Closing segmentation cursors: self._positions is None

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.3.1-arm64-arm-64bit
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 /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/composite_map/tail-
> fiber-J432-1.mrc

Opened tail-fiber-J432-1.mrc as #1, grid size 500,500,500, pixel 1.39, shown
at level 0.0519, step 2, values float32  

> open /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/composite_map/tail-
> fiber-J432-2.mrc

Opened tail-fiber-J432-2.mrc as #2, grid size 500,500,500, pixel 1.39, shown
at level 0.0507, step 2, values float32  

> open /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/composite_map/tail-
> fiber-J432-3.mrc

Opened tail-fiber-J432-3.mrc as #3, grid size 500,500,500, pixel 1.39, shown
at level 0.0498, step 2, values float32  

> open /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/composite_map/tail-
> fiber-J432-4.mrc

Opened tail-fiber-J432-4.mrc as #4, grid size 500,500,500, pixel 1.39, shown
at level 0.0492, step 2, values float32  

> open /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/composite_map/tail-
> fiber-J432-5.mrc

Opened tail-fiber-J432-5.mrc as #5, grid size 500,500,500, pixel 1.39, shown
at level 0.0488, step 2, values float32  

> open /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/composite_map/tail-
> fiber-J432-6.mrc

Opened tail-fiber-J432-6.mrc as #6, grid size 500,500,500, pixel 1.39, shown
at level 0.0484, step 2, values float32  

> open
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/composite_map/Whole_tail_J421.mrc

Opened Whole_tail_J421.mrc as #7, grid size 500,500,500, pixel 1.39, shown at
level 0.0788, step 2, values float32  

> open /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_I_capsid.mrc.mrc

Opened J474_I_capsid.mrc.mrc as #8, grid size 977,837,925, pixel
1.39,1.39,1.39, shown at step 1, values float32  

> volume #8 region 0,0,0,976,836,924 step 4

[Repeated 1 time(s)]

> volume add #1-8

Opened volume sum as #9, grid size 979,839,927, pixel 1.39, shown at step 1,
values float32  

> open /Users/xiaojiu/Desktop/cryosparc_P9_J31_002_volume_map.mrc

Opened cryosparc_P9_J31_002_volume_map.mrc as #10, grid size 800,800,800,
pixel 1.39, shown at step 1, values float32  

> hide #!10 models

> hide #!9 models

> show #!9 models

> show #!10 models

> volume #10 region 0,0,0,799,799,799 step 4

[Repeated 1 time(s)]

> select add #10

3 models selected  

> ui mousemode right "translate selected models"

> view matrix models #10,1,0,0,-221.99,0,1,0,-53.242,0,0,1,-580.28

> view matrix models #10,1,0,0,-267.08,0,1,0,-185.98,0,0,1,-582.06

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.93034,0.32342,-0.17284,-311.81,-0.30947,0.94531,0.10309,-41.077,0.19672,-0.042423,0.97954,-656.39

> view matrix models
> #10,-0.78451,0.59833,0.16294,301.27,-0.55633,-0.56301,-0.61116,1329.4,-0.27394,-0.57011,0.77455,11.498

> view matrix models
> #10,-0.89897,0.41547,0.13871,479.71,-0.39355,-0.62712,-0.67219,1308.5,-0.19229,-0.65887,0.72727,41.666

> view matrix models
> #10,-0.98865,0.13264,0.070537,724.26,-0.14149,-0.66421,-0.73404,1223.4,-0.050514,-0.73569,0.67543,34.355

> ui mousemode right "translate selected models"

> view matrix models
> #10,-0.98865,0.13264,0.070537,715.32,-0.14149,-0.66421,-0.73404,1197,-0.050514,-0.73569,0.67543,39.594

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.82996,-0.14079,-0.53976,1117.9,0.44994,-0.74092,-0.49859,780.42,-0.32972,-0.65667,0.67829,149.19

> view matrix models
> #10,-0.5056,-0.66337,-0.55165,1234.3,0.85159,-0.48629,-0.19574,247.97,-0.13841,-0.56874,0.81079,-79.39

> ui mousemode right "translate selected models"

> view matrix models
> #10,-0.5056,-0.66337,-0.55165,1294.1,0.85159,-0.48629,-0.19574,251.82,-0.13841,-0.56874,0.81079,-72.832

> ui tool show "Fit in Map"

> fitmap #10 inMap #9

Fit map cryosparc_P9_J31_002_volume_map.mrc in map volume sum using 79997
points  
correlation = 0.7173, correlation about mean = -0.018, overlap = 2241  
steps = 280, shift = 9.51, angle = 12.3 degrees  
  
Position of cryosparc_P9_J31_002_volume_map.mrc (#10) relative to volume sum
(#9) coordinates:  
Matrix rotation and translation  
-0.38033773 -0.78739735 -0.48512744 1265.46057970  
0.92484250 -0.32205701 -0.20235025 125.13676829  
0.00309136 -0.52562791 0.85070897 -196.51850309  
Axis -0.17864649 -0.26979462 0.94620098  
Axis point 612.54604180 432.18791350 0.00000000  
Rotation angle (degrees) 115.20402704  
Shift along axis -445.77731393  
  

> fitmap #10 inMap #9

Fit map cryosparc_P9_J31_002_volume_map.mrc in map volume sum using 79997
points  
correlation = 0.7173, correlation about mean = -0.01803, overlap = 2241  
steps = 40, shift = 0.0143, angle = 0.00289 degrees  
  
Position of cryosparc_P9_J31_002_volume_map.mrc (#10) relative to volume sum
(#9) coordinates:  
Matrix rotation and translation  
-0.38033602 -0.78738557 -0.48514788 1265.45728396  
0.92484310 -0.32203205 -0.20238726 125.14196679  
0.00312364 -0.52566084 0.85068850 -196.49463962  
Axis -0.17864394 -0.26982333 0.94619328  
Axis point 612.54721541 432.19609664 0.00000000  
Rotation angle (degrees) 115.20383079  
Shift along axis -445.75440869  
  

> volume resample #9 onGrid #10

Opened volume sum resampled as #11, grid size 800,800,800, pixel 1.39, shown
at step 1, values float32  

> hide #!10 models

> select add #10

3 models selected  

> select subtract #10

Nothing selected  

> save /Users/xiaojiu/Desktop/k1-1/k1_1_reference.mrc models #11

> show #!9 models

> hide #!11 models

> show #!11 models

> volume #!9,11 showOutlineBox true

> hide #!11 models

> hide #!9 models

> show #!11 models

> hide #!11 models

> show #!7 models

> close #10

> close #11

> close #9

> open /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_I_capsid.mrc.mrc

Opened J474_I_capsid.mrc.mrc as #9, grid size 977,837,925, pixel
1.39,1.39,1.39, shown at step 1, values float32  

> volume #9 region 0,0,0,976,836,924 step 4

[Repeated 1 time(s)]

> open
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_5*C6+1*C5_capsid.pdb

Chain information for J474_5*C6+1*C5_capsid.pdb #10  
---  
Chain | Description  
D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l | No description available  
  

> open /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_C6+C1_capsid.pdb

Chain information for J474_C6+C1_capsid.pdb #11  
---  
Chain | Description  
C D E F G H I | No description available  
  

