Volume Eraser: wrapped C/C++ object of type QLineEdit has been deleted

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 0.94 (2020-04-22)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Your computer has Intel graphics driver 8141 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.  
  
UCSF ChimeraX version: 0.94.dev202004220145 (2020-04-22)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Phenix_output\M49_CV3-13_C3\spike_fixed.pdb format PDB

Chain information for spike_fixed.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> close

> open C:\Users\ychen1\Desktop\spike+CV3-13.cxs format session

File not found: C:\Users\ychen1\Desktop\spike+CV3-13.cxs  

> open
> C:\Phenix_output\M49_CV3-13_C3\cryosparc_P50_J742_010_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P50_J742_010_volume_map_sharp.mrc, grid size 400,400,400,
pixel 0.889, shown at level 0.0809, step 2, values float32  

> open2 "C:/Users/ychen1/Desktop/CV3-13 spike/complete-spike_CV3-13.pdb"

Chain information for complete-spike_CV3-13.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D H L | No description available  
E I | No description available  
F J | No description available  
G K | No description available  
  

> close #2

> open2 "C:/Users/ychen1/Desktop/CV3-13 spike/complete_spike.pdb"

Chain information for complete_spike.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select #2

24830 atoms, 25393 bonds, 40 pseudobonds, 2 models selected  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode pivot

> ui mousemode rightMode pivot

> ui mousemode rightMode "rotate selected models"

> toolshed show "Fit in Map"

Fit molecule complete_spike.pdb (#2) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 24830 atoms  
average map value = 0.1601, steps = 340  
shifted from previous position = 11  
rotated from previous position = 39.7 degrees  
atoms outside contour = 5223, contour level = 0.080944  
  
Position of complete_spike.pdb (#2) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.71734290 -0.64867581 -0.25424173 190.91538506  
0.66988946 0.74244896 -0.00420164 -55.55138113  
0.19148701 -0.16729984 0.96713158 -28.62590636  
Axis -0.11638329 -0.31806224 0.94089922  
Axis point 178.88889885 210.71678170 0.00000000  
Rotation angle (degrees) 44.48272727  
Shift along axis -31.48465630  
  
Fit molecule complete_spike.pdb (#2) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 24830 atoms  
average map value = 0.1601, steps = 40  
shifted from previous position = 0.0164  
rotated from previous position = 0.0169 degrees  
atoms outside contour = 5217, contour level = 0.080944  
  
Position of complete_spike.pdb (#2) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.71732208 -0.64867773 -0.25429556 190.92643127  
0.66995581 0.74239061 -0.00392518 -55.59622020  
0.19133282 -0.16755117 0.96711859 -28.55062734  
Axis -0.11675209 -0.31796934 0.94088493  
Axis point 178.93764889 210.68985799 0.00000000  
Rotation angle (degrees) 44.48649501  
Shift along axis -31.47602209  
  
Fit molecule complete_spike.pdb (#2) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 24830 atoms  
average map value = 0.1601, steps = 40  
shifted from previous position = 0.0162  
rotated from previous position = 0.0166 degrees  
atoms outside contour = 5220, contour level = 0.080944  
  
Position of complete_spike.pdb (#2) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.71733150 -0.64867893 -0.25426595 190.92189808  
0.66989702 0.74244214 -0.00420164 -55.55337104  
0.19150327 -0.16731804 0.96712521 -28.61766015  
Axis -0.11639420 -0.31808544 0.94089003  
Axis point 178.89178047 210.72215562 0.00000000  
Rotation angle (degrees) 44.48373264  
Shift along axis -31.47755431  
  

> volume #1 level 0.1703

> undo

> ~select #2

Nothing selected  

> open2 "C:/Users/ychen1/Desktop/CV3-13 spike/CV3-13-C1.pdb"
> C:/Users/ychen1/Desktop/CV3-13 spike/CV3-13-V1.pdb

No such database 'C'  

> open2 "C:/Users/ychen1/Desktop/CV3-13 spike/CV3-13-C1.pdb"
> C:/Users/ychen1/Desktop/CV3-13 spike/CV3-13-V1.pdb

No such database 'C'  

> open2 C:/Phenix_output/CV3-13-C1.pdb C:/Phenix_output/CV3-13-V1.pdb

Chain information for CV3-13-C1.pdb #3  
---  
Chain | Description  
B | No description available  
C | No description available  
  
