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Opened 41 hours ago

#19272 new defect

ChimeraX bug report submission

Reported by:	chimerax-bug-report@…	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_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  

> set bgColor white

> ui tool show "Hide Dust"

> surface dust #1 size 6.48

> surface dust #1 size 9.08

[Repeated 1 time(s)]

> volume #1 level 0.05327

> volume #1 level 0.03181

[Repeated 1 time(s)]

> volume gaussian #1 sDev 2

Opened cryosparc_P12_J750_014_volume_map.mrc gaussian as #2, grid size
256,256,256, pixel 1.08, shown at step 1, values float32  

> volume #2 color #729fcf

> volume #2 level 0.02196

> ui tool show "Segment Map"

Segmenting cryosparc_P12_J750_014_volume_map.mrc gaussian, density threshold
0.021961  
Showing 11 region surfaces  
75 watershed regions, grouped to 11 regions  
Showing cryosparc_P12_J750_014_volume_map gaussian.seg - 11 regions, 11
surfaces  

> select #3.3

1 model selected  

> select add #3.1

2 models selected  

> select subtract #3.1

1 model selected  

> select add #3.1

2 models selected  

> select add #3.9

3 models selected  

> hide #!2 models

Saving 3 regions to mrc file...  
Opened J750-B2.mrc as #4, grid size 53,91,64, pixel 1.08, shown at step 1,
values float32  
Wrote J750-B2.mrc  

> volume resample #4 onGrid #1

Opened J750-B2.mrc resampled as #5, grid size 256,256,256, pixel 1.08, shown
at step 1, values float32  

> save /home/spuser/Downloads/J750-B2.mrc models #5

> hide #!5 models

> hide #!3 models

> open /home/spuser/Downloads/cryosparc_P12_J766_001_volume_map.mrc

Opened cryosparc_P12_J766_001_volume_map.mrc as #6, grid size 256,256,256,
pixel 1.08, shown at level 0.00593, step 1, values float32  

> volume #6 level 0.02358

> volume #6 level 0.01328

> surface dust #6 size 6.48

> volume #6 level 0.02946

> volume #6 level 0.128

> volume #6 level 0.1501

> volume #6 level 0.008872

> close #6

> open /home/spuser/Downloads/cryosparc_P12_J769_001_volume_map.mrc

Opened cryosparc_P12_J769_001_volume_map.mrc as #6, grid size 256,256,256,
pixel 1.08, shown at level 0.00982, step 1, values float32  

No surface chosen for hiding dust  

> volume #6 level 0.0199

[Repeated 1 time(s)]

> volume #6 color #729fcf

> volume #6 level 0.03755

> volume #6 level 0.02242

> volume #6 level 0.02747

> close #6

> open /home/spuser/Downloads/cryosparc_P12_J769_003_volume_map_sharp.mrc

Opened cryosparc_P12_J769_003_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.08, shown at level 0.161, step 1, values float32  

> surface dust #6 size 6.48

> volume #6 level 0.2434

> volume #6 color #729fcf

> volume #6 level 0.2707

> close

> open /home/spuser/Downloads/cryosparc_P12_J758_003_volume_map_sharp.mrc

Opened cryosparc_P12_J758_003_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 1.08, shown at level 0.0185, step 2, values float32  

> surface dust #1 size 6.48

> surface dust #1 size 48.41

> volume #1 level 0.03553

> surface dust #1 size 83.89

> volume #1 level 0.02926

> surface dust #1 size 97.32

> volume #1 level 0.02837

> volume #1 step 1

> volume #1 step 2

> save /home/spuser/Downloads/B2-TREM2-219-udpate.jpg width 1273 height 793
> supersample 3

> close

> open /home/spuser/Downloads/cryosparc_P12_J747_003_volume_map_sharp(1).mrc

Opened cryosparc_P12_J747_003_volume_map_sharp(1).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

> surface dust #1 size 70.2

> volume #1 level 0.0278

> volume #1 level 0.02942

> close

> open /home/spuser/Downloads/cryosparc_P12_J771_003_volume_map_sharp.mrc

Opened cryosparc_P12_J771_003_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.08, shown at level 0.208, step 1, values float32  

> surface dust #1 size 6.48

[Repeated 1 time(s)]

> volume #1 level 0.2079

> volume #1 level 0.1291

> surface dust #1 size 45.62

[Repeated 1 time(s)]

> volume #1 level 0.25

> volume #1 level 0.16

> close

> open /home/spuser/Downloads/cryosparc_P12_J769_003_volume_map_sharp(1).mrc

Opened cryosparc_P12_J769_003_volume_map_sharp(1).mrc as #1, grid size
256,256,256, pixel 1.08, shown at level 0.161, step 1, values float32  

> surface dust #1 size 6.48

> close

> open /home/spuser/Downloads/cryosparc_P12_J771_003_volume_map.mrc

Opened cryosparc_P12_J771_003_volume_map.mrc as #1, grid size 256,256,256,
pixel 1.08, shown at level 0.0246, step 1, values float32  

> volume #1 step 2

> surface dust #1 size 6.48

> volume #1 level 0.01997

> close

> open /home/spuser/Downloads/cryosparc_P12_J734_015_volume_map(1).mrc

Opened cryosparc_P12_J734_015_volume_map(1).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 62.33

> volume #1 level 0.02054

> surface dust #1 size 18.16

[Repeated 1 time(s)]

> surface dust #1 size 10.17

> surface dust #1 size 2.96

> close

> open /home/spuser/Downloads/cryosparc_P12_J759_003_volume_map_sharp(1).mrc

Opened cryosparc_P12_J759_003_volume_map_sharp(1).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 48.41

> volume #1 level 0.03463

> surface dust #1 size 63.24

> open /home/spuser/Downloads/8.pdb

Chain information for 8.pdb #2  
---  
Chain | Description  
A | No description available  
  

> close #2

> open /home/spuser/Downloads/B2-For-T157.pdb

Summary of feedback from opening /home/spuser/Downloads/B2-For-T157.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 52 LEU A 54 1 3  
Start residue of secondary structure not found: HELIX 2 2 TRP A 67 HIS A 69 1
3  
Start residue of secondary structure not found: HELIX 3 3 ARG A 265 TYR A 267
1 3  
Start residue of secondary structure not found: HELIX 4 4 SER A 365 HIS A 367
1 3  
Start residue of secondary structure not found: SHEET 1 1 1 THR A 7 GLU A 11 0  
End residue of secondary structure not found: SHEET 2 2 1 VAL A 15 THR A 17 0  
Start residue of secondary structure not found: SHEET 3 3 1 VAL A 22 GLN A 27
0  
Start residue of secondary structure not found: SHEET 4 4 1 GLU A 34 GLU A 40
0  
Start residue of secondary structure not found: SHEET 5 5 1 ILE A 47 ARG A 49
0  
Start residue of secondary structure not found: SHEET 6 6 1 GLN A 59 ILE A 62
0  
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 71 TYR A 78
0  
24 messages similar to the above omitted  
  
Chain information for B2-For-T157.pdb  
---  
Chain | Description  
2.1/A | No description available  
2.2/A | No description available  
  
Computing secondary structure  

> close #2

> 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 "translate selected models"

> view matrix models #2,1,0,0,-22.127,0,1,0,36.253,0,0,1,-106.05

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.93155,0.14163,-0.33491,15.689,-0.27431,-0.3309,-0.90292,400.99,-0.2387,0.93298,-0.2694,-23.497