> hide #!7 models

> hide #!9 models

> show #!9 models

> show #!8 models

> hide #!8 models

> close #8

> close #9

> close #10-11

> open /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_I_capsid.mrc.mrc

Opened J474_I_capsid.mrc.mrc as #8, grid size 977,837,925, pixel
1.39,1.39,1.39, shown at step 1, values float32  

> volume #8 region 0,0,0,976,836,924 step 4

[Repeated 1 time(s)]

> volume #8 step 1

> open
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_5*C6+1*C5_capsid.pdb

Chain information for J474_5*C6+1*C5_capsid.pdb #9  
---  
Chain | Description  
D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l | No description available  
  

> open /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_C6+C1_capsid.pdb

Chain information for J474_C6+C1_capsid.pdb #10  
---  
Chain | Description  
C D E F G H I | No description available  
  

> select add #9

90020 atoms, 91315 bonds, 12040 residues, 1 model selected  

> view matrix models #9,1,0,0,-103.59,0,1,0,-76.693,0,0,1,-530.09

> view matrix models #9,1,0,0,113.79,0,1,0,-99.471,0,0,1,-382.41

> view matrix models #9,1,0,0,7.481,0,1,0,-133.99,0,0,1,-392.37

> view matrix models #9,1,0,0,-38.223,0,1,0,-52.487,0,0,1,-430.1

> show sel cartoons

> hide sel atoms

> color #8 #d6d6d6ff models

> volume #8 change image level -0.01126,0 level 0.1156,0.8 level 0.3971,1

> volume #8 level 0.08148

> volume #8 level 0.09886

> volume #8 level 0.1359

> view matrix models #9,1,0,0,74.578,0,1,0,-207.86,0,0,1,-561.95

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.44118,0.71573,0.54138,-283.97,-0.7432,0.62952,-0.22662,504.6,-0.50301,-0.30237,0.80966,-33.314

> view matrix models
> #9,0.57595,0.68121,0.45193,-297.97,-0.73498,0.67352,-0.078562,412.77,-0.3579,-0.28691,0.88859,-152.24

> view matrix models
> #9,0.57656,0.62841,0.52219,-295.2,-0.70832,0.70299,-0.063916,374.75,-0.40726,-0.33303,0.85043,-82.404

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.57656,0.62841,0.52219,-319.79,-0.70832,0.70299,-0.063916,379.51,-0.40726,-0.33303,0.85043,-34.042

> view matrix models
> #9,0.57656,0.62841,0.52219,-326,-0.70832,0.70299,-0.063916,385.32,-0.40726,-0.33303,0.85043,-64.816

> view matrix models
> #9,0.57656,0.62841,0.52219,-328.4,-0.70832,0.70299,-0.063916,383.73,-0.40726,-0.33303,0.85043,-70.745

> view matrix models
> #9,0.57656,0.62841,0.52219,-346.05,-0.70832,0.70299,-0.063916,374.21,-0.40726,-0.33303,0.85043,-49.842

> view matrix models
> #9,0.57656,0.62841,0.52219,-349.41,-0.70832,0.70299,-0.063916,391.05,-0.40726,-0.33303,0.85043,-63.251

> fitmap #10 inMap #8

Fit molecule J474_C6+C1_capsid.pdb (#10) to map J474_I_capsid.mrc.mrc (#8)
using 18004 atoms  
average map value = 0.04646, steps = 220  
shifted from previous position = 33  
rotated from previous position = 9.94 degrees  
atoms outside contour = 18004, contour level = 0.13594  
  
Position of J474_C6+C1_capsid.pdb (#10) relative to J474_I_capsid.mrc.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.99112011 -0.12129520 -0.05448301 49.37961599  
0.12658148 0.98614137 0.10724891 -46.04721954  
0.04071918 -0.11319309 0.99273827 -6.87694409  
Axis -0.63875848 -0.27586034 0.71825391  
Axis point 442.90746698 249.45726820 -0.00000000  
Rotation angle (degrees) 9.93640845  
Shift along axis -23.77843860  
  

> view matrix models
> #9,0.57656,0.62841,0.52219,-350.43,-0.70832,0.70299,-0.063916,391.22,-0.40726,-0.33303,0.85043,-65.539

> view matrix models
> #9,0.57656,0.62841,0.52219,-351.34,-0.70832,0.70299,-0.063916,384.97,-0.40726,-0.33303,0.85043,-61.611

> fitmap #9 inMap #8

Fit molecule J474_5*C6+1*C5_capsid.pdb (#9) to map J474_I_capsid.mrc.mrc (#8)
using 90020 atoms  
average map value = 0.07534, steps = 128  
shifted from previous position = 22.8  
rotated from previous position = 4.23 degrees  
atoms outside contour = 69180, contour level = 0.13594  
  
Position of J474_5*C6+1*C5_capsid.pdb (#9) relative to J474_I_capsid.mrc.mrc
(#8) coordinates:  
Matrix rotation and translation  
0.60231780 0.62928794 0.49113130 -372.00542333  
-0.72155360 0.69235505 -0.00221143 368.05596755  
-0.34142886 -0.35304558 0.87108275 -82.14680903  
Axis -0.21588204 0.51230700 -0.83122589  
Axis point 53.54908754 509.33190236 0.00000000  
Rotation angle (degrees) 54.34679259  
Shift along axis 337.14949151  
  

> view matrix models
> #9,0.60232,0.62929,0.49113,-373.51,-0.72155,0.69236,-0.0022114,372.85,-0.34143,-0.35305,0.87108,-83.4

> view matrix models
> #9,0.60232,0.62929,0.49113,-373.27,-0.72155,0.69236,-0.0022114,373.5,-0.34143,-0.35305,0.87108,-83.21

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.66923,0.55282,0.4965,-364.76,-0.72591,0.62911,0.27798,298.99,-0.15868,-0.54645,0.82232,-43.271

> view matrix models
> #9,0.74791,0.5333,0.39525,-353.18,-0.65001,0.70913,0.27318,212.18,-0.1346,-0.46123,0.87701,-130.12

> fitmap #9 inMap #8

Fit molecule J474_5*C6+1*C5_capsid.pdb (#9) to map J474_I_capsid.mrc.mrc (#8)
using 90020 atoms  
average map value = 0.07548, steps = 76  
shifted from previous position = 2.28  
rotated from previous position = 1.65 degrees  
atoms outside contour = 69121, contour level = 0.13594  
  
Position of J474_5*C6+1*C5_capsid.pdb (#9) relative to J474_I_capsid.mrc.mrc
(#8) coordinates:  
Matrix rotation and translation  
0.76121324 0.51267272 0.39714114 -348.70198729  
-0.63064572 0.72792393 0.26909612 192.76666936  
-0.15113030 -0.45529489 0.87742019 -123.28831484  
Axis -0.49605108 0.37544728 -0.78292571  
Axis point -40.46302732 330.52924839 0.00000000  
Rotation angle (degrees) 46.89961472  
Shift along axis 341.87331068  
  

> view matrix models
> #9,0.75286,0.54617,0.3673,-352.27,-0.64487,0.72378,0.24553,212.51,-0.13174,-0.42171,0.89711,-162.01

