4 size 6.48
> surface dust #4 size 6.53
> surface dust #4 size 6.58
> surface dust #4 size 6.63
> surface dust #4 size 6.68
> surface dust #4 size 6.73
> surface dust #4 size 6.78
> surface dust #4 size 6.83
> surface dust #4 size 6.88
> surface dust #4 size 25.03
> volume #4 level 0.01238
> volume #4 style mesh
> show #2 models
> volume #4 level 0.007851
> surface dust #4 size 86.72
> volume #4 step 1
> volume #4 step 4
> surface dust #4 size 32.72
> volume #4 level 0.01157
> view matrix models
> #2,0.82922,-0.45304,-0.32735,152.04,0.24835,-0.22603,0.94193,-0.70164,-0.50072,-0.86236,-0.074914,369.77
> view matrix models
> #2,0.97837,-0.1276,-0.16281,60.122,0.14209,-0.1574,0.97726,-1.6857,-0.15032,-0.97926,-0.13586,348.81
> surface dust #4 size 11.99
> volume #4 level 0.03574
> volume #4 step 2
> view matrix models
> #2,0.98475,0.11149,0.13356,-19.412,-0.11215,-0.18012,0.97723,35.787,0.133,-0.97731,-0.16487,314.75
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.98475,0.11149,0.13356,-14.466,-0.11215,-0.18012,0.97723,36.538,0.133,-0.97731,-0.16487,312.26
> view matrix models
> #2,0.98475,0.11149,0.13356,-14.135,-0.11215,-0.18012,0.97723,35.526,0.133,-0.97731,-0.16487,313.28
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.7894,-0.37775,-0.4839,174.72,0.4053,-0.27133,0.87299,-5.2466,-0.46107,-0.88526,-0.061083,364.29
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.66019,-0.47792,-0.57943,220.81,0.50434,-0.2896,0.8135,-7.1034,-0.55659,-0.82929,0.04984,352.58
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.66019,-0.47792,-0.57943,221.22,0.50434,-0.2896,0.8135,-6.3485,-0.55659,-0.82929,0.04984,351.14
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.69194,-0.45341,-0.56182,210.77,0.48385,-0.28634,0.82698,-6.0629,-0.53583,-0.84406,0.021256,354.72
> view matrix models
> #2,0.87822,-0.24998,-0.40773,133.27,0.29822,-0.38026,0.87548,25.468,-0.37389,-0.89046,-0.2594,381.13
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.87822,-0.24998,-0.40773,132.53,0.29822,-0.38026,0.87548,24.845,-0.37389,-0.89046,-0.2594,381.14
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.93916,-0.24058,-0.24515,99.016,0.20293,-0.18722,0.96113,-3.2397,-0.27713,-0.9524,-0.12701,357.7
> view matrix models
> #2,0.88206,-0.33729,-0.32894,133.19,0.28986,-0.16189,0.94328,-15.992,-0.37141,-0.92738,-0.045028,354.61
> view matrix models
> #2,0.85171,-0.37669,-0.36427,148.24,0.32828,-0.15829,0.93123,-19.902,-0.40844,-0.91272,-0.011156,352.45
> volume #4 level 0.01307
> show #!3 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> view matrix models
> #2,0.92182,-0.24413,-0.30109,110.11,0.26059,-0.18475,0.94761,-9.3521,-0.28696,-0.95198,-0.10669,355.96
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.92182,-0.24413,-0.30109,109.72,0.26059,-0.18475,0.94761,-12.491,-0.28696,-0.95198,-0.10669,356.84
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.68438,-0.50209,-0.52871,212.91,0.49481,-0.21277,0.84255,-24.36,-0.53553,-0.83823,0.10283,342.69
> view matrix models
> #2,0.48203,-0.57119,-0.66437,270.19,0.58314,-0.35679,0.72983,1.4752,-0.65391,-0.73922,0.1611,335.5
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.48203,-0.57119,-0.66437,270.05,0.58314,-0.35679,0.72983,5.5236,-0.65391,-0.73922,0.1611,337.72
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.68807,-0.54073,-0.4839,211.33,0.44916,-0.20638,0.86929,-19.058,-0.56992,-0.81549,0.10088,346.48
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.68807,-0.54073,-0.4839,208.03,0.44916,-0.20638,0.86929,-22.29,-0.56992,-0.81549,0.10088,342.54
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.68807,-0.54073,-0.4839,207.11,0.44916,-0.20638,0.86929,-22.089,-0.56992,-0.81549,0.10088,344.95