> view matrix models
> #2,0.96002,0.17649,-0.21727,-10.575,-0.25397,0.22279,-0.94121,322.85,-0.11771,0.95876,0.2587,-121.35

> view matrix models
> #2,-0.93678,-0.13411,-0.3232,305.23,-0.10962,0.98962,-0.092888,66.183,0.3323,-0.051586,-0.94176,143.05

> view matrix models
> #2,-0.93641,-0.13608,-0.32343,305.5,-0.10857,0.98887,-0.10171,67.453,0.33368,-0.06013,-0.94077,143.97

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.93641,-0.13608,-0.32343,309.4,-0.10857,0.98887,-0.10171,84.338,0.33368,-0.06013,-0.94077,157.29

> view matrix models
> #2,-0.93641,-0.13608,-0.32343,309.45,-0.10857,0.98887,-0.10171,84.54,0.33368,-0.06013,-0.94077,157.44

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.99496,-0.099771,0.01032,-4.4169,-0.030699,-0.20496,0.97829,89.685,-0.09549,-0.97367,-0.20698,240.67

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.99496,-0.099771,0.01032,37.439,-0.030699,-0.20496,0.97829,22.095,-0.09549,-0.97367,-0.20698,328.7

> view matrix models
> #2,0.99496,-0.099771,0.01032,17.624,-0.030699,-0.20496,0.97829,20.675,-0.09549,-0.97367,-0.20698,336.06

> select add #1

3065 atoms, 3154 bonds, 396 residues, 3 models selected  

> select subtract #2

2 models selected  

> transparency #1.1 60

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99944,0.019468,-0.027269,1.1849,-0.019121,0.99973,0.01291,0.77266,0.027513,-0.012381,0.99954,-1.8735

> select add #2

3065 atoms, 3154 bonds, 396 residues, 3 models selected  

> select subtract #1

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> view matrix models
> #2,0.78144,-0.47235,-0.40772,162.45,0.31647,-0.26311,0.91138,-7.572,-0.53777,-0.84122,-0.056123,353.83

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.78144,-0.47235,-0.40772,163.11,0.31647,-0.26311,0.91138,-5.745,-0.53777,-0.84122,-0.056123,356.41

> view matrix models
> #2,0.78144,-0.47235,-0.40772,162.74,0.31647,-0.26311,0.91138,-7.2215,-0.53777,-0.84122,-0.056123,355.38

> view matrix models
> #2,0.78144,-0.47235,-0.40772,163.15,0.31647,-0.26311,0.91138,-2.5668,-0.53777,-0.84122,-0.056123,357.42

> volume #1 level 0.05475

> view matrix models
> #2,0.78144,-0.47235,-0.40772,163.5,0.31647,-0.26311,0.91138,-3.985,-0.53777,-0.84122,-0.056123,357.58

> view matrix models
> #2,0.78144,-0.47235,-0.40772,160.12,0.31647,-0.26311,0.91138,-6.321,-0.53777,-0.84122,-0.056123,359.5

> volume #1 level 0.03543

> surface dust #1 size 91.71

> volume #1 level 0.0306

> select subtract #2

Nothing selected  

> save /home/spuser/Downloads/B2-J759.pdb relModel #1

> open /home/spuser/Downloads/fold_2025_08_06_17_39_model_0_rescaled.pdb

Chain information for fold_2025_08_06_17_39_model_0_rescaled.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> select add #3

3306 atoms, 3403 bonds, 420 residues, 1 model selected  

> view matrix models #3,1,0,0,-13.515,0,1,0,165.86,0,0,1,46.372

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.97982,0.1978,-0.02888,-14.845,0.13537,-0.76288,-0.63221,166.65,-0.14708,0.61554,-0.77426,21.282

> select clear

> hide #2 models

> show #2 models

> hide #3 models

> show #3 models

> select #3/B

1732 atoms, 1785 bonds, 219 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select add #3

1574 atoms, 1618 bonds, 201 residues, 1 model selected  

> view matrix models
> #3,0.97802,-0.12189,-0.16916,-17.054,0.16293,-0.059507,0.98484,170.67,-0.13011,-0.99076,-0.03834,9.2622

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.97802,-0.12189,-0.16916,2.4652,0.16293,-0.059507,0.98484,126.33,-0.13011,-0.99076,-0.03834,105.8

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.084559,0.96259,-0.25741,-6.4326,-0.93378,0.013593,0.35758,110.09,0.3477,0.2706,0.89771,121.61

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.084559,0.96259,-0.25741,-8.8238,-0.93378,0.013593,0.35758,122.95,0.3477,0.2706,0.89771,117.97

> view matrix models
> #3,-0.084559,0.96259,-0.25741,138.28,-0.93378,0.013593,0.35758,131.08,0.3477,0.2706,0.89771,126.68

> view matrix models
> #3,-0.084559,0.96259,-0.25741,136.77,-0.93378,0.013593,0.35758,142.1,0.3477,0.2706,0.89771,97.059

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.37247,0.92293,0.097342,131.6,0.71231,0.21707,0.66745,169.34,0.59488,0.31794,-0.73826,102.83

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.37247,0.92293,0.097342,123.1,0.71231,0.21707,0.66745,131.62,0.59488,0.31794,-0.73826,111.79

> view matrix models
> #3,-0.37247,0.92293,0.097342,143.34,0.71231,0.21707,0.66745,132.65,0.59488,0.31794,-0.73826,117.93

> view matrix models
> #3,-0.37247,0.92293,0.097342,141.78,0.71231,0.21707,0.66745,126.78,0.59488,0.31794,-0.73826,114.75

> view matrix models
> #3,-0.37247,0.92293,0.097342,141.78,0.71231,0.21707,0.66745,124.85,0.59488,0.31794,-0.73826,114.21

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.47253,-0.73836,-0.48118,143.68,0.022754,-0.53558,0.84418,108.34,-0.88102,-0.40985,-0.23628,85.126

> view matrix models
> #3,0.10253,-0.97038,-0.21877,135.91,-0.039301,-0.2237,0.97386,109.49,-0.99395,-0.091248,-0.061072,85.478

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.10253,-0.97038,-0.21877,139.31,-0.039301,-0.2237,0.97386,123.78,-0.99395,-0.091248,-0.061072,117.41

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.060909,0.99799,0.01745,152.65,-0.88281,0.045705,0.4675,112.84,0.46577,-0.043881,0.88382,139.98

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.060909,0.99799,0.01745,154.72,-0.88281,0.045705,0.4675,138.15,0.46577,-0.043881,0.88382,99.681

> view matrix models
> #3,0.060909,0.99799,0.01745,147.2,-0.88281,0.045705,0.4675,138.66,0.46577,-0.043881,0.88382,102.84

> view matrix models
> #3,0.060909,0.99799,0.01745,147.37,-0.88281,0.045705,0.4675,140.68,0.46577,-0.043881,0.88382,98.356

> ui tool show "Fit in Map"

> hide #3 models

> show #3 models

> hide #2 models

> show #2 models

> fitmap #3 inMap #1

Fit molecule fold_2025_08_06_17_39_model_0_rescaled.pdb (#3) to map
cryosparc_P12_J759_003_volume_map_sharp(1).mrc (#1) using 1574 atoms  
average map value = 0.05132, steps = 144  
shifted from previous position = 5.29  
rotated from previous position = 18.6 degrees  
atoms outside contour = 700, contour level = 0.030602  
  
