Opened 13 months ago

Closed 8 months ago

#15957 closed defect (fixed)

Segmentations: self.view.drawing.parent is None

Reported by: chimerax-bug-report@… Owned by: Zach Pearson
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.9.dev202409110021 (2024-09-11 00:21:38 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9.dev202409110021 (2024-09-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/ria2/Documents/CryoEM-
> Facility/akb20/Olivia_Peduzzi/Holoenzyme/truncFhRNR.pdb format pdb

Chain information for truncFhRNR.pdb #1  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
  
Computing secondary structure  

> open /Users/ria2/Documents/CryoEM-
> Facility/akb20/Olivia_Peduzzi/Holoenzyme/cryosparc_P5_J78_class_00_00162_volume_sharp.mrc

Opened cryosparc_P5_J78_class_00_00162_volume_sharp.mrc as #2, grid size
128,128,128, pixel 2.29, shown at level 0.0485, step 1, values float32  

> surface dust #2 size 22.9

> volume #2 level 0.07279

> select #1

14478 atoms, 14789 bonds, 1805 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,146.12,0,1,0,161.76,0,0,1,174.41

> view matrix models #1,1,0,0,167.96,0,1,0,142.53,0,0,1,173.64

> ~select

Nothing selected  

> ui tool show "Fit in Map"

Opened truncFhRNR.pdb map 10 as #3, grid size 52,48,51, pixel 3.33, shown at
level 0.0836, step 1, values float32  

> fitmap #1 inMap #2 resolution 10

Fit map truncFhRNR.pdb map 10 in map
cryosparc_P5_J78_class_00_00162_volume_sharp.mrc using 8815 points  
correlation = 0.5781, correlation about mean = 0.2371, overlap = 231.8  
steps = 256, shift = 10.6, angle = 65.3 degrees  
  
Position of truncFhRNR.pdb map 10 (#3) relative to
cryosparc_P5_J78_class_00_00162_volume_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.55190599 -0.46810966 -0.69012544 154.85974942  
0.77530990 0.59278524 0.21794543 178.06998861  
0.30707381 -0.65534648 0.69009178 185.14566876  
Axis -0.48050302 -0.54867937 0.68415480  
Axis point -32.11402580 314.91147018 0.00000000  
Rotation angle (degrees) 65.32998844  
Shift along axis -45.44560837  
  
Average map value = 0.09244 for 14478 atoms, 7949 outside contour  
Opened truncFhRNR.pdb map 5 as #3, grid size 86,78,83, pixel 1.67, shown at
level 0.109, step 1, values float32  

> fitmap #1 inMap #2 resolution 5

Fit map truncFhRNR.pdb map 5 in map
cryosparc_P5_J78_class_00_00162_volume_sharp.mrc using 53218 points  
correlation = 0.5209, correlation about mean = 0.02361, overlap = 1839  
steps = 68, shift = 0.797, angle = 1.1 degrees  
  
Position of truncFhRNR.pdb map 5 (#3) relative to
cryosparc_P5_J78_class_00_00162_volume_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.53825613 -0.47017702 -0.69943828 154.14686602  
0.77988305 0.59247144 0.20189112 178.58736232  
0.31947263 -0.65414919 0.68558447 185.76240160  
Axis -0.46885140 -0.55805527 0.68465515  
Axis point -32.36343175 315.00729468 0.00000000  
Rotation angle (degrees) 65.91094849  
Shift along axis -44.75040679  
  
Average map value = 0.0926 for 14478 atoms, 7947 outside contour  

> fitmap #1 inMap #2 resolution 5 metric correlation

Fit map truncFhRNR.pdb map 5 in map
cryosparc_P5_J78_class_00_00162_volume_sharp.mrc using 53218 points  
correlation = 0.5241, correlation about mean = 0.02661, overlap = 1819  
steps = 84, shift = 2.85, angle = 7.47 degrees  
  
Position of truncFhRNR.pdb map 5 (#3) relative to
cryosparc_P5_J78_class_00_00162_volume_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.44178239 -0.49859232 -0.74581097 148.59703496  
0.80435765 0.58829495 0.08317349 177.99821879  
0.39728717 -0.63664334 0.66094490 189.10734847  
Axis -0.38352813 -0.60905813 0.69422934  
Axis point -35.81876237 311.89064367 0.00000000  
Rotation angle (degrees) 69.78700029  
Shift along axis -34.11853462  
  