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.84142,-0.2249,-0.49135,141.38,0.38837,-0.38056,0.83925,16,-0.37574,-0.89699,-0.23286,379.99
> view matrix models
> #2,0.81551,-0.36883,-0.44598,159.24,0.34836,-0.30253,0.8872,2.8836,-0.46215,-0.87889,-0.11823,372.05
> view matrix models
> #2,0.87327,-0.42066,-0.24585,129.58,0.19289,-0.16487,0.96727,-8.1915,-0.44743,-0.89211,-0.06283,363.85
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.87327,-0.42066,-0.24585,127.95,0.19289,-0.16487,0.96727,-6.07,-0.44743,-0.89211,-0.06283,361.82
[Repeated 1 time(s)]
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.59314,-0.63464,-0.4954,233.67,0.41106,-0.29035,0.86413,-1.797,-0.69225,-0.71619,0.088651,346.62
> volume #3 level 0.03976
> view matrix models
> #2,0.85862,-0.41975,-0.29425,136.92,0.22388,-0.20933,0.95187,-1.4529,-0.46114,-0.88317,-0.085762,365.73
> view matrix models
> #2,0.96918,-0.20585,-0.13536,67.341,0.083595,-0.24206,0.96665,20,-0.23175,-0.94817,-0.21739,363.84
> view matrix models
> #2,0.99656,-0.078234,0.027253,21.015,-0.045394,-0.24047,0.96959,36.655,-0.069301,-0.9675,-0.2432,348.66
> view matrix models
> #2,0.96719,-0.24169,-0.078236,64.435,0.036748,-0.17162,0.98448,13.352,-0.25137,-0.95506,-0.15711,358.6
> view matrix models
> #2,0.9552,-0.27243,-0.11565,76.058,0.072872,-0.16224,0.98406,7.1892,-0.28684,-0.9484,-0.13512,359.15
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.9552,-0.27243,-0.11565,76.3,0.072872,-0.16224,0.98406,7.3738,-0.28684,-0.9484,-0.13512,360.03
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> close #4
> close
> open /home/spuser/Downloads/cryosparc_P12_J737_class_00_00400_volume.mrc
Opened cryosparc_P12_J737_class_00_00400_volume.mrc as #1, grid size 64,64,64,
pixel 4.39, shown at level 0.0472, step 1, values float32
> surface dust #1 size 26.33
> surface dust #1 size 91.54
> close
> undo
> open /home/spuser/Downloads/cryosparc_P12_J737_class_01_00400_volume.mrc
Opened cryosparc_P12_J737_class_01_00400_volume.mrc as #1, grid size 64,64,64,
pixel 4.39, shown at level 0.0476, step 1, values float32
> surface dust #1 size 26.33
> close
> open /home/spuser/Downloads/cryosparc_P12_J737_class_02_00400_volume.mrc
Opened cryosparc_P12_J737_class_02_00400_volume.mrc as #1, grid size 64,64,64,
pixel 4.39, shown at level 0.0477, step 1, values float32
> surface dust #1 size 26.33
> close
> open /home/spuser/Downloads/cryosparc_P12_J734_015_volume_map.mrc
Opened cryosparc_P12_J734_015_volume_map.mrc as #1, grid size 280,280,280,
pixel 1.08, shown at level 0.0138, step 2, values float32
> surface dust #1 size 6.48
> surface dust #1 size 28.62
[Repeated 1 time(s)]
> volume #1 level 0.01855
> volume #1 level -0.005418
> volume #1 level 0.02335
> close #1
> open /home/spuser/Downloads/cryosparc_P12_J738_class_00_00520_volume.mrc
Opened cryosparc_P12_J738_class_00_00520_volume.mrc as #1, grid size 80,80,80,
pixel 3.78, shown at level 0.0227, step 1, values float32
> surface dust #1 size 22.68
> surface dust #1 size 96.43
> close
> open /home/spuser/Downloads/cryosparc_P12_J564_003_volume_map_sharp(1).mrc
Opened cryosparc_P12_J564_003_volume_map_sharp(1).mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.0158, step 2, values float32
> surface dust #1 size 6.48
> ui mousemode right "map eraser"
> volume erase #1 center 137.91,144.94,151.21 radius 71.497 outside true
Opened cryosparc_P12_J564_003_volume_map_sharp(1).mrc copy as #3, grid size
280,280,280, pixel 1.08, shown at step 1, values float32
> volume #3 level 0.03365
> volume #3 level 0.02688
> save /home/spuser/Downloads/Full-mask.mrc models #3
> close #3