Position of fold_2025_08_06_17_39_model_0_rescaled.pdb (#3) relative to
cryosparc_P12_J759_003_volume_map_sharp(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.19848961 0.97992800 -0.01851979 144.21605425  
-0.96479260 0.19868094 0.17234007 147.51714279  
0.17256039 -0.01633995 0.98486339 97.90979917  
Axis -0.09610971 -0.09733230 -0.99060050  
Axis point 150.23951587 -12.00475355 0.00000000  
Rotation angle (degrees) 78.98786048  
Shift along axis -125.20824067  
  

> hide #2 models

> show #2 models

> close #2

> select subtract #3

Nothing selected  

> save /home/spuser/Downloads/TREM2-J759.pdb relModel #1

> open /home/spuser/Downloads/B2-J759.pdb

Chain information for B2-J759.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open /home/spuser/Downloads/TREM2-J759-coot-0.pdb

Chain information for TREM2-J759-coot-0.pdb #4  
---  
Chain | Description  
A | No description available  
  

> hide #3 models

> color #4 #ef2929ff

> color #4 #cc0000ff

> color #4 #a40000ff

> color #4 #cc0000ff

> color #4 #a40000ff

> volume #1 level 0.0453

> volume #1 level 0.04412

> volume #1 level 0.04295

> fitmap #4 inMap #1

Fit molecule TREM2-J759-coot-0.pdb (#4) to map
cryosparc_P12_J759_003_volume_map_sharp(1).mrc (#1) using 1574 atoms  
average map value = 0.08134, steps = 56  
shifted from previous position = 1.7  
rotated from previous position = 2.85 degrees  
atoms outside contour = 246, contour level = 0.042946  
  
Position of TREM2-J759-coot-0.pdb (#4) relative to
cryosparc_P12_J759_003_volume_map_sharp(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99987827 0.01375717 -0.00736071 -0.74812773  
-0.01394609 0.99955782 -0.02626177 4.01697870  
0.00699616 0.02636122 0.99962800 -4.17339431  
Axis 0.86015950 -0.23467305 -0.45282910  
Axis point 0.00000000 155.25952952 153.05838083  
Rotation angle (degrees) 1.75289907  
Shift along axis 0.30364855  
  

> volume #1 level 0.04647

> fitmap #2 inMap #1

Fit molecule B2-J759.pdb (#2) to map
cryosparc_P12_J759_003_volume_map_sharp(1).mrc (#1) using 3065 atoms  
average map value = 0.05834, steps = 320  
shifted from previous position = 5.46  
rotated from previous position = 29 degrees  
atoms outside contour = 1278, contour level = 0.046473  
  
Position of B2-J759.pdb (#2) relative to
cryosparc_P12_J759_003_volume_map_sharp(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.85826953 -0.32484069 0.39730586 -1.02218865  
0.33448549 0.94122851 0.04699307 -51.01971821  
-0.38922086 0.09256033 0.91648225 52.66903678  
Axis 0.04435494 0.76560108 0.64178472  
Axis point 133.42650623 0.00000000 49.57776429  
Rotation angle (degrees) 30.90834047  
Shift along axis -5.30390703  
  

> volume #1 level 0.0306

> select add #2

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.89104,-0.33081,0.31083,7.8523,0.32814,0.94256,0.062486,-52.582,-0.31364,0.046318,0.94841,43.663

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.89104,-0.33081,0.31083,8.1596,0.32814,0.94256,0.062486,-42.913,-0.31364,0.046318,0.94841,44.83

> volume #1 level 0.04295

> select subtract #2

Nothing selected  

> color #2 #a40000ff

> color #2 #ef2929ff

> color #2 #a40000ff

> select add #2

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> view matrix models
> #2,0.89104,-0.33081,0.31083,8.7842,0.32814,0.94256,0.062486,-45.185,-0.31364,0.046318,0.94841,46.979

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.98138,-0.074475,-0.17707,36.345,0.08827,0.99354,0.071341,-19.979,0.17062,-0.085643,0.98161,-7.8136

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.98138,-0.074475,-0.17707,36.302,0.08827,0.99354,0.071341,-20.967,0.17062,-0.085643,0.98161,-8.9731

> select subtract #2

Nothing selected  

> color #2 #ef2929ff

> color #2 #8ae234ff

> color #2 #729fcfff

> volume #1 level 0.03237

> select add #2

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> view matrix models
> #2,0.98138,-0.074475,-0.17707,40.019,0.08827,0.99354,0.071341,-23.368,0.17062,-0.085643,0.98161,-4.9186

> view matrix models
> #2,0.98138,-0.074475,-0.17707,45.158,0.08827,0.99354,0.071341,-19.737,0.17062,-0.085643,0.98161,-9.337

> view matrix models
> #2,0.98138,-0.074475,-0.17707,46.116,0.08827,0.99354,0.071341,-21.483,0.17062,-0.085643,0.98161,-7.4468

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.97037,-0.028118,-0.23998,51.049,0.04768,0.99596,0.076103,-16.89,0.23687,-0.08529,0.96779,-14.596

> select subtract #2

Nothing selected  

> save /home/spuser/Downloads/TREM2-219-update4.jpg width 1043 height 793
> supersample 3

> select add #4

1574 atoms, 1618 bonds, 201 residues, 1 model selected  

> view matrix models
> #4,0.98954,0.069694,-0.12632,6.9916,-0.073121,0.99706,-0.022693,11.359,0.12437,0.031693,0.99173,-19.322

> view matrix models
> #4,0.99987,0.014473,0.0075401,-1.8284,-0.014403,0.99985,-0.0092678,1.8183,-0.0076732,0.009158,0.99993,0.048087

> hide #2 models

> show #2 models

> select subtract #4

Nothing selected  

> hide #4 models

> select add #2

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> select add #4

4639 atoms, 4772 bonds, 597 residues, 2 models selected  

> show #4 models

> show #3 models

> select add #3

6213 atoms, 6390 bonds, 798 residues, 3 models selected  

> hide #3 models

> close #3

> select subtract #4

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> select subtract #2

Nothing selected  

> save /home/spuser/Downloads/B2-TREM2_update4.cxs

> close #2

> close

> open /home/spuser/Downloads/cryosparc_P12_J766_011_volume_map.mrc

Opened cryosparc_P12_J766_011_volume_map.mrc as #1, grid size 256,256,256,
pixel 1.08, shown at level 0.0233, step 1, values float32  

> surface dust #1 size 6.48

> volume #1 level 0.0752

> volume #1 level 0.03197

> close

> open /home/spuser/Downloads/cryosparc_P12_J689_012_volume_map.mrc

Opened cryosparc_P12_J689_012_volume_map.mrc as #1, grid size 280,280,280,
pixel 1.08, shown at level 0.0218, step 2, values float32  

> surface dust #1 size 6.48

> volume #1 level 0.1087

> volume #1 color #729fcf

> volume #1 level 0.1421

> volume #1 level 0.09198

> volume #1 step 1

> volume #1 level 0.1419

> volume #1 level 0.2002

> volume #1 level 0.09198

> hide #!1 models

> open /home/spuser/Downloads/cryosparc_P12_J686_003_volume_map_sharp.mrc

Opened cryosparc_P12_J686_003_volume_map_sharp.mrc as #2, grid size
280,280,280, pixel 1.08, shown at level 0.0518, step 2, values float32  