Average map value = 0.09168 for 14478 atoms, 8136 outside contour  

> volume #2 color #b2b2b280

> select #1

14478 atoms, 14789 bonds, 1805 residues, 1 model selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.66183,-0.33254,-0.67187,153.99,0.68402,0.63461,0.3597,178.68,0.30676,-0.69763,0.64747,187.08

> view matrix models
> #1,0.69231,-0.48569,-0.53367,158.46,0.68845,0.66615,0.28684,177.35,0.21619,-0.56599,0.79556,185.71

> view matrix models
> #1,-0.92819,0.13277,0.34761,123.13,-0.34406,-0.66199,-0.66587,147.88,0.14171,-0.73766,0.66014,183.28

> view matrix models
> #1,-0.58194,0.50481,0.63758,133.26,-0.81234,-0.3975,-0.42673,136.6,0.038022,-0.76626,0.6414,180.5

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.58194,0.50481,0.63758,128.58,-0.81234,-0.3975,-0.42673,121.06,0.038022,-0.76626,0.6414,180.58

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.34486,0.85843,0.37971,127.41,-0.77599,-0.033129,-0.62988,115.3,-0.52812,-0.51187,0.67755,163.61

> view matrix models
> #1,-0.44193,0.74233,0.50363,127.9,-0.75964,-0.011073,-0.65025,115.21,-0.47713,-0.66994,0.56879,164.8

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.44193,0.74233,0.50363,131.25,-0.75964,-0.011073,-0.65025,118.74,-0.47713,-0.66994,0.56879,155.41

> volume #2 level 0.04266

> surface dust #2 size 22.9

> volume #2 level 0.07826

> open /Users/ria2/Documents/CryoEM-
> Facility/akb20/Olivia_Peduzzi/Holoenzyme/cryosparc_P5_J78_class_01_00162_volume_sharp.mrc

Opened cryosparc_P5_J78_class_01_00162_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.29, shown at level 0.0516, step 1, values float32  

> volume #4 level 0.1866

> volume #4 level 0.07935

> open /Users/ria2/Documents/CryoEM-
> Facility/akb20/Olivia_Peduzzi/Holoenzyme/cryosparc_P5_J78_class_02_00162_volume_sharp.mrc

Opened cryosparc_P5_J78_class_02_00162_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.29, shown at level 0.0712, step 1, values float32  

> fitmap #1 inMap #5 resolution 5 metric correlation

Fit map truncFhRNR.pdb map 5 in map
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc using 53218 points  
correlation = 0.6704, correlation about mean = 0.03358, overlap = 2885  
steps = 224, shift = 16.7, angle = 61.4 degrees  
  
Position of truncFhRNR.pdb map 5 (#3) relative to
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.97814738 0.20149375 -0.05126370 124.41393475  
-0.13532957 -0.80419894 -0.57874862 141.10201360  
-0.15784044 -0.55916396 0.81389315 163.45359442  
Axis 0.05535128 0.30121318 -0.95194898  
Axis point 75.06498170 90.30917744 0.00000000  
Rotation angle (degrees) 169.81002791  
Shift along axis -106.21122558  
  
Average map value = 0.1464 for 14478 atoms, 5214 outside contour  

> fitmap #1 inMap #5 resolution 5

Fit map truncFhRNR.pdb map 5 in map
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc using 53218 points  
correlation = 0.6676, correlation about mean = 0.03457, overlap = 2924  
steps = 80, shift = 3.13, angle = 8.34 degrees  
  
Position of truncFhRNR.pdb map 5 (#3) relative to
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.96667995 0.24084267 0.08674495 124.08392459  
-0.24724972 -0.79065892 -0.56011253 138.34585899  
-0.06631333 -0.56289722 0.82386241 165.83151341  
Axis -0.00544378 0.29921329 -0.95417072  
Axis point 73.39279943 86.76175151 0.00000000  
Rotation angle (degrees) 165.18091134  
Shift along axis -117.51214060  
  
Average map value = 0.1484 for 14478 atoms, 5121 outside contour  

> view matrix models
> #1,-0.96668,0.24084,0.086745,125.04,-0.24725,-0.79066,-0.56011,138.91,-0.066313,-0.5629,0.82386,165.41

> fitmap #1 inMap #5 resolution 5

Fit map truncFhRNR.pdb map 5 in map
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc using 53218 points  
correlation = 0.6676, correlation about mean = 0.03457, overlap = 2924  
steps = 88, shift = 1.19, angle = 0.0191 degrees  
  