> close #1
> open /home/spuser/Downloads/cryosparc_P12_J747_002_volume_map_sharp.mrc
Opened cryosparc_P12_J747_002_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.0108, step 2, values float32
> surface dust #1 size 6.48
> surface dust #1 size 47.02
> open /home/spuser/Downloads/fold_4_B2_only_573.pdb
Chain information for fold_4_B2_only_573.pdb #2
---
Chain | Description
A | No description available
> select add #2
3065 atoms, 3154 bonds, 396 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.93424,0.15778,0.31984,189.52,0.093962,0.97403,-0.20602,21.547,-0.34404,-0.16242,-0.9248,353.65
> view matrix models
> #2,-0.90436,-0.34029,-0.25756,343.51,-0.31011,0.9386,-0.15119,72.914,0.29319,-0.056853,-0.95436,256.98
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.90436,-0.34029,-0.25756,362.7,-0.31011,0.9386,-0.15119,66.636,0.29319,-0.056853,-0.95436,272.63
> volume #1 style mesh
> view matrix models
> #2,-0.90436,-0.34029,-0.25756,360.67,-0.31011,0.9386,-0.15119,68.459,0.29319,-0.056853,-0.95436,271.58
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.54388,-0.4082,-0.73319,392.3,-0.38029,0.89874,-0.21828,93.606,0.74805,0.1601,-0.64404,133
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.54388,-0.4082,-0.73319,391.82,-0.38029,0.89874,-0.21828,100.09,0.74805,0.1601,-0.64404,135.54
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.26612,-0.64061,-0.72028,386.64,-0.64015,0.67611,-0.36481,189.17,0.72069,0.364,-0.59001,101.4
> view matrix models
> #2,-0.8386,-0.33644,-0.42843,375.98,-0.30243,0.94169,-0.14752,72.919,0.45308,0.0058576,-0.89145,234.19
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.8386,-0.33644,-0.42843,374.03,-0.30243,0.94169,-0.14752,70.754,0.45308,0.0058576,-0.89145,236.48
> view matrix models
> #2,-0.8386,-0.33644,-0.42843,373.94,-0.30243,0.94169,-0.14752,70.973,0.45308,0.0058576,-0.89145,234.96
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.8486,-0.090803,-0.52119,352.99,-0.064403,0.99556,-0.068589,19.487,0.52511,-0.024638,-0.85068,223.75
> view matrix models
> #2,-0.68397,-0.26555,-0.67946,379.79,-0.3672,0.93012,0.0061186,58.72,0.63035,0.25368,-0.73369,151.63
> view matrix models
> #2,-0.25486,-0.36226,-0.89656,368.32,-0.53257,0.82647,-0.18255,123.91,0.8071,0.43095,-0.40356,53.288
> view matrix models
> #2,0.095993,-0.4273,-0.899,331.08,-0.58802,0.70438,-0.39759,180.92,0.80313,0.5668,-0.18365,1.5248
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.095993,-0.4273,-0.899,330.04,-0.58802,0.70438,-0.39759,177,0.80313,0.5668,-0.18365,8.8711
> view matrix models
> #2,0.095993,-0.4273,-0.899,327.09,-0.58802,0.70438,-0.39759,180.17,0.80313,0.5668,-0.18365,8.6279
> volume #1 level 0.009323
> volume #1 level 0.01299
> view matrix models
> #2,0.095993,-0.4273,-0.899,327.39,-0.58802,0.70438,-0.39759,179.31,0.80313,0.5668,-0.18365,9.3586
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.016854,-0.46529,-0.885,341.51,-0.5847,0.71342,-0.38621,175.87,0.81107,0.52397,-0.26003,25.818
> view matrix models
> #2,-0.17995,-0.44947,-0.87498,364.15,-0.51785,0.79955,-0.30422,142.2,0.83633,0.39837,-0.37664,57.999
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.17995,-0.44947,-0.87498,362.32,-0.51785,0.79955,-0.30422,146.38,0.83633,0.39837,-0.37664,57.404
> view matrix models
> #2,-0.17995,-0.44947,-0.87498,362.87,-0.51785,0.79955,-0.30422,146.61,0.83633,0.39837,-0.37664,57.831
> close #1
> hide #2 models
> select subtract #2
Nothing selected
> open /home/spuser/Downloads/cryosparc_P12_J564_003_volume_map_sharp(1).mrc
Opened cryosparc_P12_J564_003_volume_map_sharp(1).mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.0158, step 2, values float32