> fitmap #9 inMap #8

Fit molecule J474_5*C6+1*C5_capsid.pdb (#9) to map J474_I_capsid.mrc.mrc (#8)
using 90020 atoms  
average map value = 0.07589, steps = 84  
shifted from previous position = 2.06  
rotated from previous position = 2.11 degrees  
atoms outside contour = 68836, contour level = 0.13594  
  
Position of J474_5*C6+1*C5_capsid.pdb (#9) relative to J474_I_capsid.mrc.mrc
(#8) coordinates:  
Matrix rotation and translation  
0.75240504 0.52867191 0.39292832 -350.82304024  
-0.63709814 0.73559023 0.23024546 208.83798047  
-0.16730993 -0.42357175 0.89027769 -137.56426697  
Axis -0.45113768 0.38656765 -0.80438812  
Axis point -30.08747339 351.12738615 0.00000000  
Rotation angle (degrees) 46.43820730  
Shift along axis 349.65456233  
  

> show #!7 models

> view matrix models
> #9,0.67986,0.60942,0.40792,-367.29,-0.7245,0.64428,0.24496,304.53,-0.11353,-0.46207,0.87954,-138.44

> view matrix models
> #9,0.75742,0.55672,0.34114,-349.19,-0.65182,0.61431,0.4447,201.97,0.038007,-0.55919,0.82817,-139.12

> view matrix models
> #9,0.76511,0.55339,0.32918,-346.35,-0.64276,0.62607,0.44147,191.36,0.03822,-0.54936,0.83471,-147.87

> fitmap #9 inMap #8

Fit molecule J474_5*C6+1*C5_capsid.pdb (#9) to map J474_I_capsid.mrc.mrc (#8)
using 90020 atoms  
average map value = 0.1096, steps = 88  
shifted from previous position = 3.78  
rotated from previous position = 4.15 degrees  
atoms outside contour = 55571, contour level = 0.13594  
  
Position of J474_5*C6+1*C5_capsid.pdb (#9) relative to J474_I_capsid.mrc.mrc
(#8) coordinates:  
Matrix rotation and translation  
0.79982770 0.51038980 0.31587640 -330.43173251  
-0.60022954 0.67978758 0.42144197 139.22171552  
0.00037083 -0.52667931 0.85006398 -148.53320470  
Axis -0.63463113 0.21118570 -0.74340025  
Axis point -3.76856988 211.32645146 0.00000000  
Rotation angle (degrees) 48.32997650  
Shift along axis 349.52351946  
  

> view matrix models
> #9,0.80892,0.50272,0.30481,-326.08,-0.58791,0.69372,0.41607,126.44,-0.0022856,-0.51577,0.85672,-156.46

> view matrix models
> #9,0.8166,0.49715,0.29327,-322.05,-0.5772,0.70049,0.41971,115.16,0.00323,-0.51201,0.85897,-162.59

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.8166,0.49715,0.29327,-321.49,-0.5772,0.70049,0.41971,116.82,0.00323,-0.51201,0.85897,-163.68

> view matrix models
> #9,0.8166,0.49715,0.29327,-322.14,-0.5772,0.70049,0.41971,115.4,0.00323,-0.51201,0.85897,-165.5

> view matrix models
> #9,0.8166,0.49715,0.29327,-321.7,-0.5772,0.70049,0.41971,117.13,0.00323,-0.51201,0.85897,-165.44

> view matrix models
> #9,0.8166,0.49715,0.29327,-321.29,-0.5772,0.70049,0.41971,115.74,0.00323,-0.51201,0.85897,-164.35

> fitmap #9 inMap #8

Fit molecule J474_5*C6+1*C5_capsid.pdb (#9) to map J474_I_capsid.mrc.mrc (#8)
using 90020 atoms  
average map value = 0.1096, steps = 60  
shifted from previous position = 2.11  
rotated from previous position = 1.91 degrees  
atoms outside contour = 55576, contour level = 0.13594  
  
Position of J474_5*C6+1*C5_capsid.pdb (#9) relative to J474_I_capsid.mrc.mrc
(#8) coordinates:  
Matrix rotation and translation  
0.79980164 0.51040807 0.31591285 -330.44279213  
-0.60026431 0.67981467 0.42134876 139.26460628  
0.00029762 -0.52662664 0.85009664 -148.54343376  
Axis -0.63454621 0.21126334 -0.74345068  
Axis point -3.76700449 211.38181407 0.00000000  
Rotation angle (degrees) 48.32868440  
Shift along axis 349.53744363  
  

> volume resample #9 onGrid #7

> volume resample #9 onGrid #8

> save
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_5*C6+1*C5_capsid.pdb
> models #9 relModel #8

> select subtract #9

Nothing selected  

> select add #9

90020 atoms, 91315 bonds, 12040 residues, 1 model selected  

> view matrix models
> #9,0.7998,0.51041,0.31591,-329.73,-0.60026,0.67981,0.42135,140.27,0.00029762,-0.52663,0.8501,-148.87

> view matrix models
> #9,0.7998,0.51041,0.31591,-323.61,-0.60026,0.67981,0.42135,141.63,0.00029762,-0.52663,0.8501,-149.51

> view matrix models
> #9,0.7998,0.51041,0.31591,-324.62,-0.60026,0.67981,0.42135,146.04,0.00029762,-0.52663,0.8501,-149.53

> view matrix models
> #9,0.7998,0.51041,0.31591,-324.22,-0.60026,0.67981,0.42135,141.53,0.00029762,-0.52663,0.8501,-150.77

> view matrix models
> #9,0.7998,0.51041,0.31591,-324.49,-0.60026,0.67981,0.42135,141.86,0.00029762,-0.52663,0.8501,-151.08

> fitmap #9 inMap #8

Fit molecule J474_5*C6+1*C5_capsid.pdb (#9) to map J474_I_capsid.mrc.mrc (#8)
using 90020 atoms  
average map value = 0.1096, steps = 68  
shifted from previous position = 6.98  
rotated from previous position = 0.00686 degrees  
atoms outside contour = 55576, contour level = 0.13594  
  
Position of J474_5*C6+1*C5_capsid.pdb (#9) relative to J474_I_capsid.mrc.mrc
(#8) coordinates:  
Matrix rotation and translation  
0.79981083 0.51045439 0.31581474 -330.44342878  
-0.60025200 0.67979632 0.42139589 139.24935649  
0.00041368 -0.52660543 0.85010973 -148.62930315  
Axis -0.63456505 0.21112048 -0.74347518  
Axis point -3.69791623 211.31475217 0.00000000  
Rotation angle (degrees) 48.32853362  
Shift along axis 349.58843819  
  

> fitmap #9 inMap #8

Fit molecule J474_5*C6+1*C5_capsid.pdb (#9) to map J474_I_capsid.mrc.mrc (#8)
using 90020 atoms  
average map value = 0.1096, steps = 44  
shifted from previous position = 0.0028  
rotated from previous position = 0.000897 degrees  
atoms outside contour = 55571, contour level = 0.13594  
  