> volume #2 color #729fcf

> volume #2 level 0.0562

> surface dust #1 size 6.48

> surface dust #2 size 6.48

> volume #2 level 0.1042

> volume #2 step 1

> volume #2 level 0.1271

> volume #2 level 0.1248

> volume #2 level 0.1202

> hide #!2 models

> open /home/spuser/Downloads/cryosparc_P12_J583_011_volume_map_sharp(2).mrc

Opened cryosparc_P12_J583_011_volume_map_sharp(2).mrc as #3, grid size
256,256,256, pixel 1.08, shown at level 0.0586, step 1, values float32  

> volume #3 color #729fcf

> surface dust #2 size 6.48

> surface dust #3 size 6.48

> surface dust #3 size 14.9

> surface dust #3 size 22.16

> surface dust #3 size 25.73

> volume #3 level 0.09282

> volume #3 level 0.1185

> volume #3 level 0.1099

> close #3

> open /home/spuser/Downloads/B2-J759.pdb

Chain information for B2-J759.pdb #3  
---  
Chain | Description  
A | No description available  
  

> show #!1 models

> select add #3

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,6.7772,0,1,0,5.5349,0,0,1,10.167

> volume #1 level 0.06701

> select subtract #3

Nothing selected  

> select add #3

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> view matrix models #3,1,0,0,-21.255,0,1,0,28.515,0,0,1,-11.577

> volume #1 level 0.07117

> select #3/100-220

Nothing selected  

> select #3/A 100-220

Expected a keyword  

> select #3/A:100-220

909 atoms, 935 bonds, 121 residues, 1 model selected  

> select #3/A:200-320

903 atoms, 923 bonds, 121 residues, 1 model selected  

> hide #3/A

> select #3/A

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> hide sel target a

> cartoon hide sel

> select #3/A:200-320

903 atoms, 923 bonds, 121 residues, 1 model selected  

> cartoon sel

> hide #3/A:305-320

> select #3/A:305-320

108 atoms, 109 bonds, 16 residues, 1 model selected  

> cartoon hide sel

> select add #3

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select add #3

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> view matrix models #3,1,0,0,-18.666,0,1,0,25.063,0,0,1,-11.301

> view matrix models #3,1,0,0,-34.656,0,1,0,23.805,0,0,1,-5.2898

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.51378,-0.3481,0.78413,89.123,0.83339,0.014482,0.55249,-35.366,-0.20368,0.93735,0.28266,3.8622

> view matrix models
> #3,0.98019,0.027232,0.19616,-68.318,-0.19758,0.20157,0.95934,8.1941,-0.013414,-0.9791,0.20295,270.41

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.98019,0.027232,0.19616,-31.547,-0.19758,0.20157,0.95934,11.359,-0.013414,-0.9791,0.20295,256.81

> view matrix models
> #3,0.98019,0.027232,0.19616,-8.8953,-0.19758,0.20157,0.95934,-10.049,-0.013414,-0.9791,0.20295,281.08

> view matrix models
> #3,0.98019,0.027232,0.19616,-17.194,-0.19758,0.20157,0.95934,-9.5415,-0.013414,-0.9791,0.20295,285.52

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.97922,-0.18038,0.092702,30.206,-0.065215,0.15276,0.98611,-24.557,-0.19203,-0.97166,0.13782,319.06

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.97922,-0.18038,0.092702,29.605,-0.065215,0.15276,0.98611,-25.259,-0.19203,-0.97166,0.13782,318.7

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.94215,-0.22132,-0.25173,97.321,0.24955,-0.038243,0.96761,-36.51,-0.22378,-0.97445,0.0192,342.92

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.94215,-0.22132,-0.25173,91.136,0.24955,-0.038243,0.96761,-38.576,-0.22378,-0.97445,0.0192,342.23

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.96434,-0.12245,-0.23463,70.962,0.23058,-0.046445,0.97194,-35.561,-0.12991,-0.99139,-0.016554,338.04

> select subtract #3

Nothing selected  

> select add #2

2 models selected  

> transparency #2.1 50

> transparency #2.1 0

> view matrix models
> #2,0.99273,0.090995,-0.078803,0.26801,-0.091987,0.99572,-0.0090426,14.607,0.077643,0.016226,0.99685,-12.452

> select add #3

3065 atoms, 3154 bonds, 396 residues, 3 models selected  

> view matrix models
> #2,0.99209,0.10015,-0.075652,-1.3112,-0.10215,0.9945,-0.023097,18.198,0.072923,0.030643,0.99687,-13.713,#3,0.96598,-0.12608,-0.22578,70.057,0.2237,-0.030633,0.97418,-37.8,-0.12974,-0.99155,-0.0013864,335.75

> select subtract #2

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> view matrix models
> #3,0.99778,0.014406,-0.065051,18.857,0.066093,-0.090682,0.99368,-11.203,0.0084162,-0.99578,-0.091433,332.74

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.99778,0.014406,-0.065051,-18.512,0.066093,-0.090682,0.99368,-14.787,0.0084162,-0.99578,-0.091433,349.62

> view matrix models
> #3,0.99778,0.014406,-0.065051,-7.2749,0.066093,-0.090682,0.99368,-33.372,0.0084162,-0.99578,-0.091433,348.93

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.38253,0.80729,0.44939,-125.2,-0.89547,0.20413,0.39555,150.97,0.22759,-0.55373,0.80099,108.13

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.38253,0.80729,0.44939,-97.018,-0.89547,0.20413,0.39555,151.77,0.22759,-0.55373,0.80099,108.43

> view matrix models
> #3,0.38253,0.80729,0.44939,-104.74,-0.89547,0.20413,0.39555,162.43,0.22759,-0.55373,0.80099,101.3

> view matrix models
> #3,0.38253,0.80729,0.44939,-99.77,-0.89547,0.20413,0.39555,171.95,0.22759,-0.55373,0.80099,92.791

> view matrix models
> #3,0.38253,0.80729,0.44939,-96.923,-0.89547,0.20413,0.39555,170.83,0.22759,-0.55373,0.80099,93.065

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.57862,0.58327,0.57008,-110.45,-0.74507,0.093704,0.66037,123.11,0.33175,-0.80686,0.4888,167.45

> view matrix models
> #3,0.64995,0.50038,0.572,-108.25,-0.70291,0.10965,0.70278,108.16,0.28894,-0.85883,0.42299,191.59

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.64995,0.50038,0.572,-104.32,-0.70291,0.10965,0.70278,107.49,0.28894,-0.85883,0.42299,191.07

> view matrix models
> #3,0.64995,0.50038,0.572,-107.34,-0.70291,0.10965,0.70278,113.35,0.28894,-0.85883,0.42299,183.4

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.20438,0.20128,0.95797,-67.883,-0.92448,-0.28203,0.2565,273.57,0.3218,-0.93805,0.12844,239.11

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.20438,0.20128,0.95797,-63.896,-0.92448,-0.28203,0.2565,272.39,0.3218,-0.93805,0.12844,239.55

> view matrix models
> #3,0.20438,0.20128,0.95797,-62.751,-0.92448,-0.28203,0.2565,267.63,0.3218,-0.93805,0.12844,237

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.57102,0.6028,0.55728,-104.12,-0.37685,-0.41061,0.83029,118.47,0.72933,-0.68413,-0.0073007,167.94

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.57102,0.6028,0.55728,-106.56,-0.37685,-0.41061,0.83029,123.51,0.72933,-0.68413,-0.0073007,168.57

> volume #1 level 0.1419

> volume #2 level 0.1708

> view matrix models
> #3,0.57102,0.6028,0.55728,-133.95,-0.37685,-0.41061,0.83029,142.38,0.72933,-0.68413,-0.0073007,157.04