Chain information for CV3-13-V1.pdb #4  
---  
Chain | Description  
A | No description available  
D | No description available  
  

> select #3

1543 atoms, 1577 bonds, 1 model selected  

> select #4

1789 atoms, 1832 bonds, 1 model selected  

> select #3

1543 atoms, 1577 bonds, 1 model selected  

> select #4

1789 atoms, 1832 bonds, 1 model selected  

> select #3

1543 atoms, 1577 bonds, 1 model selected  

> select #4

1789 atoms, 1832 bonds, 1 model selected  

> ui mousemode rightMode "translate selected models"

> volume #1 level 0.1071

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

Fit molecule CV3-13-V1.pdb (#4) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.08637, steps = 104  
shifted from previous position = 5.49  
rotated from previous position = 14.5 degrees  
atoms outside contour = 1236, contour level = 0.10705  
  
Position of CV3-13-V1.pdb (#4) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.79988674 -0.59144693 0.10184166 91.72758807  
0.52918080 0.77511654 0.34519853 -89.76195750  
-0.28310577 -0.22222708 0.93298781 101.26347617  
Axis -0.43190995 0.29301220 0.85299335  
Axis point 221.37780942 95.12742321 0.00000000  
Rotation angle (degrees) 41.06231994  
Shift along axis 20.45766500  
  
Fit molecule CV3-13-V1.pdb (#4) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09357, steps = 112  
shifted from previous position = 5.35  
rotated from previous position = 20.1 degrees  
atoms outside contour = 1164, contour level = 0.10705  
  
Position of CV3-13-V1.pdb (#4) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.35685612 -0.65900425 -0.66209297 357.05661814  
-0.83809766 -0.53890857 0.08467506 399.05144567  
-0.41260880 0.52468175 -0.74462274 401.15565414  
Axis 0.82001414 -0.46494871 -0.33376566  
Axis point 0.00000000 268.06701759 305.46108564  
Rotation angle (degrees) 164.43733541  
Shift along axis -26.63896126  
  

> volume #1 level 0.14

> volume #1 level 0.1304

> ~select #4

Nothing selected  

> select #3

1543 atoms, 1577 bonds, 1 model selected  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

Fit molecule CV3-13-C1.pdb (#3) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1543 atoms  
average map value = 0.06662, steps = 84  
shifted from previous position = 2.41  
rotated from previous position = 7.68 degrees  
atoms outside contour = 1510, contour level = 0.13041  
  
Position of CV3-13-C1.pdb (#3) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.87825723 -0.12581024 -0.46134154 153.48586929  
-0.16621922 0.82428890 -0.54121990 256.82872368  
0.44836972 0.55201412 0.70302561 -84.85685983  
Axis 0.76836645 -0.63937968 -0.02840097  
Axis point 0.00000000 326.38519364 316.74950461  
Rotation angle (degrees) 45.34905575  
Shift along axis -43.86765743  
  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

Fit molecule CV3-13-C1.pdb (#3) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1543 atoms  
average map value = 0.07182, steps = 184  
shifted from previous position = 6.14  
rotated from previous position = 46.2 degrees  
atoms outside contour = 1498, contour level = 0.13041  
  
Position of CV3-13-C1.pdb (#3) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.33500544 -0.92496575 -0.17947067 289.96277804  
-0.74629570 -0.37676223 0.54871937 277.80886759  
-0.57516440 -0.04988578 -0.81651536 492.06361380  
Axis -0.80949918 0.53510021 0.24161712  
Axis point 0.00000000 292.05348336 258.49710059  
Rotation angle (degrees) 158.30054244  
Shift along axis 32.82194651  
  
Fit molecule CV3-13-C1.pdb (#3) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1543 atoms  
average map value = 0.07182, steps = 40  
shifted from previous position = 0.00531  
rotated from previous position = 0.0256 degrees  
atoms outside contour = 1497, contour level = 0.13041  
  
Position of CV3-13-C1.pdb (#3) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.33459077 -0.92509574 -0.17957420 290.09502078  
-0.74638046 -0.37648181 0.54879656 277.80165187  
-0.57529578 -0.04959159 -0.81644072 492.06515463  
Axis -0.80936970 0.53524632 0.24172727  
Axis point 0.00000000 292.13090711 258.54886591  
Rotation angle (degrees) 158.30516159  
Shift along axis 32.84375795  
  