Position of J474_5*C6+1*C5_capsid.pdb (#9) relative to J474_I_capsid.mrc.mrc
(#8) coordinates:  
Matrix rotation and translation  
0.79981083 0.51044669 0.31582717 -330.44446728  
-0.60025200 0.67979337 0.42140064 139.24878959  
0.00040535 -0.52661669 0.85010275 -148.61731301  
Axis -0.63457202 0.21113313 -0.74346564  
Axis point -3.70732036 211.31862808 0.00000000  
Rotation angle (degrees) 48.32891419  
Shift along axis 349.58271077  
  

> view matrix models
> #9,0.79981,0.51045,0.31583,-330.45,-0.60025,0.67979,0.4214,139.88,0.00040535,-0.52662,0.8501,-149.41

> view matrix models
> #9,0.79981,0.51045,0.31583,-331.11,-0.60025,0.67979,0.4214,139.47,0.00040535,-0.52662,0.8501,-150.89

> fitmap #9 inMap #8

Fit molecule J474_5*C6+1*C5_capsid.pdb (#9) to map J474_I_capsid.mrc.mrc (#8)
using 90020 atoms  
average map value = 0.1096, steps = 56  
shifted from previous position = 2.36  
rotated from previous position = 0.00524 degrees  
atoms outside contour = 55565, contour level = 0.13594  
  
Position of J474_5*C6+1*C5_capsid.pdb (#9) relative to J474_I_capsid.mrc.mrc
(#8) coordinates:  
Matrix rotation and translation  
0.79979152 0.51044565 0.31587776 -330.46549031  
-0.60027778 0.67981578 0.42132777 139.28136335  
0.00032624 -0.52658878 0.85012008 -148.61564209  
Axis -0.63451227 0.21122251 -0.74349124  
Axis point -3.73119728 211.37240756 0.00000000  
Rotation angle (degrees) 48.32813089  
Shift along axis 349.59819723  
  

> save
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_5*C6+1*C5_capsid.pdb
> models #9 relModel #8

> select subtract #9

Nothing selected  

> select add #10

18004 atoms, 18263 bonds, 2408 residues, 1 model selected  

> view matrix models
> #10,0.99112,-0.1213,-0.054483,232.91,0.12658,0.98614,0.10725,-353.97,0.040719,-0.11319,0.99274,35.198

> select add #9

108024 atoms, 109578 bonds, 14448 residues, 2 models selected  

> select subtract #10

90020 atoms, 91315 bonds, 12040 residues, 1 model selected  

> select subtract #9

Nothing selected  

> select add #10

18004 atoms, 18263 bonds, 2408 residues, 1 model selected  

> view matrix models
> #10,0.99112,-0.1213,-0.054483,210.41,0.12658,0.98614,0.10725,-327.92,0.040719,-0.11319,0.99274,-24.166

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.067702,0.76133,0.64482,191.34,-0.96612,-0.1113,0.23285,423.09,0.24905,-0.63874,0.72801,98.029

> view matrix models
> #10,-0.95878,0.27042,0.087216,745.25,-0.28413,-0.91032,-0.30097,488.75,-0.001996,-0.31335,0.94964,61.809

> view matrix models
> #10,-0.76147,0.49085,0.42337,583.68,-0.60763,-0.76796,-0.20252,547.01,0.22572,-0.41147,0.88303,19.94

> view matrix models
> #10,-0.91593,0.20506,0.345,739.74,-0.32679,-0.88009,-0.34446,495.36,0.23299,-0.42824,0.87311,23.699

> ui mousemode right "translate selected models"

> view matrix models
> #10,-0.91593,0.20506,0.345,790.36,-0.32679,-0.88009,-0.34446,580.34,0.23299,-0.42824,0.87311,15.283

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.6769,0.60412,0.42053,566.06,-0.6831,-0.72839,-0.053158,636.95,0.2742,-0.32325,0.90572,-36.852

> ui mousemode right "translate selected models"

> view matrix models
> #10,-0.6769,0.60412,0.42053,563.95,-0.6831,-0.72839,-0.053158,648.81,0.2742,-0.32325,0.90572,-29.892

> show sel cartoons

> hide sel atoms

> view matrix models
> #10,-0.6769,0.60412,0.42053,577.11,-0.6831,-0.72839,-0.053158,636.1,0.2742,-0.32325,0.90572,-67.024

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.77856,0.33966,-0.52771,752.79,-0.06569,-0.88037,-0.46972,495.31,-0.62413,-0.33104,0.70773,258.42

> view matrix models
> #10,-0.65807,0.60397,-0.44963,615.33,-0.34457,-0.77251,-0.53339,558.27,-0.66949,-0.19608,0.71647,227.02

> view matrix models
> #10,-0.49272,0.86954,-0.033588,444.47,-0.72756,-0.43283,-0.53227,573.87,-0.47736,-0.23782,0.84591,167.97

> view matrix models
> #10,-0.4447,0.89561,0.011077,416.44,-0.6658,-0.32226,-0.67295,521.33,-0.59913,-0.30663,0.73961,239.63

> ui mousemode right "translate selected models"

> view matrix models
> #10,-0.4447,0.89561,0.011077,405.46,-0.6658,-0.32226,-0.67295,610.2,-0.59913,-0.30663,0.73961,263.84

> view matrix models
> #10,-0.4447,0.89561,0.011077,450.06,-0.6658,-0.32226,-0.67295,592.93,-0.59913,-0.30663,0.73961,254.62

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.36243,0.93101,0.043116,407.53,-0.219,-0.040105,-0.9749,355.31,-0.90592,-0.36277,0.21843,407.6

> view matrix models
> #10,-0.2391,0.96619,0.096436,349.7,-0.26348,0.031031,-0.96417,345.6,-0.93456,-0.25595,0.24715,379.1

> ui mousemode right "translate selected models"

> view matrix models
> #10,-0.2391,0.96619,0.096436,351.17,-0.26348,0.031031,-0.96417,423.82,-0.93456,-0.25595,0.24715,432.94

> view matrix models
> #10,-0.2391,0.96619,0.096436,293.48,-0.26348,0.031031,-0.96417,297.66,-0.93456,-0.25595,0.24715,330.97

> view matrix models
> #10,-0.2391,0.96619,0.096436,305.2,-0.26348,0.031031,-0.96417,280.7,-0.93456,-0.25595,0.24715,315.8

> view matrix models
> #10,-0.2391,0.96619,0.096436,281.55,-0.26348,0.031031,-0.96417,393.18,-0.93456,-0.25595,0.24715,409.95

> view matrix models
> #10,-0.2391,0.96619,0.096436,307.27,-0.26348,0.031031,-0.96417,365.81,-0.93456,-0.25595,0.24715,386.92

> view matrix models
> #10,-0.2391,0.96619,0.096436,357.12,-0.26348,0.031031,-0.96417,345.91,-0.93456,-0.25595,0.24715,377.27

> view matrix models
> #10,-0.2391,0.96619,0.096436,329.19,-0.26348,0.031031,-0.96417,386.66,-0.93456,-0.25595,0.24715,410.45

> view matrix models
> #10,-0.2391,0.96619,0.096436,360.18,-0.26348,0.031031,-0.96417,389.84,-0.93456,-0.25595,0.24715,406.58