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.51442,0.83667,0.18804,38.07,0.09853,-0.16016,0.98216,17.32,0.85186,0.52377,-4.5928e-05,-36.294

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.51442,0.83667,0.18804,70.41,0.09853,-0.16016,0.98216,-6.9487,0.85186,0.52377,-4.5928e-05,-21.84

> ui tool show "Fit in Map"

> fitmap #3 inMap #2

Fit molecule B2-J759.pdb (#3) to map
cryosparc_P12_J686_003_volume_map_sharp.mrc (#2) using 3065 atoms  
average map value = 0.04894, steps = 140  
shifted from previous position = 4.59  
rotated from previous position = 16.9 degrees  
atoms outside contour = 2806, contour level = 0.17075  
  
Position of B2-J759.pdb (#3) relative to
cryosparc_P12_J686_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.68688138 0.72670735 -0.00950829 143.67852596  
0.01814980 0.03023105 0.99937814 -25.75644866  
0.72654288 0.68628166 -0.03395474 -21.03233947  
Axis -0.29300349 -0.68881503 -0.66308582  
Axis point 83.18857636 0.00000000 31.43714412  
Rotation angle (degrees) 147.70436409  
Shift along axis -10.41063481  
  

> close #2

> close #3

> close #1

> open /home/spuser/Downloads/cryosparc_P12_J479_008_volume_map_sharp.mrc

Opened cryosparc_P12_J479_008_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.08, shown at level 0.0999, step 1, values float32  

> surface dust #1 size 6.48

> surface dust #1 size 10.62

> surface dust #1 size 15.81

> volume #1 level 0.2089

> open /home/spuser/Downloads/TREM2-J759.pdb

Chain information for TREM2-J759.pdb #2  
---  
Chain | Description  
A | No description available  
  

> close #2

> open /home/spuser/Downloads/B2-J759.pdb

Chain information for B2-J759.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,-0.79457,-0.49572,0.35059,261.75,-0.4361,0.86771,0.23854,41.884,-0.42246,0.036643,-0.90564,343.29

> view matrix models
> #2,-0.9816,-0.14397,-0.12546,313.38,-0.12346,0.97965,-0.15827,43.889,0.14569,-0.13987,-0.97939,299.01

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.9816,-0.14397,-0.12546,307.11,-0.12346,0.97965,-0.15827,44.022,0.14569,-0.13987,-0.97939,291.31

> view matrix models
> #2,-0.9816,-0.14397,-0.12546,313.34,-0.12346,0.97965,-0.15827,44.838,0.14569,-0.13987,-0.97939,288.75

> view matrix models
> #2,-0.9816,-0.14397,-0.12546,312.11,-0.12346,0.97965,-0.15827,41.307,0.14569,-0.13987,-0.97939,284.13

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule B2-J759.pdb (#2) to map
cryosparc_P12_J479_008_volume_map_sharp.mrc (#1) using 3065 atoms  
average map value = 0.06135, steps = 68  
shifted from previous position = 1.92  
rotated from previous position = 3.02 degrees  
atoms outside contour = 2586, contour level = 0.20889  
  
Position of B2-J759.pdb (#2) relative to
cryosparc_P12_J479_008_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98570893 -0.12981274 -0.10736177 306.17506647  
-0.10606251 0.97338529 -0.20315466 47.20870905  
0.13087643 -0.18886431 -0.97324284 292.08281269  
Axis 0.05958157 -0.99329978 0.09902314  
Axis point 145.65639505 0.00000000 157.66877102  
Rotation angle (degrees) 173.11236373  
Shift along axis 0.27294939  
  

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.98571,-0.12981,-0.10736,312.08,-0.10606,0.97339,-0.20315,45.114,0.13088,-0.18886,-0.97324,289.22

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.76015,0.2931,-0.57989,296.42,0.4229,0.90074,-0.099077,-34.524,0.49329,-0.32055,-0.80865,231.35

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.76015,0.2931,-0.57989,295.89,0.4229,0.90074,-0.099077,-35.327,0.49329,-0.32055,-0.80865,231.78

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.80549,0.23883,-0.54235,303.68,0.35194,0.92911,-0.11356,-27.035,0.47678,-0.28234,-0.83244,232.62

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.80549,0.23883,-0.54235,305.32,0.35194,0.92911,-0.11356,-23.461,0.47678,-0.28234,-0.83244,231.42

> volume #1 step 2

> volume #1 step 1

> volume #1 level 0.1726

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.062782,-0.75375,0.65416,134.66,-0.58576,0.50285,0.63563,49.518,-0.80805,-0.42308,-0.40994,364.35

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.062782,-0.75375,0.65416,126.54,-0.58576,0.50285,0.63563,70.998,-0.80805,-0.42308,-0.40994,389.96

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.46484,0.51818,-0.71792,110.38,0.79857,0.10479,0.5927,-61.935,0.38236,-0.84882,-0.3651,274.29

> view matrix models
> #2,-0.45822,-0.62975,0.62725,186.54,-0.61631,0.73361,0.28631,97.69,-0.64047,-0.25539,-0.72428,392.18

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.45822,-0.62975,0.62725,205.63,-0.61631,0.73361,0.28631,123.28,-0.64047,-0.25539,-0.72428,403.87

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.96443,-0.2323,0.12615,299.33,-0.24417,0.9657,-0.088344,97.714,-0.1013,-0.116,-0.98807,350.57

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.96443,-0.2323,0.12615,263.8,-0.24417,0.9657,-0.088344,54.293,-0.1013,-0.116,-0.98807,327.1

> view matrix models
> #2,-0.96443,-0.2323,0.12615,282.94,-0.24417,0.9657,-0.088344,44.001,-0.1013,-0.116,-0.98807,309.16

> select subtract #2

Nothing selected  

> select add #1

2 models selected  

> transparency #1.1 50

> close

> open /home/spuser/Downloads/cryosparc_P12_J498_002_volume_map_sharp.mrc

Opened cryosparc_P12_J498_002_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.08, shown at level 0.0138, step 1, values float32  

> surface dust #1 size 6.48

> surface dust #1 size 41.87

> volume #1 level 0.0361

> volume #1 level 0.04638

> open /home/spuser/Downloads/B2-J759.pdb

Chain information for B2-J759.pdb #2  
---  
Chain | Description  
A | No description available  
  

> select add #2

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> view matrix models #2,1,0,0,-41.796,0,1,0,-19.286,0,0,1,-43.273

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.83073,-0.043836,0.55495,133.98,-0.19117,0.95874,-0.21043,44.705,-0.52282,-0.2809,-0.80483,340.77

> view matrix models
> #2,-0.99976,-0.0038112,-0.021478,239.71,-0.0017557,0.99548,-0.094922,-4.0238,0.021743,-0.094861,-0.99525,269.39

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.99976,-0.0038112,-0.021478,271.55,-0.0017557,0.99548,-0.094922,17.194,0.021743,-0.094861,-0.99525,298.42

> view matrix models
> #2,-0.99976,-0.0038112,-0.021478,279.55,-0.0017557,0.99548,-0.094922,12.223,0.021743,-0.094861,-0.99525,287.4

> view matrix models
> #2,-0.99976,-0.0038112,-0.021478,281.62,-0.0017557,0.99548,-0.094922,10.546,0.021743,-0.094861,-0.99525,291.78

> fitmap #2 inMap #1

Fit molecule B2-J759.pdb (#2) to map
cryosparc_P12_J498_002_volume_map_sharp.mrc (#1) using 3065 atoms  
average map value = 0.06452, steps = 100  
shifted from previous position = 2.2  
rotated from previous position = 7.02 degrees  
atoms outside contour = 1393, contour level = 0.046376  
  