> volume #1 level 0.1208

> ui mousemode rightMode "rotate selected models"

> ~select #3

Nothing selected  

> select #4

1789 atoms, 1832 bonds, 1 model selected  
Fit molecule CV3-13-V1.pdb (#4) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.07875, steps = 72  
shifted from previous position = 2.68  
rotated from previous position = 3.66 degrees  
atoms outside contour = 1491, contour level = 0.12079  
  
Position of CV3-13-V1.pdb (#4) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.68987983 0.31457095 -0.65200532 196.36512578  
0.19100981 0.78964046 0.58308078 -54.40252443  
0.69827005 -0.52679508 0.48467089 -28.25587326  
Axis -0.63340502 -0.77060077 -0.07051621  
Axis point 157.78323187 0.00000000 147.95486504  
Rotation angle (degrees) 61.17764203  
Shift along axis -80.46353123  
  
Fit molecule CV3-13-V1.pdb (#4) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09357, steps = 148  
shifted from previous position = 1.44  
rotated from previous position = 33.1 degrees  
atoms outside contour = 1427, contour level = 0.12079  
  
Position of CV3-13-V1.pdb (#4) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.35671136 -0.65900738 -0.66216786 357.10754403  
-0.83815152 -0.53881612 0.08473022 399.04576004  
-0.41262456 0.52477277 -0.74454987 401.13762105  
Axis 0.81996813 -0.46499493 -0.33381429  
Axis point 0.00000000 268.08957635 305.48278023  
Rotation angle (degrees) 164.43513988  
Shift along axis -26.64292060  
  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

Fit molecule CV3-13-V1.pdb (#4) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09356, steps = 116  
shifted from previous position = 2.38  
rotated from previous position = 25.6 degrees  
atoms outside contour = 1422, contour level = 0.12079  
  
Position of CV3-13-V1.pdb (#4) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.35735093 -0.65888165 -0.66194809 356.89005773  
-0.83802492 -0.53909701 0.08419413 399.15783040  
-0.41232821 0.52464215 -0.74480606 401.11477816  
Axis 0.82016154 -0.46481906 -0.33358401  
Axis point 0.00000000 268.00741905 305.38525395  
Rotation angle (degrees) 164.42420106  
Shift along axis -26.63414336  
  

> volume #1 level 0.1455

> volume #1 level 0.1716

> volume #1 level 0.195

> volume #1 level 0.1606

> select #3

1543 atoms, 1577 bonds, 1 model selected  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> volume #1 level 0.09743

Fit molecule CV3-13-C1.pdb (#3) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1543 atoms  
average map value = 0.07495, steps = 60  
shifted from previous position = 0.814  
rotated from previous position = 6.83 degrees  
atoms outside contour = 1186, contour level = 0.097434  
  
Position of CV3-13-C1.pdb (#3) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.12531489 -0.98395228 -0.12702007 337.97995406  
-0.93507523 -0.15992430 0.31632032 358.47057059  
-0.33155769 0.07913367 -0.94011029 445.78798358  
Axis -0.74824851 0.64525122 0.15419156  
Axis point 0.00000000 348.33310801 240.23538399  
Rotation angle (degrees) 170.88047372  
Shift along axis 47.14732332  
  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

Fit molecule CV3-13-C1.pdb (#3) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1543 atoms  
average map value = 0.07377, steps = 172  
shifted from previous position = 1.92  
rotated from previous position = 15 degrees  
atoms outside contour = 1215, contour level = 0.097434  
  
Position of CV3-13-C1.pdb (#3) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.07619505 -0.98894417 -0.12721535 392.98998277  
-0.99150040 0.06165433 0.11456743 396.78266075  
-0.10545741 0.13486354 -0.98523630 391.14956039  
Axis 0.67961200 -0.72856092 -0.08559509  
Axis point 379.57728316 0.00000000 174.47368300  
Rotation angle (degrees) 179.14441997  
Shift along axis -55.48010936  
  

> volume #1 level 0.1318

> volume #1 level 0.1455

> volume #1 level 0.1771

> volume #1 level 0.1758

> undo

> ~select #3

Nothing selected  

> volume #1 level 0.1689

> open2 C:/Phenix_output/CV3-13-C2.pdb C:/Phenix_output/CV3-13-V2.pdb

Chain information for CV3-13-C2.pdb #5  
---  
Chain | Description  
E | No description available  
F | No description available  
  