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.14752,0.96812,-0.20245,343.02,-0.11666,-0.2203,-0.96843,426,-0.98215,-0.11925,0.14544,381.04

> view matrix models
> #10,0.036506,0.99928,-0.010696,258.34,-0.1952,-0.0033668,-0.98076,378.85,-0.98008,0.037892,0.19493,323.36

> view matrix models
> #10,-0.014416,0.99382,-0.11002,283.05,-0.15845,-0.11091,-0.98112,403.32,-0.98726,0.0032888,0.15907,339.69

> view matrix models
> #10,0.066762,0.99576,0.063287,245.22,-0.22163,0.076643,-0.97211,359.9,-0.97284,0.050874,0.22581,314.76

> view matrix models
> #10,0.08989,0.97081,0.22238,237.64,0.26604,0.19177,-0.94469,148.95,-0.95976,0.14408,-0.24103,301.94

> view matrix models
> #10,0.12628,0.96206,0.24186,227,0.25795,0.20358,-0.94447,147.66,-0.95787,0.18165,-0.22246,287.32

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.12628,0.96206,0.24186,231.64,0.25795,0.20358,-0.94447,153.64,-0.95787,0.18165,-0.22246,274.58

> fitmap #10 inMap #8

Fit molecule J474_C6+C1_capsid.pdb (#10) to map J474_I_capsid.mrc.mrc (#8)
using 18004 atoms  
average map value = 0.07744, steps = 160  
shifted from previous position = 13.2  
rotated from previous position = 11.9 degrees  
atoms outside contour = 13470, contour level = 0.13594  
  
Position of J474_C6+C1_capsid.pdb (#10) relative to J474_I_capsid.mrc.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.20954075 0.97633145 0.05356834 192.78669412  
0.24415512 0.00080577 -0.96973586 228.33987446  
-0.94682678 0.21627817 -0.23820748 265.55213140  
Axis 0.69128585 0.58309512 -0.42675983  
Axis point -0.00000000 -102.74482457 249.28157199  
Rotation angle (degrees) 120.92599348  
Shift along axis 153.08759865  
  

> view matrix models
> #10,0.20954,0.97633,0.053568,190.34,0.24416,0.00080577,-0.96974,217.74,-0.94683,0.21628,-0.23821,265.82

> fitmap #10 inMap #8

Fit molecule J474_C6+C1_capsid.pdb (#10) to map J474_I_capsid.mrc.mrc (#8)
using 18004 atoms  
average map value = 0.1203, steps = 112  
shifted from previous position = 2.53  
rotated from previous position = 7.67 degrees  
atoms outside contour = 10075, contour level = 0.13594  
  
Position of J474_C6+C1_capsid.pdb (#10) relative to J474_I_capsid.mrc.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.14549876 0.98739488 -0.06230144 213.88164290  
0.21142189 -0.09254771 -0.97300345 262.77532643  
-0.96650447 0.12839891 -0.22222247 301.20970264  
Axis 0.67879199 0.55725845 -0.47823054  
Axis point 0.00000000 -96.61321962 294.03471187  
Rotation angle (degrees) 125.77725872  
Shift along axis 147.56723802  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.19706,0.98018,-0.020336,196.28,0.19766,-0.060038,-0.97843,256.59,-0.96026,0.18879,-0.20557,277.27

> fitmap #10 inMap #8

Fit molecule J474_C6+C1_capsid.pdb (#10) to map J474_I_capsid.mrc.mrc (#8)
using 18004 atoms  
average map value = 0.1203, steps = 104  
shifted from previous position = 1.13  
rotated from previous position = 3.99 degrees  
atoms outside contour = 10082, contour level = 0.13594  
  
Position of J474_C6+C1_capsid.pdb (#10) relative to J474_I_capsid.mrc.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.14548741 0.98739745 -0.06228710 213.88701196  
0.21136314 -0.09252321 -0.97301854 262.79203673  
-0.96651903 0.12839675 -0.22216039 301.22260386  
Axis 0.67877728 0.55725764 -0.47825236  
Axis point 0.00000000 -96.62540555 294.06049696  
Rotation angle (degrees) 125.77460244  
Shift along axis 147.56409542  
  

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.14549,0.9874,-0.062287,214.28,0.21136,-0.092523,-0.97302,264.11,-0.96652,0.1284,-0.22216,301.35

> view matrix models
> #10,0.14549,0.9874,-0.062287,214.96,0.21136,-0.092523,-0.97302,266.58,-0.96652,0.1284,-0.22216,302.33

> fitmap #10 inMap #8

Fit molecule J474_C6+C1_capsid.pdb (#10) to map J474_I_capsid.mrc.mrc (#8)
using 18004 atoms  
average map value = 0.1203, steps = 88  
shifted from previous position = 4.1  
rotated from previous position = 0.00461 degrees  
atoms outside contour = 10077, contour level = 0.13594  
  
Position of J474_C6+C1_capsid.pdb (#10) relative to J474_I_capsid.mrc.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.14552029 0.98739339 -0.06227463 213.87172839  
0.21143369 -0.09252774 -0.97300278 262.76151069  
-0.96649865 0.12842469 -0.22223290 301.20014682  
Axis 0.67879810 0.55726370 -0.47821576  
Axis point 0.00000000 -96.61322291 294.01949683  
Rotation angle (degrees) 125.77616153  
Shift along axis 147.56451821  
  

> ui tool show "Color Zone"

> color zone #7 near #10 distance 8.33

> ui tool show "Surface Color"

> color radial #7.1 palette #ff0000:#ffffff:#0000ff

> color radial #7.1 palette 307.5,#ff0000:556.1,#ffffff:804.8,#0000ff

> hide #!7 models

> color radial #8.2 palette 307.5,#ff0000:556.1,#ffffff:804.8,#0000ff

> color radial #8.2 palette 307.5,#ff0000:556.1,#ffffff:804.8,#0000ff center
> 347.54,347.89,-13.603

> color single #8.2

> color cylindrical #8.2 palette 307.5,#ff0000:556.1,#ffffff:804.8,#0000ff
> center 347.54,347.89,-13.603

Surface Color: could not parse center "" as 3 numbers  

> color cylindrical #8.2 palette 307.5,#ff0000:556.1,#ffffff:804.8,#0000ff

Surface Color: could not parse center "" as 3 numbers  

> color cylindrical #8.2 palette 307.5,#ff0000:556.1,#ffffff:804.8,#0000ff

Surface Color: could not parse center "" as 3 numbers  

> color cylindrical #8.2 palette #ff0000:#ffffff:#0000ff

Surface Color: could not parse center "" as 3 numbers  

> color cylindrical #8.2 palette 192.4,#ff0000:492.9,#ffffff:793.5,#0000ff

> color single #8.2

> view matrix models
> #10,0.14552,0.98739,-0.062275,140.74,0.21143,-0.092528,-0.973,166.91,-0.9665,0.12842,-0.22223,318.42

> view matrix models
> #10,0.14552,0.98739,-0.062275,142.16,0.21143,-0.092528,-0.973,163.96,-0.9665,0.12842,-0.22223,315.9