Position of truncFhRNR.pdb map 5 (#3) relative to
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.96675111 0.24064569 0.08649829 124.08551566  
-0.24695406 -0.79078035 -0.56007154 138.34635958  
-0.06637765 -0.56281089 0.82391621 165.82941447  
Axis -0.00536064 0.29916380 -0.95418671  
Axis point 73.38766439 86.76523078 0.00000000  
Rotation angle (degrees) 165.19646435  
Shift along axis -117.50917900  
  
Average map value = 0.1484 for 14478 atoms, 5121 outside contour  

> view matrix models
> #1,-0.96675,0.24065,0.086498,124.53,-0.24695,-0.79078,-0.56007,138.94,-0.066378,-0.56281,0.82392,167.92

> fitmap #1 inMap #5 resolution 5

Fit map truncFhRNR.pdb map 5 in map
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc using 53218 points  
correlation = 0.6676, correlation about mean = 0.03456, overlap = 2924  
steps = 84, shift = 2.23, angle = 0.0174 degrees  
  
Position of truncFhRNR.pdb map 5 (#3) relative to
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.96672001 0.24077042 0.08649867 124.09783149  
-0.24707527 -0.79090915 -0.55983616 138.31490147  
-0.06637940 -0.56257650 0.82407613 165.82904978  
Axis -0.00536012 0.29903025 -0.95422858  
Axis point 73.39648696 86.73223527 0.00000000  
Rotation angle (degrees) 165.18949135  
Shift along axis -117.54365832  
  
Average map value = 0.1484 for 14478 atoms, 5124 outside contour  
Opened truncFhRNR.pdb map 10 as #3, grid size 52,48,51, pixel 3.33, shown at
level 0.0836, step 1, values float32  

> fitmap #1 inMap #5 resolution 10

Fit map truncFhRNR.pdb map 10 in map
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc using 8815 points  
correlation = 0.7367, correlation about mean = 0.2765, overlap = 366.2  
steps = 64, shift = 0.283, angle = 0.599 degrees  
  
Position of truncFhRNR.pdb map 10 (#3) relative to
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.96566389 0.24108743 0.09679931 124.04933364  
-0.25322240 -0.79017977 -0.55811678 138.14656290  
-0.05806609 -0.56346497 0.82409681 166.07284035  
Axis -0.01032412 0.29895117 -0.95421256  
Axis point 73.10845720 86.60848254 0.00000000  
Rotation angle (degrees) 164.98840417  
Shift along axis -118.45041315  
  
Average map value = 0.1483 for 14478 atoms, 5127 outside contour  

> fitmap #1 inMap #5 resolution 10

Fit map truncFhRNR.pdb map 10 in map
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc using 8815 points  
correlation = 0.7367, correlation about mean = 0.2767, overlap = 366.2  
steps = 64, shift = 0.0535, angle = 0.0478 degrees  
  
Position of truncFhRNR.pdb map 10 (#3) relative to
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.96553462 0.24137018 0.09738244 124.03674211  
-0.25375453 -0.78975208 -0.55848034 138.16675132  
-0.05789252 -0.56394333 0.82378175 166.07777032  
Axis -0.01052742 0.29922123 -0.95412569  
Axis point 73.11006635 86.63168885 0.00000000  
Rotation angle (degrees) 164.96167234  
Shift along axis -118.42242843  
  
Average map value = 0.1483 for 14478 atoms, 5130 outside contour  

> fitmap #1 inMap #5 resolution 10

Fit map truncFhRNR.pdb map 10 in map
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc using 8815 points  
correlation = 0.7367, correlation about mean = 0.2765, overlap = 366.2  
steps = 64, shift = 0.0457, angle = 0.0281 degrees  
  
Position of truncFhRNR.pdb map 10 (#3) relative to
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.96558513 0.24129185 0.09707526 124.05013796  
-0.25353830 -0.79002049 -0.55819886 138.14048410  
-0.05799739 -0.56360081 0.82400876 166.07238198  
Axis -0.01041665 0.29902858 -0.95418730  
Axis point 73.11466238 86.60379737 0.00000000  
Rotation angle (degrees) 164.97182323  
Shift along axis -118.44839271  
  
Average map value = 0.1483 for 14478 atoms, 5129 outside contour  

> volume #5 color #ffb2ff80

> ~select #1

Nothing selected  

> fitmap #1 inMap #5 resolution 10 metric correlation

Fit map truncFhRNR.pdb map 10 in map
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc using 8815 points  
correlation = 0.7379, correlation about mean = 0.2741, overlap = 364.7  
steps = 136, shift = 1.69, angle = 4.36 degrees  
  