Chain information for CV3-13-V2.pdb #6  
---  
Chain | Description  
G | No description available  
H | No description available  
  

> select /C:27-1147

9092 atoms, 9296 bonds, 14 pseudobonds, 3 models selected  

> select /B:27-1147

9019 atoms, 9226 bonds, 12 pseudobonds, 3 models selected  

> select /B:27-1147

9019 atoms, 9226 bonds, 12 pseudobonds, 3 models selected  

> select /B:27-1147

9019 atoms, 9226 bonds, 12 pseudobonds, 3 models selected  

> select /B:27-1147

9019 atoms, 9226 bonds, 12 pseudobonds, 3 models selected  

> select /B:27-1147

9019 atoms, 9226 bonds, 12 pseudobonds, 3 models selected  

> select /C:27-1147

9092 atoms, 9296 bonds, 14 pseudobonds, 3 models selected  

> select /B:27-1147

9019 atoms, 9226 bonds, 12 pseudobonds, 3 models selected  

> select /A:27-1147

9040 atoms, 9249 bonds, 14 pseudobonds, 3 models selected  

> select /C:27-1147

9092 atoms, 9296 bonds, 14 pseudobonds, 3 models selected  

> volume #1 level 0.129

> select #6

1789 atoms, 1832 bonds, 1 model selected  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

Fit molecule CV3-13-V2.pdb (#6) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09832, steps = 184  
shifted from previous position = 6.14  
rotated from previous position = 44.7 degrees  
atoms outside contour = 1485, contour level = 0.12904  
  
Position of CV3-13-V2.pdb (#6) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.59099325 -0.75120561 -0.29396788 252.89440995  
0.78124366 0.62378698 -0.02341259 -51.84381625  
0.20096100 -0.21582386 0.95552851 -18.75018379  
Axis -0.11863736 -0.30516432 0.94488090  
Axis point 188.96603600 228.72788031 0.00000000  
Rotation angle (degrees) 54.18610396  
Shift along axis -31.89853274  
  

> undo

> ui mousemode rightMode select

> volume #1 level 0.1469

> ui mousemode rightMode "rotate selected models"

Fit molecule CV3-13-V2.pdb (#6) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09832, steps = 184  
shifted from previous position = 2.1  
rotated from previous position = 46 degrees  
atoms outside contour = 1650, contour level = 0.1469  
  
Position of CV3-13-V2.pdb (#6) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.59116687 -0.75119157 -0.29365449 252.78203409  
0.78119129 0.62385917 -0.02323594 -51.89440984  
0.20065369 -0.21566401 0.95562918 -18.74376553  
Axis -0.11866601 -0.30482861 0.94498566  
Axis point 188.95849366 228.63041869 0.00000000  
Rotation angle (degrees) 54.17386267  
Shift along axis -31.89032431  
  

> volume #1 level 0.1304

> undo

> ~select #6

Nothing selected  

> select #5

1543 atoms, 1577 bonds, 1 model selected  

> ui mousemode rightMode "translate selected models"

Fit molecule CV3-13-C2.pdb (#5) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1543 atoms  
average map value = 0.0775, steps = 136  
shifted from previous position = 1.42  
rotated from previous position = 35.1 degrees  
atoms outside contour = 1498, contour level = 0.13041  
  
Position of CV3-13-C2.pdb (#5) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.85653256 -0.48761771 -0.16905900 99.66222340  
0.42969500 0.85523408 -0.28971861 32.25927235  
0.28585694 0.17550961 0.94206273 -132.38429023  
Axis 0.41366313 -0.40449384 0.81563935  
Axis point 83.43985234 247.53327142 0.00000000  
Rotation angle (degrees) 34.21690625  
Shift along axis -79.79992650  
  

> ui mousemode rightMode select

> ~select #5

Nothing selected  

> open2 C:/Phenix_output/CV3-13-V3.pdb

Chain information for CV3-13-V3.pdb #7  
---  
Chain | Description  
K | No description available  
L | No description available  
  

> open2 C:/Phenix_output/CV3-13-C3.pdb

Chain information for CV3-13-C3.pdb #8  
---  
Chain | Description  
I | No description available  
J | No description available  
  