> fitmap #10 inMap #8

Fit molecule J474_C6+C1_capsid.pdb (#10) to map J474_I_capsid.mrc.mrc (#8)
using 18004 atoms  
average map value = 0.08312, steps = 244  
shifted from previous position = 12.3  
rotated from previous position = 29.8 degrees  
atoms outside contour = 13072, contour level = 0.13594  
  
Position of J474_C6+C1_capsid.pdb (#10) relative to J474_I_capsid.mrc.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.31352464 0.80617682 -0.50177807 161.43961565  
-0.00741124 -0.52632748 -0.85024964 374.46298405  
-0.94955114 0.27029301 -0.15904187 256.09786713  
Axis 0.76994747 0.30767392 -0.55903278  
Axis point 0.00000000 68.09718661 283.30668266  
Rotation angle (degrees) 133.30818819  
Shift along axis 96.34541478  
  

> view matrix models
> #10,0.31352,0.80618,-0.50178,156.58,-0.0074112,-0.52633,-0.85025,383.47,-0.94955,0.27029,-0.15904,285.04

> view matrix models
> #10,0.31352,0.80618,-0.50178,160.67,-0.0074112,-0.52633,-0.85025,376.73,-0.94955,0.27029,-0.15904,283.72

> fitmap #10 inMap #8

Fit molecule J474_C6+C1_capsid.pdb (#10) to map J474_I_capsid.mrc.mrc (#8)
using 18004 atoms  
average map value = 0.1735, steps = 104  
shifted from previous position = 14.7  
rotated from previous position = 3.91 degrees  
atoms outside contour = 5487, contour level = 0.13594  
  
Position of J474_C6+C1_capsid.pdb (#10) relative to J474_I_capsid.mrc.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.35706748 0.79808421 -0.48534977 157.09749211  
-0.04993986 -0.50254860 -0.86310539 394.28495672  
-0.93274264 0.33242517 -0.13958755 259.66618973  
Axis 0.78011080 0.29193399 -0.55335494  
Axis point 0.00000000 74.55934741 295.23922542  
Rotation angle (degrees) 129.98105889  
Shift along axis 93.97106118  
  

> volume resample #10 onGrid #8

> save /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_C6+C1_capsid.pdb
> models #10 relModel #8

> select subtract #10

Nothing selected  

> hide #9 models

> hide #10 models

> show #!7 models

> hide #!7 models

> open /Users/xiaojiu/Downloads/overall_pbd.pdb

Chain information for overall_pbd.pdb #11  
---  
Chain | Description  
0 3 4 5 9 AA AE AF AG e f g k l m q r s w x y | No description available  
1 2 6 7 8 AB AC AD AH AI AJ h i j n o p t u v z | No description available  
A B C D E F G H I J K L | No description available  
A0 A1 A2 A3 A4 A5 A6 A7 A8 A9 AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ Aa Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax Ay Az B0 B1 B2 B3 B4 B5 B6 B7 B8 B9 BA BB BC BD BE BF BG BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX BY BZ Ba Bb Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp Bq Br Bs Bt Bu Bv Bw Bx By Bz C0 C1 C2 C3 C4 C5 C6 C7 C8 C9 CA CB CC CD CE CF CG CH CI CJ CK CL CM CN CO CP CQ CR CS CT CU CV CW CX CY CZ Ca Cb Cc Cd Ce Cf Cg Ch Ci Cj Ck Cl Cm Cn Co Cp Cq Cr Cs Ct Cu Cv Cw Cx Cy Cz D0 D1 D2 D3 D4 D5 D6 D7 D8 D9 DA DB DC DD DE DF DG DH DI DJ DK DL DM DN DO DP DQ DR DS DT DU DV DW DX DY DZ Da Db Dc Dd De Df Dg Dh Di Dj Dk Dl Dm Dn Do Dp Dq Dr Ds Dt Du Dv Dw Dx Dy Dz E0 E1 E2 E3 E4 E5 E6 E7 E8 E9 EA EB EC ED EE EF EG EH EI EJ EK EL EM EN EO EP EQ ER ES ET EU EV EW EX EY EZ Ea Eb Ec Ed Ee Ef Eg Eh Ei Ej Ek El Em En Eo Ep Eq Er Es Et Eu Ev Ew Ex Ey Ez F0 F1 F2 F3 F4 F5 F6 F7 F8 F9 FA FB FC FD FE FF FG FH FI FJ FK FL FM FN FO FP FQ FR FS FT FU FV FW FX FY FZ Fa Fb Fc Fd Fe Ff Fg Fh Fi Fj Fk Fl Fm Fn Fo Fp Fq Fr Fs Ft Fu Fv Fw Fx Fy Fz G1 GA GB GC GD GE GF GG GH GI GJ GK GL GM GN GO GP GQ GR GS GT GU GV GW GX GY GZ Ga Gb Gc Gd Ge Gf Gg Gh Gi Gj Gk Gl Gm Gn Go Gp Gq Gr Gs Gt Gu Gv Gw Gx Gy Gz | No description available  
M N O P Q R S T U V W X | No description available  
Y Z a b c d | No description available  
  

> show #!7 models

> select add #11

1334880 atoms, 1355695 bonds, 177482 residues, 1 model selected  

> view matrix models #11,1,0,0,342.09,0,1,0,-402.77,0,0,1,-101.89

> view matrix models #11,1,0,0,360.18,0,1,0,-407.79,0,0,1,-110.78

> fitmap #11 inMap #7

Fit molecule overall_pbd.pdb (#11) to map Whole_tail_J421.mrc (#7) using
1334880 atoms  
average map value = 0.01764, steps = 712  
shifted from previous position = 51.3  
rotated from previous position = 22.6 degrees  
atoms outside contour = 1300906, contour level = 0.078793  
  
Position of overall_pbd.pdb (#11) relative to Whole_tail_J421.mrc (#7)
coordinates:  
Matrix rotation and translation  
0.96176541 0.24057701 -0.13088165 211.60965410  
-0.26749964 0.92767830 -0.26049361 -278.01763468  
0.05874730 0.28554454 0.95656316 -303.38468314  
Axis 0.70952429 -0.24640466 -0.66019696  
Axis point 0.00000000 -7.87751106 -668.80328890  
Rotation angle (degrees) 22.63081082  
Shift along axis 418.94067587  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #11,0.97101,0.21724,0.099727,190.98,-0.22294,0.97355,0.049964,-358.62,-0.086235,-0.070749,0.99376,-65.723

> view matrix models
> #11,0.96794,0.19935,0.15284,194.79,-0.2192,0.96747,0.12633,-366.57,-0.12268,-0.15578,0.98014,-5.4332

> view matrix models
> #11,0.96344,0.20966,0.16683,185.24,-0.23051,0.96599,0.1172,-364.4,-0.13658,-0.15137,0.979,-8.7189

> ui mousemode right "translate selected models"

> view matrix models
> #11,0.96344,0.20966,0.16683,188.7,-0.23051,0.96599,0.1172,-361.34,-0.13658,-0.15137,0.979,-0.86988