Position of B2-J759.pdb (#2) relative to
cryosparc_P12_J498_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98972604 -0.01533566 -0.14215196 302.80397034  
0.00015940 0.99411206 -0.10835674 11.69127030  
0.14297670 -0.10726615 -0.98389615 274.86353689  
Axis 0.00381925 -0.99851934 0.05426362  
Axis point 141.55681945 0.00000000 148.62886508  
Rotation angle (degrees) 171.79150201  
Shift along axis 4.39761670  
  

> volume #1 level 0.04409

> select add #1

3065 atoms, 3154 bonds, 396 residues, 3 models selected  

> select subtract #2

2 models selected  

> transparency #1.1 60

> volume #1 level 0.06692

> volume #1 level 0.04352

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.98655,-0.16344,-0.0011817,25.133,0.16332,0.9861,-0.030589,-15.624,0.0061646,0.029984,0.99953,-5.0103

> select add #2

3065 atoms, 3154 bonds, 396 residues, 3 models selected  

> select subtract #1

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.42,0.55536,-0.71776,118.74,-0.68149,-0.32929,-0.65356,364.76,-0.59931,0.76364,0.24017,76.47

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.42,0.55536,-0.71776,117.1,-0.68149,-0.32929,-0.65356,367.14,-0.59931,0.76364,0.24017,73.094

> view matrix models
> #2,0.42,0.55536,-0.71776,121.91,-0.68149,-0.32929,-0.65356,365.9,-0.59931,0.76364,0.24017,69.204

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.98854,0.014795,0.1502,257.41,-0.019323,0.97459,-0.22317,35.569,-0.14969,-0.22352,-0.96314,320.52

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.98854,0.014795,0.1502,260.04,-0.019323,0.97459,-0.22317,35.017,-0.14969,-0.22352,-0.96314,327.4

> view matrix models
> #2,-0.98854,0.014795,0.1502,255.15,-0.019323,0.97459,-0.22317,39.997,-0.14969,-0.22352,-0.96314,329.43

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.80861,-0.58183,0.087337,318.86,-0.5817,0.81287,0.029548,101.17,-0.088185,-0.026912,-0.99574,299.75

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.80861,-0.58183,0.087337,318.18,-0.5817,0.81287,0.029548,98.47,-0.088185,-0.026912,-0.99574,297.85

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.91358,-0.40218,-0.060137,331.33,-0.4016,0.91555,-0.022062,67.672,0.063931,0.0039959,-0.99795,272.95

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.91358,-0.40218,-0.060137,333.93,-0.4016,0.91555,-0.022062,65.915,0.063931,0.0039959,-0.99795,269.01

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.93206,-0.20117,-0.30132,346.46,-0.15761,0.974,-0.16275,45.646,0.32622,-0.1042,-0.93953,238.06

> view matrix models
> #2,-0.96569,-0.20278,-0.16226,330.22,-0.1872,0.97656,-0.10627,40.838,0.18001,-0.07225,-0.98101,260.43

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.96569,-0.20278,-0.16226,329.78,-0.1872,0.97656,-0.10627,43.608,0.18001,-0.07225,-0.98101,263.76

> fitmap #2 inMap #1

Fit molecule B2-J759.pdb (#2) to map
cryosparc_P12_J498_002_volume_map_sharp.mrc (#1) using 3065 atoms  
average map value = 0.06452, steps = 60  
shifted from previous position = 2.2  
rotated from previous position = 2.79 degrees  
atoms outside contour = 1358, contour level = 0.043522  
  
Position of B2-J759.pdb (#2) relative to
cryosparc_P12_J498_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98952249 -0.01431163 -0.14366766 302.88182401  
0.00141477 0.99406599 -0.10876942 11.59607263  
0.14437180 -0.10783305 -0.98363042 274.70239683  
Axis 0.00324601 -0.99850759 0.05451658  
Axis point 141.49606210 0.00000000 148.66259311  
Rotation angle (degrees) 171.70701856  
Shift along axis 4.38022499  
  

> volume #1 level 0.04809

> volume #1 level 0.07263

> volume #1 level 0.04409

> open /home/spuser/Downloads/cryosparc_P12_J448_004_volume_map.mrc

Opened cryosparc_P12_J448_004_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.08, shown at level 0.00264, step 1, values float32  

> volume #3 color #729fcf

> hide #!1 models

> surface dust #3 size 6.48

> surface dust #3 size 27.04

> volume #3 level 0.01475

> volume #3 level 0.02594

> transparency sel 60

> select add #3

3065 atoms, 3154 bonds, 396 residues, 3 models selected  

> select subtract #2

2 models selected  

> transparency #3.1 70

> fitmap #2 inMap #3

Fit molecule B2-J759.pdb (#2) to map cryosparc_P12_J448_004_volume_map.mrc
(#3) using 3065 atoms  
average map value = 0.05919, steps = 272  
shifted from previous position = 4.88  
rotated from previous position = 9.68 degrees  
atoms outside contour = 1172, contour level = 0.025938  
  
Position of B2-J759.pdb (#2) relative to cryosparc_P12_J448_004_volume_map.mrc
(#3) coordinates:  
Matrix rotation and translation  
-0.99074361 -0.13427517 0.01993149 292.59158572  
-0.13468103 0.99067394 -0.02064307 15.17103400  
-0.01697376 -0.02313638 -0.99958820 288.61454402  
Axis -0.06740213 0.99766557 -0.01097144  
Axis point 148.14565133 0.00000000 143.03690209  
Rotation angle (degrees) 178.94020826  
Shift along axis -7.75219383  
  

> volume #3 level 0.05809

> volume #3 level 0.00823

> surface dust #3 size 118.91

> ui mousemode right "rotate selected 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,-0.69427,-0.46151,0.55227,213.96,-0.42842,0.88159,0.19814,37.206,-0.57831,-0.099041,-0.80978,347.81

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.69427,-0.46151,0.55227,213.07,-0.42842,0.88159,0.19814,34.2,-0.57831,-0.099041,-0.80978,344.74

> view matrix models
> #2,-0.69427,-0.46151,0.55227,211.75,-0.42842,0.88159,0.19814,34.583,-0.57831,-0.099041,-0.80978,344.06

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.054655,0.80707,-0.58792,112.63,0.80177,0.31546,0.50758,-108.17,0.59512,-0.49912,-0.62984,206.83

> view matrix models
> #2,-0.62253,0.40426,-0.6701,272.61,0.52121,0.85289,0.030327,-68.008,0.58378,-0.33038,-0.74165,203

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.62253,0.40426,-0.6701,272.7,0.52121,0.85289,0.030327,-59.402,0.58378,-0.33038,-0.74165,205.87

> view matrix models
> #2,-0.62253,0.40426,-0.6701,279.95,0.52121,0.85289,0.030327,-57.531,0.58378,-0.33038,-0.74165,202.29

> view matrix models
> #2,-0.62253,0.40426,-0.6701,279.94,0.52121,0.85289,0.030327,-56.802,0.58378,-0.33038,-0.74165,202.63

> view matrix models
> #2,-0.62253,0.40426,-0.6701,280.1,0.52121,0.85289,0.030327,-57.484,0.58378,-0.33038,-0.74165,202.86

> view matrix models
> #2,-0.62253,0.40426,-0.6701,280.72,0.52121,0.85289,0.030327,-57.748,0.58378,-0.33038,-0.74165,203.22