> select #7

1789 atoms, 1832 bonds, 1 model selected  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09334, steps = 112  
shifted from previous position = 4.47  
rotated from previous position = 18.9 degrees  
atoms outside contour = 1528, contour level = 0.13041  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.46897592 0.82560997 0.31373519 -100.36098473  
0.81954092 -0.53921445 0.19390836 47.61581933  
0.32926322 0.16618047 -0.92949975 355.37560549  
Axis -0.85701261 -0.47993999 -0.18758198  
Axis point 0.00000000 53.58377689 188.45447591  
Rotation angle (degrees) 179.07308221  
Shift along axis -3.50416684  
  

> volume #1 level 0.1345

Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09333, steps = 156  
shifted from previous position = 0.407  
rotated from previous position = 27.1 degrees  
atoms outside contour = 1576, contour level = 0.13454  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.46907012 0.82541583 0.31410497 -100.43334975  
0.81948219 -0.53939335 0.19365884 47.70466751  
0.32927520 0.16656385 -0.92942688 355.30428747  
Axis -0.85704054 -0.47984917 -0.18768666  
Axis point 0.00000000 53.60357580 188.43705719  
Rotation angle (degrees) 179.09427082  
Shift along axis -3.50146888  
  

> volume #1 level 0.1167

Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09334, steps = 108  
shifted from previous position = 0.579  
rotated from previous position = 23.3 degrees  
atoms outside contour = 1342, contour level = 0.11667  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.46920192 0.82524877 0.31434700 -100.49959848  
0.81939701 -0.53958049 0.19349792 47.78148749  
0.32929942 0.16678540 -0.92937857 355.27925923  
Axis -0.85707926 -0.47975307 -0.18775551  
Axis point 0.00000000 53.63028553 188.43798222  
Rotation angle (degrees) 179.10709745  
Shift along axis -3.49283386  
  
Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.07781, steps = 128  
shifted from previous position = 8.7  
rotated from previous position = 16.3 degrees  
atoms outside contour = 1398, contour level = 0.11667  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.78689103 -0.27946473 0.55018357 -43.61316354  
0.61638259 0.39869037 -0.67905705 157.22743900  
-0.02958040 0.87346748 0.48598307 -21.80331041  
Axis 0.82411042 0.30775007 0.47553330  
Axis point 0.00000000 106.36603550 136.40897514  
Rotation angle (degrees) 70.37988757  
Shift along axis 2.07649229  
  
Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.08067, steps = 64  
shifted from previous position = 2.65  
rotated from previous position = 8.22 degrees  
atoms outside contour = 1405, contour level = 0.11667  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.22642776 0.96758929 -0.11180979 10.85117706  
0.77976987 -0.11128266 0.61609668 -97.09809734  
0.58368606 -0.22668730 -0.77969446 350.29603302  
Axis -0.76013664 -0.62729227 -0.16940097  
Axis point 0.00000000 16.46196833 194.09664206  
Rotation angle (degrees) 146.33311646  
Shift along axis -6.67997887  
  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09828, steps = 128  
shifted from previous position = 5.02  
rotated from previous position = 21.7 degrees  
atoms outside contour = 1301, contour level = 0.11667  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.59948381 -0.76041749 -0.24976869 217.90019089  
0.76642285 0.63531919 -0.09468653 -28.03383799  
0.23068413 -0.13466539 0.96366491 -37.81634365  
Axis -0.02496888 -0.30006773 0.95359106  
Axis point 148.21806368 207.39953917 0.00000000  
Rotation angle (degrees) 53.18494641  
Shift along axis -33.09000000  
  
Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09828, steps = 44  
shifted from previous position = 0.00461  
rotated from previous position = 0.00542 degrees  
atoms outside contour = 1302, contour level = 0.11667  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.59949366 -0.76038360 -0.24984819 217.91093363  
0.76639232 0.63535203 -0.09471322 -28.02484915  
0.23075994 -0.13470176 0.96364168 -37.81502449  
Axis -0.02497515 -0.30016746 0.95355951  
Axis point 148.21898466 207.42410053 0.00000000  
Rotation angle (degrees) 53.18425019  
Shift along axis -33.08908564  
  
Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09828, steps = 44  
shifted from previous position = 0.00735  
rotated from previous position = 0.0115 degrees  
atoms outside contour = 1301, contour level = 0.11667  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.59963130 -0.76025396 -0.24991243 217.90214313  
0.76626997 0.63550304 -0.09469015 -28.03407017  
0.23080867 -0.13472121 0.96362729 -37.81365318  
Axis -0.02500491 -0.30027652 0.95352439  
Axis point 148.23672390 207.46417873 0.00000000  
Rotation angle (degrees) 53.17443556  
Shift along axis -33.08689143  
  