> fitmap #11 inMap #7

Fit molecule overall_pbd.pdb (#11) to map Whole_tail_J421.mrc (#7) using
1334880 atoms  
average map value = 0.05142, steps = 2000  
shifted from previous position = 33  
rotated from previous position = 6.87 degrees  
atoms outside contour = 1207775, contour level = 0.078793  
  
Position of overall_pbd.pdb (#11) relative to Whole_tail_J421.mrc (#7)
coordinates:  
Matrix rotation and translation  
0.95030349 0.29172795 0.10871097 163.56250584  
-0.29773171 0.95365903 0.04347752 -320.43930809  
-0.09098959 -0.07368354 0.99312216 -53.06752996  
Axis -0.18500069 0.31533295 -0.93077380  
Axis point -886.82082268 -659.79596715 0.00000000  
Rotation angle (degrees) 18.46047139  
Shift along axis -81.91038230  
  

> fitmap #11 inMap #7

Fit molecule overall_pbd.pdb (#11) to map Whole_tail_J421.mrc (#7) using
1334880 atoms  
average map value = 0.05229, steps = 2000  
shifted from previous position = 0.422  
rotated from previous position = 0.0667 degrees  
atoms outside contour = 1206510, contour level = 0.078793  
  
Position of overall_pbd.pdb (#11) relative to Whole_tail_J421.mrc (#7)
coordinates:  
Matrix rotation and translation  
0.95040144 0.29183705 0.10755576 163.38064761  
-0.29775677 0.95365050 0.04349294 -320.54894689  
-0.08987776 -0.07336121 0.99324726 -53.56027291  
Axis -0.18470359 0.31207005 -0.93193179  
Axis point -889.62051690 -660.20935223 0.00000000  
Rotation angle (degrees) 18.44105378  
Shift along axis -80.29619832  
  

> show #9 models

> show sel cartoons

> show sel atoms

> hide #11 models

> show #9 atoms

> show #11 models

> hide #11 models

> show #11 models

> select subtract #11

Nothing selected  

> hide #11 models

> show #11 models

> hide #9 models

> fitmap #11 inMap #8

Fit molecule overall_pbd.pdb (#11) to map J474_I_capsid.mrc.mrc (#8) using
1334880 atoms  
average map value = 0.0447, steps = 104  
shifted from previous position = 7.24  
rotated from previous position = 1.9 degrees  
atoms outside contour = 1163131, contour level = 0.13594  
  
Position of overall_pbd.pdb (#11) relative to J474_I_capsid.mrc.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.94051193 0.32241614 0.10716878 141.13070180  
-0.32735619 0.94436727 0.03175511 -317.47939373  
-0.09096833 -0.06494842 0.99373360 -53.47508407  
Axis -0.14093462 0.28876274 -0.94697071  
Axis point -820.49301636 -562.48274488 0.00000000  
Rotation angle (degrees) 20.06460083  
Shift along axis -60.92708145  
  

> ui mousemode right "rotate selected models"

> select add #11

1334880 atoms, 1355695 bonds, 177482 residues, 1 model selected  

> view matrix models
> #11,0.94437,0.32814,0.022035,150.97,-0.32027,0.93283,-0.1651,-277.56,-0.07473,0.14886,0.98603,-200.48

> view matrix models
> #11,0.83594,0.54782,-0.03312,3.9107,-0.54274,0.8162,-0.19814,-197.55,-0.081514,0.18361,0.97961,-223.81

> fitmap #11 inMap #8

Fit molecule overall_pbd.pdb (#11) to map J474_I_capsid.mrc.mrc (#8) using
1334880 atoms  
average map value = 0.05666, steps = 332  
shifted from previous position = 17.2  
rotated from previous position = 11.9 degrees  
atoms outside contour = 1100079, contour level = 0.13594  
  
Position of overall_pbd.pdb (#11) relative to J474_I_capsid.mrc.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.71570797 0.69839746 0.00175649 -117.74924058  
-0.69274026 0.71022559 -0.12526190 -155.10617322  
-0.08873009 0.08843415 0.99212216 -157.28521412  
Axis 0.15151869 0.06415846 -0.98637000  
Axis point -271.54228167 85.69284277 0.00000000  
Rotation angle (degrees) 44.84412571  
Shift along axis 127.34883307  
  

> color #11 #929000ff

> color #11 #531b93ff

> show sel cartoons

> hide sel atoms

[Repeated 1 time(s)]

> ui mousemode right "translate selected models"

> view matrix models
> #11,0.71571,0.6984,0.0017565,-105.29,-0.69274,0.71023,-0.12526,-171.57,-0.08873,0.088434,0.99212,-159.69

> view matrix models
> #11,0.71571,0.6984,0.0017565,-110.95,-0.69274,0.71023,-0.12526,-168.69,-0.08873,0.088434,0.99212,-160.68

> view matrix models
> #11,0.71571,0.6984,0.0017565,-103.5,-0.69274,0.71023,-0.12526,-175.11,-0.08873,0.088434,0.99212,-177.39

> view matrix models
> #11,0.71571,0.6984,0.0017565,-111.42,-0.69274,0.71023,-0.12526,-159.43,-0.08873,0.088434,0.99212,-165.44

> fitmap #11 inMap #8

Fit molecule overall_pbd.pdb (#11) to map J474_I_capsid.mrc.mrc (#8) using
1334880 atoms  
average map value = 0.05666, steps = 188  
shifted from previous position = 11.2  
rotated from previous position = 0.000652 degrees  
atoms outside contour = 1100067, contour level = 0.13594  
  
Position of overall_pbd.pdb (#11) relative to J474_I_capsid.mrc.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.71570190 0.69840369 0.00175234 -117.74904189  
-0.69274628 0.71021866 -0.12526790 -155.10315675  
-0.08873211 0.08844055 0.99212141 -157.29104361  
Axis 0.15152600 0.06415631 -0.98636902  
Axis point -271.53702763 85.69405169 0.00000000  
Rotation angle (degrees) 44.84468427  
Shift along axis 127.35412415  
  

> fitmap #11 inMap #8

Fit molecule overall_pbd.pdb (#11) to map J474_I_capsid.mrc.mrc (#8) using
1334880 atoms  
average map value = 0.05666, steps = 76  
shifted from previous position = 0.0152  
rotated from previous position = 0.00161 degrees  
atoms outside contour = 1100131, contour level = 0.13594  
  
Position of overall_pbd.pdb (#11) relative to J474_I_capsid.mrc.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.71569073 0.69841518 0.00173670 -117.76344353  
-0.69276055 0.71020769 -0.12525116 -155.09112228  
-0.08871073 0.08843798 0.99212355 -157.29903843  
Axis 0.15151015 0.06412915 -0.98637322  
Axis point -271.52064708 85.71556549 0.00000000  
Rotation angle (degrees) 44.84549690  
Shift along axis 127.36733917  
  

> view matrix models
> #11,0.71569,0.69842,0.0017367,-110.07,-0.69276,0.71021,-0.12525,-164.2,-0.088711,0.088438,0.99212,-158.77

> fitmap #11 inMap #8

Fit molecule overall_pbd.pdb (#11) to map J474_I_capsid.mrc.mrc (#8) using
1334880 atoms  
average map value = 0.08546, steps = 192  
shifted from previous position = 13.2  
rotated from previous position = 5.79 degrees  
atoms outside contour = 939286, contour level = 0.13594  
  