> view matrix models
> #2,-0.62253,0.40426,-0.6701,281.11,0.52121,0.85289,0.030327,-57.221,0.58378,-0.33038,-0.74165,204.97

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.7345,0.38545,-0.55851,282.21,0.4738,0.8805,-0.015429,-47.349,0.48582,-0.27596,-0.82935,224.68

> view matrix models
> #2,-0.67277,0.40476,-0.61931,280.31,0.49597,0.86787,0.028431,-55.416,0.54899,-0.28803,-0.78463,210.71

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.67277,0.40476,-0.61931,278.23,0.49597,0.86787,0.028431,-54.686,0.54899,-0.28803,-0.78463,208.6

> view matrix models
> #2,-0.67277,0.40476,-0.61931,278.73,0.49597,0.86787,0.028431,-56.963,0.54899,-0.28803,-0.78463,210.57

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.85684,0.066793,-0.51124,332.72,0.17903,0.96842,-0.17353,4.3955,0.4835,-0.24021,-0.84174,222

> view matrix models
> #2,-0.76837,0.35868,-0.53006,284.56,0.42044,0.90731,0.0044935,-48.068,0.48254,-0.2194,-0.84795,220.31

> view matrix models
> #2,-0.78934,0.41428,-0.45312,268.41,0.4503,0.89233,0.031417,-54.317,0.41735,-0.17924,-0.89089,230.56

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.78934,0.41428,-0.45312,267.7,0.4503,0.89233,0.031417,-51.292,0.41735,-0.17924,-0.89089,229.32

> show #!1 models

> hide #!3 models

> volume #1 level 0.02754

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.9982,0.048432,0.035507,271.02,0.043984,0.99218,-0.11683,14.412,-0.040887,-0.11506,-0.99252,299.88

> surface dust #1 size 89.09

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.97737,0.11926,-0.17469,290.66,0.13624,0.9867,-0.088647,-1.9561,0.1618,-0.11044,-0.98062,269.31

> view matrix models
> #2,-0.8807,0.24759,-0.40381,295.01,0.29951,0.95153,-0.069808,-22.829,0.36695,-0.18243,-0.91218,239.97

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.8807,0.24759,-0.40381,294.06,0.29951,0.95153,-0.069808,-17.143,0.36695,-0.18243,-0.91218,240.14

> view matrix models
> #2,-0.8807,0.24759,-0.40381,293.25,0.29951,0.95153,-0.069808,-16.126,0.36695,-0.18243,-0.91218,240.97

> view matrix models
> #2,-0.8807,0.24759,-0.40381,294.98,0.29951,0.95153,-0.069808,-20.357,0.36695,-0.18243,-0.91218,241.53

> view matrix models
> #2,-0.8807,0.24759,-0.40381,295.15,0.29951,0.95153,-0.069808,-20.856,0.36695,-0.18243,-0.91218,241.74

> view matrix models
> #2,-0.8807,0.24759,-0.40381,296.96,0.29951,0.95153,-0.069808,-18.692,0.36695,-0.18243,-0.91218,241.31

> view matrix models
> #2,-0.8807,0.24759,-0.40381,297.02,0.29951,0.95153,-0.069808,-18.844,0.36695,-0.18243,-0.91218,241.38

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.83264,0.41451,-0.36727,262.65,0.45152,0.8921,-0.016807,-40.122,0.32068,-0.17983,-0.92996,250.17

> ui mousemode right "rotate selected models"

[Repeated 1 time(s)]

> view matrix models
> #2,-0.99232,0.10932,-0.057816,278.31,0.10667,0.99317,0.047224,-15.362,0.062584,0.040695,-0.99721,266.97

> view matrix models
> #2,-0.94457,-0.29832,0.13708,296.15,-0.30818,0.94962,-0.057009,63.868,-0.11316,-0.096094,-0.98892,308.27

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.94457,-0.29832,0.13708,295.13,-0.30818,0.94962,-0.057009,62.143,-0.11316,-0.096094,-0.98892,303.97

> view matrix models
> #2,-0.94457,-0.29832,0.13708,291.81,-0.30818,0.94962,-0.057009,61.674,-0.11316,-0.096094,-0.98892,306.54

> hide #!1 models

> hide #2 models

> open /home/spuser/Downloads/cryosparc_P12_J759_003_volume_map_sharp(1).mrc

Opened cryosparc_P12_J759_003_volume_map_sharp(1).mrc as #4, grid size
256,256,256, pixel 1.08, shown at level 0.0217, step 1, values float32  

> volume #4 color #729fcf

> surface dust #4 size 6.48

> surface dust #4 size 32.99

> volume #4 level 0.04467

> show #2 models

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.89756,-0.35403,0.26276,24.266,0.35096,0.93445,0.060199,-45.665,-0.26685,0.038186,0.96298,13.567

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.89756,-0.35403,0.26276,43.472,0.35096,0.93445,0.060199,-82.44,-0.26685,0.038186,0.96298,62.277

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.61446,-0.54457,0.57085,61.268,0.61486,0.78393,0.08601,-103.04,-0.49435,0.29814,0.81654,81.63

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.61446,-0.54457,0.57085,68.051,0.61486,0.78393,0.08601,-98.504,-0.49435,0.29814,0.81654,88.959

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.86728,-0.34824,0.35573,39.569,0.36486,0.93081,0.021659,-73.494,-0.33866,0.11101,0.93434,74.268

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.86728,-0.34824,0.35573,-0.93743,0.36486,0.93081,0.021659,-52.296,-0.33866,0.11101,0.93434,53.783

> view matrix models
> #2,0.86728,-0.34824,0.35573,10.076,0.36486,0.93081,0.021659,-48.044,-0.33866,0.11101,0.93434,45.875

> select add #4

3065 atoms, 3154 bonds, 396 residues, 3 models selected  

> select subtract #2

2 models selected  

> transparency #4.1 60

> select subtract #4

Nothing selected  

> select add #2

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> view matrix models
> #2,0.86728,-0.34824,0.35573,9.2601,0.36486,0.93081,0.021659,-48.809,-0.33866,0.11101,0.93434,45.377

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.81866,-0.25927,0.51243,-19.594,0.34561,0.93504,-0.079054,-31.398,-0.45865,0.24182,0.85508,56.726

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.81866,-0.25927,0.51243,-23.307,0.34561,0.93504,-0.079054,-29.229,-0.45865,0.24182,0.85508,58.033

> view matrix models
> #2,0.81866,-0.25927,0.51243,-23.341,0.34561,0.93504,-0.079054,-24.128,-0.45865,0.24182,0.85508,54.9

> volume #4 level 0.04996

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.89796,-0.22862,0.37603,-17.701,0.28916,0.95064,-0.11254,-13.27,-0.33174,0.20979,0.91975,31.701

> view matrix models
> #2,0.88163,-0.2961,0.36749,-5.183,0.3296,0.94363,-0.03041,-30.433,-0.33777,0.14794,0.92953,39.258

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.88163,-0.2961,0.36749,-6.1751,0.3296,0.94363,-0.03041,-32.38,-0.33777,0.14794,0.92953,37.536

> view matrix models
> #2,0.88163,-0.2961,0.36749,-6.3954,0.3296,0.94363,-0.03041,-30.667,-0.33777,0.14794,0.92953,35.17

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.87817,-0.2923,0.37867,-8.1176,0.32805,0.94412,-0.032008,-30.273,-0.34815,0.15233,0.92498,36.721