> ui mousemode right "map eraser"
> volume erase #1 center 228.24,137.06,153 radius 37.565
Opened cryosparc_P12_J564_003_volume_map_sharp(1).mrc copy as #4, grid size
280,280,280, pixel 1.08, shown at step 1, values float32
> volume gaussian #4 sDev 2
Opened cryosparc_P12_J564_003_volume_map_sharp(1).mrc copy gaussian as #5,
grid size 280,280,280, pixel 1.08, shown at step 1, values float32
> close #5
> close #3
> show #!4 models
> close #4
> show #!1 models
> ui mousemode right "map eraser"
> volume erase #1 center 223.79,131.85,154.37 radius 31.601 outside true
Opened cryosparc_P12_J564_003_volume_map_sharp(1).mrc copy as #4, grid size
280,280,280, pixel 1.08, shown at step 1, values float32
> save /home/spuser/Downloads/blob-remove.mrc models #4
> close #3
> close #4
> show #2 models
> show #!1 models
> close #1
> open /home/spuser/Downloads/cryosparc_P12_J747_002_volume_map_sharp.mrc
Opened cryosparc_P12_J747_002_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.0108, step 2, values float32
> surface dust #1 size 6.48
> surface dust #1 size 25.76
> ui mousemode right "translate selected models"
> select add #2
3065 atoms, 3154 bonds, 396 residues, 1 model selected
> view matrix models
> #2,-0.17995,-0.44947,-0.87498,392.24,-0.51785,0.79955,-0.30422,117.24,0.83633,0.39837,-0.37664,105.57
> volume #1 level 0.01445
> view matrix models
> #2,-0.17995,-0.44947,-0.87498,355.79,-0.51785,0.79955,-0.30422,145.39,0.83633,0.39837,-0.37664,62.026
> view matrix models
> #2,-0.17995,-0.44947,-0.87498,358.64,-0.51785,0.79955,-0.30422,141.16,0.83633,0.39837,-0.37664,60.39
> view matrix models
> #2,-0.17995,-0.44947,-0.87498,359.66,-0.51785,0.79955,-0.30422,143.08,0.83633,0.39837,-0.37664,55.793
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.7675,-0.41533,-0.4883,376.58,-0.36653,0.90925,-0.19728,90.943,0.52593,0.027561,-0.85008,221.53
> view matrix models
> #2,-0.3709,-0.57237,-0.73132,382.12,-0.49913,0.78694,-0.36277,151.04,0.78314,0.23047,-0.57756,117.13
> close #2
> close #1
> close #
Expected a models specifier or a keyword
> open /home/spuser/Downloads/fold_4_B2_only_573.pdb format pdb
Chain information for fold_4_B2_only_573.pdb #1
---
Chain | Description
A | No description available
> open /home/spuser/Downloads/cryosparc_P12_J759_003_volume_map.mrc
Opened cryosparc_P12_J759_003_volume_map.mrc as #2, grid size 256,256,256,
pixel 1.08, shown at level 0.00794, step 1, values float32
> close #2
> close
> open /home/spuser/Downloads/cryosparc_P12_J564_003_volume_map_sharp(1).mrc
Opened cryosparc_P12_J564_003_volume_map_sharp(1).mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.0158, step 2, values float32
> ui mousemode right "map eraser"
> volume erase #1 center 221.33,134.39,152.63 radius 32.81 outside true
Opened cryosparc_P12_J564_003_volume_map_sharp(1).mrc copy as #3, grid size
280,280,280, pixel 1.08, shown at step 1, values float32
> save /home/spuser/Downloads/Full-mask.mrc models #3
> close #3
> close #2
> show #!1 models
> close #1
> open /home/spuser/Downloads/cryosparc_P12_J759_003_volume_map_sharp.mrc
Opened cryosparc_P12_J759_003_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.08, shown at level 0.0217, step 1, values float32
> surface dust #1 size 6.48
> surface dust #1 size 97.26
[Repeated 1 time(s)]
> volume #1 level 0.02403
> volume #1 step 2
> volume #1 level 0.04898
> volume #1 level 0.06229
> volume #1 level 0.06007
> volume #1 level 0.06617
> volume #1 level 0.02403
> close
> open /home/spuser/Downloads/cryosparc_P12_J750_004_volume_map.mrc
Opened cryosparc_P12_J750_004_volume_map.mrc as #1, grid size 256,256,256,
pixel 1.08, shown at level 0.00426, step 1, values float32