> volume #1 level 0.1524

> volume #1 level 0.1208

Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09828, steps = 76  
shifted from previous position = 0.305  
rotated from previous position = 10.8 degrees  
atoms outside contour = 1384, contour level = 0.12079  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.59950251 -0.76046052 -0.24959274 217.86047685  
0.76646347 0.63528330 -0.09459848 -28.05474556  
0.23050051 -0.13459169 0.96371914 -37.81801728  
Axis -0.02497827 -0.29984836 0.95365982  
Axis point 148.21222311 207.34172285 0.00000000  
Rotation angle (degrees) 53.18362094  
Shift along axis -33.09513217  
  
Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09828, steps = 76  
shifted from previous position = 0.161  
rotated from previous position = 5.86 degrees  
atoms outside contour = 1384, contour level = 0.12079  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.59944746 -0.76048198 -0.24965956 217.88531619  
0.76648126 0.63525259 -0.09466054 -28.03878013  
0.23058452 -0.13461535 0.96369574 -37.81840894  
Axis -0.02495301 -0.29992725 0.95363567  
Axis point 148.20786517 207.36129129 0.00000000  
Rotation angle (degrees) 53.18752730  
Shift along axis -33.09228472  
  

> volume #1 level 0.1414

Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09828, steps = 140  
shifted from previous position = 0.895  
rotated from previous position = 30.1 degrees  
atoms outside contour = 1610, contour level = 0.14141  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.59934389 -0.76059061 -0.24957729 217.88757954  
0.76660254 0.63511766 -0.09458382 -28.05517973  
0.23045051 -0.13463835 0.96372458 -37.80705943  
Axis -0.02501284 -0.29976280 0.95368581  
Axis point 148.21207865 207.30952265 -0.00000000  
Rotation angle (degrees) 53.19502905  
Shift along axis -33.09614340  
  
Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09828, steps = 112  
shifted from previous position = 0.488  
rotated from previous position = 26.5 degrees  
atoms outside contour = 1610, contour level = 0.14141  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.59967272 -0.76023602 -0.24986762 217.88598522  
0.76627651 0.63551516 -0.09455567 -28.06577724  
0.23067929 -0.13476523 0.96365211 -37.79988829  
Axis -0.02511733 -0.30017872 0.95355223  
Axis point 148.25936256 207.43891059 -0.00000000  
Rotation angle (degrees) 53.17163050  
Shift along axis -33.09213210  
  

> ui mousemode rightMode "translate selected models"

Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.07262, steps = 148  
shifted from previous position = 2.78  
rotated from previous position = 21 degrees  
atoms outside contour = 1673, contour level = 0.14141  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97633731 -0.17719924 0.12395915 18.00959137  
0.01835492 -0.50324154 -0.86395083 375.88704752  
0.21547283 0.84578270 -0.48808102 178.18585071  
Axis 0.99212060 -0.05310336 0.11347576  
Axis point 0.00000000 137.68965127 196.61862673  
Rotation angle (degrees) 120.49695852  
Shift along axis 18.12659473  
  

> ui mousemode rightMode "rotate selected models"

> volume #1 level 0.1002

> ui mousemode rightMode "translate selected models"

Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09828, steps = 108  
shifted from previous position = 1.71  
rotated from previous position = 19 degrees  
atoms outside contour = 972, contour level = 0.10018  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.59968305 -0.76017968 -0.25001415 217.91305032  
0.76620212 0.63558222 -0.09470766 -28.02973313  
0.23089939 -0.13476680 0.96359918 -37.81358171  
Axis -0.02502365 -0.30041118 0.95348148  
Axis point 148.24695219 207.50268213 0.00000000  
Rotation angle (degrees) 53.17075528  
Shift along axis -33.08708459  
  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.07664, steps = 264  
shifted from previous position = 7.58  
rotated from previous position = 44.8 degrees  
atoms outside contour = 1224, contour level = 0.10018  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.57860770 0.45853470 0.67450652 -148.89751235  
0.25354524 0.68490207 -0.68309880 157.96554487  
-0.77519541 0.56626415 0.28003033 137.90380527  
Axis 0.64911263 0.75319973 -0.10650328  
Axis point -20.82479900 0.00000000 215.09364309  
Rotation angle (degrees) 74.23037781  
Shift along axis 7.64114219  
  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09334, steps = 96  
shifted from previous position = 4.17  
rotated from previous position = 15.7 degrees  
atoms outside contour = 1056, contour level = 0.10018  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.46923369 0.82526363 0.31426052 -100.48345318  
0.81942199 -0.53956859 0.19342526 47.79729988  
0.32919194 0.16675033 -0.92942293 355.30725544  
Axis -0.85708852 -0.47975945 -0.18769696  
Axis point 0.00000000 53.63156322 188.44689966  
Rotation angle (degrees) 179.10836364  
Shift along axis -3.49808278  
  