> view matrix models
> #2,0.78334,-0.37179,0.49814,-2.5499,0.43514,0.90028,-0.012332,-42.319,-0.44388,0.22642,0.86701,48.993

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.78334,-0.37179,0.49814,-1.5308,0.43514,0.90028,-0.012332,-42.921,-0.44388,0.22642,0.86701,52.744

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.87305,-0.31294,0.37397,-2.9356,0.34958,0.93634,-0.03258,-32.747,-0.33997,0.15918,0.92687,38.141

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.87305,-0.31294,0.37397,-1.5606,0.34958,0.93634,-0.03258,-28.939,-0.33997,0.15918,0.92687,34.404

> view matrix models
> #2,0.87305,-0.31294,0.37397,0.91737,0.34958,0.93634,-0.03258,-30.265,-0.33997,0.15918,0.92687,35.279

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.8821,-0.234,0.40884,-16.11,0.26703,0.96337,-0.024757,-23.575,-0.38807,0.13101,0.91227,47.915

> view matrix models
> #2,0.91363,-0.20216,0.35272,-16.188,0.23207,0.97169,-0.044191,-16.871,-0.3338,0.12223,0.93468,38.137

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.91363,-0.20216,0.35272,-15.423,0.23207,0.97169,-0.044191,-18.962,-0.3338,0.12223,0.93468,36.954

> view matrix models
> #2,0.91363,-0.20216,0.35272,-14.602,0.23207,0.97169,-0.044191,-15.562,-0.3338,0.12223,0.93468,37.97

> view matrix models
> #2,0.91363,-0.20216,0.35272,-15.232,0.23207,0.97169,-0.044191,-16.47,-0.3338,0.12223,0.93468,38.971

> fitmap #2 inMap #4

Fit molecule B2-J759.pdb (#2) to map
cryosparc_P12_J759_003_volume_map_sharp(1).mrc (#4) using 3065 atoms  
average map value = 0.05834, steps = 112  
shifted from previous position = 10.3  
rotated from previous position = 8.51 degrees  
atoms outside contour = 1367, contour level = 0.049964  
  
Position of B2-J759.pdb (#2) relative to
cryosparc_P12_J759_003_volume_map_sharp(1).mrc (#4) coordinates:  
Matrix rotation and translation  
0.85832925 -0.32473792 0.39726083 -1.02935345  
0.33438177 0.94126699 0.04696015 -50.99707438  
-0.38917825 0.09252951 0.91650344 52.65386252  
Axis 0.04436560 0.76566447 0.64170835  
Axis point 133.40468666 0.00000000 49.57343545  
Rotation angle (degrees) 30.90167942  
Shift along axis -5.30389254  
  

> view matrix models
> #2,0.85833,-0.32474,0.39726,-1.4111,0.33438,0.94127,0.04696,-42.259,-0.38918,0.09253,0.9165,54.112

> color #2 #a40000ff

> color #2 #cc0000ff

> open /home/spuser/Downloads/cryosparc_P12_J689_011_volume_map_sharp.mrc

Opened cryosparc_P12_J689_011_volume_map_sharp.mrc as #5, grid size
280,280,280, pixel 1.08, shown at level 0.1, step 2, values float32  

> volume #5 level 0.1351

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> select subtract #2

Nothing selected  

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> surface dust #5 size 6.48

> select add #4

2 models selected  

> select subtract #4

Nothing selected  

> select add #5

2 models selected  

> view matrix models #5,1,0,0,-8.1873,0,1,0,-9.4899,0,0,1,-17.105

> select add #2

3065 atoms, 3154 bonds, 396 residues, 3 models selected  

> show #2 models

> select subtract #2

2 models selected  

> fitmap #5 inMap #4

Fit map cryosparc_P12_J689_011_volume_map_sharp.mrc in map
cryosparc_P12_J759_003_volume_map_sharp(1).mrc using 6742 points  
correlation = 0.5835, correlation about mean = 0.335, overlap = 73.44  
steps = 88, shift = 7.92, angle = 2.64 degrees  
  
Position of cryosparc_P12_J689_011_volume_map_sharp.mrc (#5) relative to
cryosparc_P12_J759_003_volume_map_sharp(1).mrc (#4) coordinates:  
Matrix rotation and translation  
0.99899834 0.04473515 -0.00104400 -20.12798656  
-0.04474402 0.99893614 -0.01116060 -5.34863413  
0.00054362 0.01119613 0.99993717 -15.65800850  
Axis 0.24236642 -0.01721111 -0.97003211  
Axis point -127.50720929 503.44038360 0.00000000  
Rotation angle (degrees) 2.64351977  
Shift along axis 10.40247891  
  

> hide #!4 models

> volume #5 color #888a85

> volume #5 level 0.0733

> hide #!5 models

> select subtract #5

Nothing selected  

> show #!4 models

> ui mousemode right "rotate selected models"

> select add #2

3065 atoms, 3154 bonds, 396 residues, 1 model selected  

> view matrix models
> #2,0.79584,-0.36041,0.48656,-1.5661,0.37745,0.92362,0.066774,-48.908,-0.47347,0.13051,0.87109,67.679

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.79584,-0.36041,0.48656,-1.6066,0.37745,0.92362,0.066774,-48.8,-0.47347,0.13051,0.87109,67.01

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models
> #2,0.79584,-0.36041,0.48656,-1.6937,0.37745,0.92362,0.066774,-49.902,-0.47347,0.13051,0.87109,66.349

> volume #1 level 0.02869

> volume #5 level 0.1008

> show #!3 models

> 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,-0.008684,0,1,0,-15.589,0,0,1,50.046

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.97493,0.15985,0.15481,219.84,0.12975,0.97353,-0.18815,-2.9722,-0.18079,-0.16335,-0.96986,371.83

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.97493,0.15985,0.15481,219.76,0.12975,0.97353,-0.18815,9.4613,-0.18079,-0.16335,-0.96986,323.48

> view matrix models
> #3,-0.97493,0.15985,0.15481,229.86,0.12975,0.97353,-0.18815,10.542,-0.18079,-0.16335,-0.96986,322.99

> hide #!4 models

> show #!4 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> select subtract #3

Nothing selected  

> select add #3

2 models selected  

> hide #!3 models

> show #!3 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> hide #!4 models

> show #!4 models

> select subtract #3

Nothing selected  

> hide #2 models

> show #!5 models

> hide #!5 models

> close #5

> ui mousemode right "crop volume"

> ui mousemode right zone

[Repeated 1 time(s)]

> ui mousemode right "contour level"

> ui mousemode right "move planes"

[Repeated 1 time(s)]

> ui mousemode right "rotate slab"

> ui mousemode right "crop volume"

> select add #4

2 models selected  

> ui mousemode right "crop volume"

> select subtract #4

Nothing selected  

> close #1

> close #2

> close #3

> ui tool show Segmentations

Created segmentation sphere cursor with ID #1  
Created segmentation sphere cursor with ID #2  
Created segmentation sphere cursor with ID #3  

> ui view fourup

> segmentations create #4

Opened segmentation 1 of cryosparc_P12_J759_003_volume_map_sharp(1).mrc as #5,
grid size 256,256,256, pixel 1.08, shown at level 0.501, step 1, values
float64  

> close #1

> close #2

> close #3

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> close #5

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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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 "axial segmentation
cursor"  
  
RuntimeError: Tried to get the position of deleted drawing "axial 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.  
  




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       276Gi        26Gi       1.0Gi       199Gi       222Gi
	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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