> surface dust #1 size 6.48
> surface dust #1 size 60.89
> volume #1 level 0.0184
> volume #1 level 0.02244
> volume #1 level 0.08506
> volume #1 level 0.02648
> close
> open /home/spuser/Downloads/cryosparc_P12_J747_003_volume_map_sharp.mrc
Opened cryosparc_P12_J747_003_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.0148, step 2, values float32
> surface dust #1 size 6.48
[Repeated 1 time(s)]
> surface dust #1 size 63.24
> volume #1 level 0.03088
> volume #1 level 0.03775
> surface dust #1 size 27.28
> close
> open /home/spuser/Downloads/cryosparc_P12_J761_component_000.cs
Unrecognized file suffix '.cs'
> toolshed show
> open /home/spuser/Downloads/J761_component_001_frame_019.mrc
Opened J761_component_001_frame_019.mrc as #1, grid size 280,280,280, pixel
1.08, shown at level 0.0237, step 2, values float32
> volume #1 level 0.06169
> open /home/spuser/Downloads/J761_component_001_frame_009.mrc
> /home/spuser/Downloads/J761_component_001_frame_008.mrc
> /home/spuser/Downloads/J761_component_001_frame_007.mrc
> /home/spuser/Downloads/J761_component_001_frame_011.mrc
> /home/spuser/Downloads/J761_component_001_frame_006.mrc
> /home/spuser/Downloads/J761_component_001_frame_005.mrc
> /home/spuser/Downloads/J761_component_001_frame_004.mrc
> /home/spuser/Downloads/J761_component_001_frame_003.mrc
> /home/spuser/Downloads/J761_component_001_frame_002.mrc
> /home/spuser/Downloads/J761_component_001_frame_001.mrc
> /home/spuser/Downloads/J761_component_001_frame_000.mrc
Opened J761_component_001_frame_009.mrc as #2.1, grid size 280,280,280, pixel
1.08, shown at level 0.0213, step 2, values float32
Opened J761_component_001_frame_008.mrc as #2.2, grid size 280,280,280, pixel
1.08, shown at level 0.0213, step 2, values float32
Opened J761_component_001_frame_007.mrc as #2.3, grid size 280,280,280, pixel
1.08, shown at level 0.0214, step 2, values float32
Opened J761_component_001_frame_011.mrc as #2.4, grid size 280,280,280, pixel
1.08, shown at level 0.0214, step 2, values float32
Opened J761_component_001_frame_006.mrc as #2.5, grid size 280,280,280, pixel
1.08, shown at level 0.0216, step 2, values float32
Opened J761_component_001_frame_005.mrc as #2.6, grid size 280,280,280, pixel
1.08, shown at level 0.0218, step 2, values float32
Opened J761_component_001_frame_004.mrc as #2.7, grid size 280,280,280, pixel
1.08, shown at level 0.022, step 2, values float32
Opened J761_component_001_frame_003.mrc as #2.8, grid size 280,280,280, pixel
1.08, shown at level 0.0223, step 2, values float32
Opened J761_component_001_frame_002.mrc as #2.9, grid size 280,280,280, pixel
1.08, shown at level 0.0226, step 2, values float32
Opened J761_component_001_frame_001.mrc as #2.10, grid size 280,280,280, pixel
1.08, shown at level 0.0229, step 2, values float32
Opened J761_component_001_frame_000.mrc as #2.11, grid size 280,280,280, pixel
1.08, shown at level 0.0233, step 2, values float32
> surface dust #2.11 size 6.48
> volume #2.1 level 0.03631
> volume #2.2 level 0.03208
> volume #1 level 0.06999
> volume #2.3 level 0.03181
> volume #2.4 level 0.03725
> volume #2.5 level 0.03723
> volume #2.6 level 0.03895
> volume #2.7 level 0.04248
> volume #2.8 level 0.03989
> volume #2.9 level 0.03621
> volume #2.10 level 0.03159
> volume #2.11 level 0.03448
> volume #1 level 0.04167
> volume #2.1 color #729fcf
> volume #1 color #729fcf
> volume #2.11 color #ef2929
> volume #2.11 color #888a85
> volume #2.11 color #ad7fa8
> volume #2.11 color #e9b96e
> volume #2.11 color #ef2929
> volume #2.11 color #555753
> volume #2.11 color #888a85
> volume #2.11 level 0.04262
> close #2.1
> close #2.2
> close #2.3
> close #2.4
> close #2.5