Position of truncFhRNR.pdb map 10 (#3) relative to
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.97546396 0.21856675 0.02643198 124.11685730  
-0.19394948 -0.79630775 -0.57295512 139.87732448  
-0.10418095 -0.56402354 0.81916041 165.28115074  
Axis 0.02063712 0.30179126 -0.95315064  
Axis point 73.83675749 88.84196553 0.00000000  
Rotation angle (degrees) 167.50255157  
Shift along axis -112.76266636  
  
Average map value = 0.1479 for 14478 atoms, 5209 outside contour  
Opened truncFhRNR.pdb map 8 as #3, grid size 61,56,59, pixel 2.67, shown at
level 0.0977, step 1, values float32  

> fitmap #1 inMap #5 resolution 8

Fit map truncFhRNR.pdb map 8 in map
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc using 15892 points  
correlation = 0.7226, correlation about mean = 0.1751, overlap = 718.6  
steps = 72, shift = 1.56, angle = 4.14 degrees  
  
Position of truncFhRNR.pdb map 8 (#3) relative to
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.96566083 0.24272420 0.09265054 124.09071447  
-0.25216263 -0.78976430 -0.55918366 138.19708897  
-0.06255532 -0.56334476 0.82385042 165.95129122  
Axis -0.00802263 0.29923784 -0.95414483  
Axis point 73.34227907 86.60803861 0.00000000  
Rotation angle (degrees) 164.96937655  
Shift along axis -117.98330142  
  
Average map value = 0.1483 for 14478 atoms, 5111 outside contour  

> select #1

14478 atoms, 14789 bonds, 1805 residues, 1 model selected  

> ~select

Nothing selected  

> volume #5 level 0.05463

> select #1

14478 atoms, 14789 bonds, 1805 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.98761,0.095632,-0.1244,121.54,-0.023007,-0.8725,-0.48807,146.21,-0.15522,-0.47917,0.86389,163.29

> view matrix models
> #1,-0.61152,-0.39179,-0.68742,127.47,0.73928,-0.59254,-0.31995,166.4,-0.28197,-0.70385,0.65199,158.79

> ~select

Nothing selected  

> fitmap #1 inMap #5 resolution 8

Fit map truncFhRNR.pdb map 8 in map
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc using 15892 points  
correlation = 0.6793, correlation about mean = 0.1384, overlap = 660.3  
steps = 100, shift = 6.1, angle = 15.9 degrees  
  
Position of truncFhRNR.pdb map 8 (#3) relative to
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.50251993 -0.61821058 -0.60439176 128.62915594  
0.82907228 -0.54282381 -0.13409501 170.97784915  
-0.24517928 -0.56846987 0.78532103 160.52480249  
Axis -0.27966954 -0.23127671 0.93182403  
Axis point 40.31544488 143.58836550 0.00000000  
Rotation angle (degrees) 129.05096025  
Shift along axis 74.06401683  
  
Average map value = 0.1363 for 14478 atoms, 5302 outside contour  

> fitmap #1 inMap #5 resolution 8

Fit map truncFhRNR.pdb map 8 in map
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc using 15892 points  
correlation = 0.6794, correlation about mean = 0.1385, overlap = 660.3  
steps = 40, shift = 0.0411, angle = 0.0393 degrees  
  
Position of truncFhRNR.pdb map 8 (#3) relative to
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.50258885 -0.61797256 -0.60457784 128.63224391  
0.82914109 -0.54257560 -0.13467287 171.00477953  
-0.24480505 -0.56896541 0.78507888 160.54260940  
Axis -0.27962572 -0.23164508 0.93174568  
Axis point 40.30609356 143.63431133 0.00000000  
Rotation angle (degrees) 129.05327891  
Shift along axis 74.00358345  
  
Average map value = 0.1363 for 14478 atoms, 5301 outside contour  

> fitmap #1 inMap #5 resolution 8 metric correlation

Fit map truncFhRNR.pdb map 8 in map
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc using 15892 points  
correlation = 0.6826, correlation about mean = 0.1458, overlap = 654.2  
steps = 56, shift = 2.23, angle = 6.1 degrees  
  