Position of overall_pbd.pdb (#11) relative to J474_I_capsid.mrc.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.64214307 0.76651397 -0.01042156 -166.60334013  
-0.76114719 0.63591286 -0.12755306 -106.11154837  
-0.09114400 0.08983965 0.99177700 -158.72458339  
Axis 0.14069254 0.05224207 -0.98867405  
Axis point -215.31009298 140.31555545 0.00000000  
Rotation angle (degrees) 50.58621090  
Shift along axis 127.94354236  
  

> show #9 models

> open
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_5*C6+1*C5_capsid.pdb

Chain information for J474_5*C6+1*C5_capsid.pdb #12  
---  
Chain | Description  
D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l | No description available  
  

> open
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_5*C6+1*C5_capsid.pdb

Chain information for J474_5*C6+1*C5_capsid.pdb #13  
---  
Chain | Description  
D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l | No description available  
  

> open
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_5*C6+1*C5_capsid.pdb

Chain information for J474_5*C6+1*C5_capsid.pdb #14  
---  
Chain | Description  
D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l | No description available  
  

> open
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_5*C6+1*C5_capsid.pdb

Chain information for J474_5*C6+1*C5_capsid.pdb #15  
---  
Chain | Description  
D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l | No description available  
  

> open
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_5*C6+1*C5_capsid.pdb

Chain information for J474_5*C6+1*C5_capsid.pdb #16  
---  
Chain | Description  
D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l | No description available  
  

> open
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_5*C6+1*C5_capsid.pdb

Chain information for J474_5*C6+1*C5_capsid.pdb #17  
---  
Chain | Description  
D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l | No description available  
  

> open
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_5*C6+1*C5_capsid.pdb

Chain information for J474_5*C6+1*C5_capsid.pdb #18  
---  
Chain | Description  
D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l | No description available  
  

> open
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_5*C6+1*C5_capsid.pdb

Chain information for J474_5*C6+1*C5_capsid.pdb #19  
---  
Chain | Description  
D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l | No description available  
  

> open
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_5*C6+1*C5_capsid.pdb

Chain information for J474_5*C6+1*C5_capsid.pdb #20  
---  
Chain | Description  
D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l | No description available  
  

> open
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_5*C6+1*C5_capsid.pdb

Chain information for J474_5*C6+1*C5_capsid.pdb #21  
---  
Chain | Description  
D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l | No description available  
  

> open
> /Users/xiaojiu/Desktop/k1-1/K1_1_right_position/J474_5*C6+1*C5_capsid.pdb

Chain information for J474_5*C6+1*C5_capsid.pdb #22  
---  
Chain | Description  
D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l | No description available  
  

> ui tool show "Map Coordinates"

> ui tool show Segmentations

Created segmentation sphere cursor with ID #23  
Created segmentation sphere cursor with ID #24  
Created segmentation sphere cursor with ID #25  

> ui view fourup

> segmentations create #6

Opened segmentation 1 of tail-fiber-J432-6.mrc as #26, grid size 500,500,500,
pixel 1.39, shown at level 0.501, step 1, values float64  

> select down

1334880 atoms, 1355695 bonds, 177482 residues, 1 model selected  

> close #23-25#26

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 659, in
_on_plane_viewer_enter_event  
self.make_puck_visible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 933, in
make_puck_visible  
self.segmentation_cursors[axis].display = True  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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()  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 659, in
_on_plane_viewer_enter_event  
self.make_puck_visible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 933, in
make_puck_visible  
self.segmentation_cursors[axis].display = True  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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()  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 662, in
_on_plane_viewer_leave_event  
self.make_puck_invisible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 937, in
make_puck_invisible  
self.segmentation_cursors[axis].display = False  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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.  
  
Error processing trigger "plane viewer enter":  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 659, in
_on_plane_viewer_enter_event  
self.make_puck_visible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 933, in
make_puck_visible  
self.segmentation_cursors[axis].display = True  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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()  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 659, in
_on_plane_viewer_enter_event  
self.make_puck_visible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 933, in
make_puck_visible  
self.segmentation_cursors[axis].display = True  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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()  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 662, in
_on_plane_viewer_leave_event  
self.make_puck_invisible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 937, in
make_puck_invisible  
self.segmentation_cursors[axis].display = False  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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.  
  
Error processing trigger "plane viewer enter":  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 659, in
_on_plane_viewer_enter_event  
self.make_puck_visible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 933, in
make_puck_visible  
self.segmentation_cursors[axis].display = True  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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()  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 659, in
_on_plane_viewer_enter_event  
self.make_puck_visible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 933, in
make_puck_visible  
self.segmentation_cursors[axis].display = True  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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()  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 662, in
_on_plane_viewer_leave_event  
self.make_puck_invisible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 937, in
make_puck_invisible  
self.segmentation_cursors[axis].display = False  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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.  
  
Error processing trigger "plane viewer enter":  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 659, in
_on_plane_viewer_enter_event  
self.make_puck_visible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 933, in
make_puck_visible  
self.segmentation_cursors[axis].display = True  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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()  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 659, in
_on_plane_viewer_enter_event  
self.make_puck_visible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 933, in
make_puck_visible  
self.segmentation_cursors[axis].display = True  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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()  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 662, in
_on_plane_viewer_leave_event  
self.make_puck_invisible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 937, in
make_puck_invisible  
self.segmentation_cursors[axis].display = False  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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.  
  
Error processing trigger "plane viewer enter":  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 659, in
_on_plane_viewer_enter_event  
self.make_puck_visible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 933, in
make_puck_visible  
self.segmentation_cursors[axis].display = True  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent  
self.moveSegmentationPuck(x, y, record_seg=False)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin  
return self.position.origin()  
^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 662, in
_on_plane_viewer_leave_event  
self.make_puck_invisible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 937, in
make_puck_invisible  
self.segmentation_cursors[axis].display = False  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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.  
  
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 659, in
_on_plane_viewer_enter_event  
self.make_puck_visible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 933, in
make_puck_visible  
self.segmentation_cursors[axis].display = True  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1398, in
mouseMoveEvent  
self.moveSegmentationPuck(x, y, record_seg=False)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin  
return self.position.origin()  
^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 662, in
_on_plane_viewer_leave_event  
self.make_puck_invisible(axis)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 937, in
make_puck_invisible  
self.segmentation_cursors[axis].display = False  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display  
Drawing.set_display(self, display)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display  
dp = self.display_positions  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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.  
  
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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.  
  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac16,8
      Model Number: MX2J3ZP/A
      Chip: Apple M4 Pro
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.1 (24D70)
      Kernel Version: Darwin 24.3.0
      Time since boot: 8小时15分钟

Graphics/Displays:

    Apple M4 Pro:

      Chipset Model: Apple M4 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 20
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        VX2776 Series:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    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: 2023.11.17
    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-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-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
    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
    OpenMM: 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

[Zach Pearson]

This happens if you close a segmentation cursor while the four panel view is open.

[Zach Pearson]

If you accidentally close a segmentation cursor, but the tool is open and a four panel view is up, it will be recreated the next time you move your mouse into the relevant panel.