> close #2.6
> close #2.7
> close #2.8
> close #2.9
> close #2.10
> volume #1 level 0.05801
> volume #2.11 level 0.07069
> volume #2.11 level 0.05265
> volume #1 level 0.06137
> close #1
> close #2.11
> open /home/spuser/Downloads/cryosparc_P12_J750_014_volume_map.mrc
Opened cryosparc_P12_J750_014_volume_map.mrc as #1, grid size 256,256,256,
pixel 1.08, shown at level 0.0175, step 1, values float32
> surface dust #1 size 6.48
> surface dust #1 size 34.32
> volume gaussian #1 sDev 2
Opened cryosparc_P12_J750_014_volume_map.mrc gaussian as #3, grid size
256,256,256, pixel 1.08, shown at step 1, values float32
> volume #3 level 0.0278
> volume #3 color #729fcf
> volume #3 level 0.01999
> volume #3 level 0.02183
> ui tool show Segmentations
Created segmentation sphere cursor with ID #4
Created segmentation sphere cursor with ID #5
Created segmentation sphere cursor with ID #6
> ui view fourup
> close #6
> close #5
> close #4
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 659, in
_on_plane_viewer_enter_event
self.make_puck_visible(axis)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 933, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Error processing trigger "plane viewer enter":
TypeError: object of type 'NoneType' has no len()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 662, in
_on_plane_viewer_leave_event
self.make_puck_invisible(axis)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 937, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Error processing trigger "plane viewer leave":
TypeError: object of type 'NoneType' has no len()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 659, in
_on_plane_viewer_enter_event
self.make_puck_visible(axis)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 933, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Error processing trigger "plane viewer enter":
TypeError: object of type 'NoneType' has no len()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1323, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 662, in
_on_plane_viewer_leave_event
self.make_puck_invisible(axis)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 937, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Error processing trigger "plane viewer leave":
TypeError: object of type 'NoneType' has no len()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 659, in
_on_plane_viewer_enter_event
self.make_puck_visible(axis)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 933, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Error processing trigger "plane viewer enter":
TypeError: object of type 'NoneType' has no len()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 662, in
_on_plane_viewer_leave_event
self.make_puck_invisible(axis)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 937, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Error processing trigger "plane viewer leave":
TypeError: object of type 'NoneType' has no len()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 550.67
OpenGL renderer: NVIDIA GeForce RTX 4090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:1
Manufacturer: Supermicro
Model: Super Server
OS: Rocky Linux 8.9
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 Intel(R) Xeon(R) Silver 4314 CPU @ 2.40GHz
Cache Size: 24576 KB
Memory:
total used free shared buff/cache available
Mem: 502Gi 282Gi 21Gi 1.1Gi 198Gi 216Gi
Swap: 31Gi 0B 31Gi
Graphics:
05:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)
DeviceName: ASPEED Video AST2500
Subsystem: Super Micro Computer Inc Device [15d9:1b57]
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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