Position of truncFhRNR.pdb map 8 (#3) relative to
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.56673318 -0.59313731 -0.57184057 127.47724855  
0.80600879 -0.54299910 -0.23558821 169.64702929  
-0.17077276 -0.59442418 0.78580949 164.73325123  
Axis -0.23937146 -0.26754337 0.93333909  
Axis point 38.84354230 143.73528679 0.00000000  
Rotation angle (degrees) 131.44963190  
Shift along axis 77.84962934  
  
Average map value = 0.135 for 14478 atoms, 5232 outside contour  

> select #1

14478 atoms, 14789 bonds, 1805 residues, 1 model selected  

> view matrix models
> #1,0.080124,-0.8129,-0.57687,146.75,0.82293,-0.27262,0.49846,178.96,-0.56246,-0.51466,0.64712,151.37

> fitmap #1 inMap #5 resolution 8 metric correlation

Fit map truncFhRNR.pdb map 8 in map
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc using 15892 points  
correlation = 0.6934, correlation about mean = 0.1814, overlap = 669.2  
steps = 148, shift = 6.8, angle = 26.2 degrees  
  
Position of truncFhRNR.pdb map 8 (#3) relative to
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.23085634 -0.75913870 -0.60861629 152.26020071  
0.96010898 0.07629668 0.26901593 180.89815736  
-0.15778500 -0.64644200 0.74646945 164.06221930  
Axis -0.45789357 -0.22549671 0.85993297  
Axis point 7.65197460 211.25688246 0.00000000  
Rotation angle (degrees) 88.46364527  
Shift along axis 30.57160586  
  
Average map value = 0.1371 for 14478 atoms, 4916 outside contour  

> view matrix models
> #1,0.074909,-0.23958,-0.96798,137.43,0.8876,-0.4264,0.17422,182.38,-0.45448,-0.87223,0.18071,149.51

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.074909,-0.23958,-0.96798,137.54,0.8876,-0.4264,0.17422,180.89,-0.45448,-0.87223,0.18071,141.18

> view matrix models
> #1,0.074909,-0.23958,-0.96798,136.23,0.8876,-0.4264,0.17422,182.37,-0.45448,-0.87223,0.18071,139.71

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.59957,-0.37096,-0.70916,123.62,0.75937,-0.54352,-0.3577,171.77,-0.25275,-0.75298,0.60757,150.6

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.59957,-0.37096,-0.70916,127.37,0.75937,-0.54352,-0.3577,166.91,-0.25275,-0.75298,0.60757,158.28

> fitmap #1 inMap #5 resolution 8 metric correlation

Fit map truncFhRNR.pdb map 8 in map
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc using 15892 points  
correlation = 0.7242, correlation about mean = 0.1719, overlap = 712.3  
steps = 240, shift = 2.66, angle = 60 degrees  
  
Position of truncFhRNR.pdb map 8 (#3) relative to
cryosparc_P5_J78_class_02_00162_volume_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.97800974 0.20752120 -0.02078245 124.15949501  
-0.15769029 -0.80100210 -0.57752005 140.73385957  
-0.13649444 -0.56154304 0.81611193 164.28518432  
Axis 0.04166788 0.30177572 -0.95246795  
Axis point 74.48969112 89.85590287 0.00000000  
Rotation angle (degrees) 168.94690797  
Shift along axis -108.83284733  
  
Average map value = 0.1472 for 14478 atoms, 4601 outside contour  

> ~select

Nothing selected  

> volume #5 level 0.04042

> ui tool show "Segment Map"

Segmenting cryosparc_P5_J78_class_02_00162_volume_sharp.mrc, density threshold
0.040420  
Showing 50 region surfaces  
162 watershed regions, grouped to 50 regions  
Showing cryosparc_P5_J78_class_02_00162_volume_sharp.seg - 50 regions, 50
surfaces  
Segmenting cryosparc_P5_J78_class_02_00162_volume_sharp.mrc, density threshold
0.040420  
Only showing 60 of 110 regions.  
Showing 60 of 110 region surfaces  
162 watershed regions, grouped to 110 regions  
Showing cryosparc_P5_J78_class_02_00162_volume_sharp.seg - 110 regions, 60
surfaces  

> select #6.1

1 model selected  

> select #6.3

1 model selected  

> select add #6.1

2 models selected  

> select subtract #6.3

1 model selected  

> select add #6.33

2 models selected  

> select add #6.3

3 models selected  
Grouped 3 regions  
Showing 19 grouped regions  
Deleted 57 regions  