> volume #1 level 0.1304

> ui mousemode rightMode "rotate selected models"

Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09334, steps = 136  
shifted from previous position = 0.245  
rotated from previous position = 30.7 degrees  
atoms outside contour = 1530, contour level = 0.13041  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.46920017 0.82516813 0.31456121 -100.53640212  
0.81933835 -0.53965928 0.19352654 47.78933502  
0.32944781 0.16692938 -0.92930012 355.21941401  
Axis -0.85707879 -0.47971247 -0.18786138  
Axis point 0.00000000 53.63491375 188.41916766  
Rotation angle (degrees) 179.11095321  
Shift along axis -3.48953203  
  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected atoms"

> ui mousemode rightMode "rotate selected models"

Fit molecule CV3-13-V3.pdb (#7) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09333, steps = 120  
shifted from previous position = 1.47  
rotated from previous position = 29.2 degrees  
atoms outside contour = 1529, contour level = 0.13041  
  
Position of CV3-13-V3.pdb (#7) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.46910111 0.82538502 0.31413962 -100.44401044  
0.81947326 -0.53942653 0.19360422 47.72394114  
0.32925327 0.16660907 -0.92942654 355.30401062  
Axis -0.85704961 -0.47983230 -0.18768839  
Axis point 0.00000000 53.60884936 188.43876640  
Rotation angle (degrees) 179.09761796  
Shift along axis -3.50042646  
  

> ~select #7

Nothing selected  

> select #8

1543 atoms, 1577 bonds, 1 model selected  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

Fit molecule CV3-13-C3.pdb (#8) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1543 atoms  
average map value = 0.07766, steps = 76  
shifted from previous position = 1.97  
rotated from previous position = 10.5 degrees  
atoms outside contour = 1495, contour level = 0.13041  
  
Position of CV3-13-C3.pdb (#8) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.83650098 -0.54789840 0.00857019 110.19438761  
0.52395561 0.80432968 0.28022185 -116.24824971  
-0.16042636 -0.22991545 0.95989701 6.89090313  
Axis -0.42545863 0.14094449 0.89393490  
Axis point 238.47631279 85.61220110 0.00000000  
Rotation angle (degrees) 36.83514005  
Shift along axis -57.10768388  
  

> undo

> ~select #8

Nothing selected  

> volume #1 level 0.1661

> volume #1 level 0.2184

> volume #1 level 0.1551

> volume #1 level 0.1455

> volume #1 level 0.173

> volume #1 level 0.1359

> volume #1 level 0.1565

> volume #1 level 0.151

> ui mousemode rightMode "translate selected models"

> select #4

1789 atoms, 1832 bonds, 1 model selected  

> ui mousemode rightMode "rotate selected models"

Fit molecule CV3-13-V1.pdb (#4) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09357, steps = 116  
shifted from previous position = 1.14  
rotated from previous position = 17.9 degrees  
atoms outside contour = 1686, contour level = 0.15102  
  
Position of CV3-13-V1.pdb (#4) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.35672968 -0.65904343 -0.66212211 357.09707123  
-0.83806808 -0.53892057 0.08489114 399.00389208  
-0.41277817 0.52462022 -0.74457222 401.19306173  
Axis 0.81997934 -0.46496101 -0.33383400  
Axis point 0.00000000 268.07735458 305.48360940  
Rotation angle (degrees) 164.44672619  
Shift along axis -26.64091625  
  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

Fit molecule CV3-13-V1.pdb (#4) to map
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) using 1789 atoms  
average map value = 0.09357, steps = 120  
shifted from previous position = 0.753  
rotated from previous position = 20.4 degrees  
atoms outside contour = 1686, contour level = 0.15102  
  