> select #6.1

1 model selected  

> select #6.1

1 model selected  
Select one or more regions to delete  

> hide #!6 models

> show #!6 models

> color #6 #b2b2b20d

> color #6 #b2b2b280

> color #6 #6674bf80

> ui tool show "Fit in Map"

> ui tool show Segmentations

> ui view fourup

> segmentations mouseModes false

Mouse bindings not saved; ignoring 'mouseModes false'  

> ui view fourup

> segmentations create #2

Opened segmentation 1 of cryosparc_P5_J78_class_00_00162_volume_sharp.mrc as
#10, grid size 128,128,128, pixel 2.29, shown at level 0.501, step 1, values
float64  

> segmentations mouseModes false

Mouse bindings not saved; ignoring 'mouseModes false'  

> close #10

> hide #6.1 models

> show #6.1 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> ui tool show "Show Volume Menu"

> ui tool show "Segment Map"

> select add #6

2 models selected  
Saving 1 regions to mrc file...  
Opened cryosparc_P5_J78_class_02_volume_sharp_segment.mrc as #7, grid size
50,41,54, pixel 2.29, shown at step 1, values float32  
Wrote cryosparc_P5_J78_class_02_volume_sharp_segment.mrc  

> hide #!6 models

> hide #6.1 models

> volume #7 level 0.07897

> volume #7 level 0.04151

> help mask

No help found for 'mask'  

> help volume mask

> volume mask #7 surfaces #7 fullMap true extend 7

Opened cryosparc_P5_J78_class_02_volume_sharp_segment.mrc masked as #8, grid
size 50,41,54, pixel 2.29, shown at step 1, values float32  

> show #!7 models

> hide #!8 models

> hide #!7 models

> show #!8 models

> volume #8 level 0.04492

> close #8

> volume onemask #7 onGrid #5 extend 10

Expected a density maps specifier or a keyword  

> close session

> open /Users/ria2/Documents/CryoEM-
> Facility/akb20/Olivia_Peduzzi/Holoenzyme/truncFhRNR.pdb format pdb

Chain information for truncFhRNR.pdb #1  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
  
Computing secondary structure  

> open /Users/ria2/Documents/CryoEM-
> Facility/akb20/Olivia_Peduzzi/Holoenzyme/cryosparc_P5_J78_class_02_00162_volume_sharp.mrc

Opened cryosparc_P5_J78_class_02_00162_volume_sharp.mrc as #2, grid size
128,128,128, pixel 2.29, shown at level 0.0712, step 1, values float32  

> open /Users/ria2/Documents/CryoEM-
> Facility/akb20/Olivia_Peduzzi/Holoenzyme/cryosparc_P5_J78_class_02_volume_sharp_segment.mrc

Opened cryosparc_P5_J78_class_02_volume_sharp_segment.mrc as #3, grid size
50,41,54, pixel 2.29,2.29,2.29, shown at level 0.368, step 1, values float32  

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2182, in _drag  
cb(event)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb  
cb(m)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1624, in
moved_marker_cb  
self.plane_viewer.update_and_rerender()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 644, in
update_and_rerender  
self.view.drawing.parent.update_drawings()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'update_drawings'  
  
AttributeError: 'NoneType' object has no attribute 'update_drawings'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 644, in
update_and_rerender  
self.view.drawing.parent.update_drawings()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,6
      Model Number: Z1760005VLL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 10 hours, 54 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 38
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          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: 2.4.1
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.14
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.3.4
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9.dev202409110021
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-DeepMutationalScan: 1.0
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-Foldseek: 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
    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-Label: 1.1.11
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.2.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.13
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    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
    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: 1.40.1
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.5
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.53.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.8
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.1
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.2
    prompt_toolkit: 3.0.47
    psutil: 6.0.0
    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: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.4
    pyproject_hooks: 1.1.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.2
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.2
    PyQt6-WebEngineSubwheel-Qt6: 6.7.2
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.1
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.2
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (3)

comment:1 by pett, 13 months ago

Cc: Tom Goddard added
Component: Unassigned → Volume Data
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Segmentations: self.view.drawing.parent is None

comment:2 by Zach Pearson, 11 months ago

I'm not sure how to reproduce this one, but I can add a guard that suppresses this traceback? There should never be a histogram that has no drawing. It should be deleted when the drawing goes away

comment:3 by Zach Pearson, 8 months ago

Resolution: → fixed
Status: assigned → closed

This is fixed in newer daily builds.

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