Position of CV3-13-V1.pdb (#4) relative to
cryosparc_P50_J742_010_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.35677891 -0.65904542 -0.66209360 357.07869025  
-0.83804806 -0.53895378 0.08487795 399.00598358  
-0.41277627 0.52458360 -0.74459908 401.20053087  
Axis 0.81999518 -0.46494515 -0.33381719  
Axis point 0.00000000 268.07020750 305.47570590  
Rotation angle (degrees) 164.44788392  
Shift along axis -26.64072235  
  

> undo

> undo

> volume #1 level 0.1304

> volume #1 level 0.1167

> volume #1 level 0.1813

> volume #1 level 0.2252

> volume #1 level 0.1332

> ui mousemode rightMode "map eraser"

> volume #1 level 0.151

> ui mousemode rightMode "map eraser"

> close #9

> ui mousemode rightMode "map eraser"

> close

> open "C:\Users\ychen1\Desktop\CV3-13 spike\complete-spike_CV3-13.pdb" format
> PDB

Chain information for complete-spike_CV3-13.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D H L | No description available  
E I | No description available  
F J | No description available  
G K | No description available  
  

> close

> open C:\Phenix_output\CV3-13-V3.pdb format PDB

Chain information for CV3-13-V3.pdb #1  
---  
Chain | Description  
K | No description available  
L | No description available  
  

> close

> open "C:\Users\ychen1\Desktop\CV3-13 spike\complete_spike.pdb" format PDB

Chain information for complete_spike.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open2 "C:/Users/ychen1/Desktop/CV3-13
> spike/cryosparc_P50_J742_010_volumne_map_sharp.mrc"

Opened cryosparc_P50_J742_010_volumne_map_sharp.mrc, grid size 400,400,400,
pixel 0.889, shown at level 0.0809, step 2, values float32  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 109, in mouse_drag  
c = self.settings.sphere_center  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 298, in sphere_center  
return self.sphere_model.scene_position.origin()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 254, in sphere_model  
center, self._radius_value())  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 109, in mouse_drag  
c = self.settings.sphere_center  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 298, in sphere_center  
return self.sphere_model.scene_position.origin()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 254, in sphere_model  
center, self._radius_value())  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 109, in mouse_drag  
c = self.settings.sphere_center  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 298, in sphere_center  
return self.sphere_model.scene_position.origin()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 254, in sphere_model  
center, self._radius_value())  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 109, in mouse_drag  
c = self.settings.sphere_center  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 298, in sphere_center  
return self.sphere_model.scene_position.origin()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 254, in sphere_model  
center, self._radius_value())  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 109, in mouse_drag  
c = self.settings.sphere_center  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 298, in sphere_center  
return self.sphere_model.scene_position.origin()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 254, in sphere_model  
center, self._radius_value())  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 109, in mouse_drag  
c = self.settings.sphere_center  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 298, in sphere_center  
return self.sphere_model.scene_position.origin()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 254, in sphere_model  
center, self._radius_value())  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 109, in mouse_drag  
c = self.settings.sphere_center  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 298, in sphere_center  
return self.sphere_model.scene_position.origin()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 254, in sphere_model  
center, self._radius_value())  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 109, in mouse_drag  
c = self.settings.sphere_center  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 298, in sphere_center  
return self.sphere_model.scene_position.origin()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 254, in sphere_model  
center, self._radius_value())  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 109, in mouse_drag  
c = self.settings.sphere_center  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 298, in sphere_center  
return self.sphere_model.scene_position.origin()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 254, in sphere_model  
center, self._radius_value())  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 109, in mouse_drag  
c = self.settings.sphere_center  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 298, in sphere_center  
return self.sphere_model.scene_position.origin()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 254, in sphere_model  
center, self._radius_value())  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 109, in mouse_drag  
c = self.settings.sphere_center  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 298, in sphere_center  
return self.sphere_model.scene_position.origin()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 254, in sphere_model  
center, self._radius_value())  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 109, in mouse_drag  
c = self.settings.sphere_center  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 298, in sphere_center  
return self.sphere_model.scene_position.origin()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 254, in sphere_model  
center, self._radius_value())  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLineEdit has been deleted  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 269, in _radius_value  
rt = self._radius_entry.text()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 26.20.100.8141
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Latitude 7300
OS: Microsoft Windows 10 Enterprise (Build 17763)
Memory: 8,429,592,576
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz"

[Tom Goddard]

Fixed long ago. #3115. User is on old ChimeraX 0.94.