Opened 2 years ago

Closed 2 years ago

#9852 closed defect (can't reproduce)

Crash using File→Open on Windows and/or in return statement

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010e

Thread 0x00004ae4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004ae4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004ae4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004ae4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004ae4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\molc.py", line 36 in c_function
Windows fatal exception: access violation

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/rnwok/Documents/Tomo-
> Processing/20230419-CP01_TEM4/Lam_10/corrected_tomos-v6/crop/segmentations/Lam_102_ccRedo_corrected_crop_preproc__actin-
> positive_seg.hdf

Opened Lam_102_ccRedo_corrected_crop_preproc__actin-positive_seg.hdf as #1,
grid size 440,440,288, pixel 8.8, shown at level 0.479, step 2, values float32  

> open C:/Users/rnwok/Documents/Tomo-
> Processing/20230419-CP01_TEM4/Lam_10/corrected_tomos-v6/crop/segmentations/Lam_102_ccRedo_corrected_crop_preproc__mt-
> positive_seg.hdf

Opened Lam_102_ccRedo_corrected_crop_preproc__mt-positive_seg.hdf as #2, grid
size 440,440,288, pixel 8.8, shown at level 0.197, step 2, values float32  

> open C:/Users/rnwok/Documents/Tomo-
> Processing/20230419-CP01_TEM4/Lam_10/corrected_tomos-v6/crop/segmentations/Lam_102_ccRedo_corrected_crop_preproc__ribo-
> positive_seg.hdf

Opened Lam_102_ccRedo_corrected_crop_preproc__ribo-positive_seg.hdf as #3,
grid size 440,440,288, pixel 8.8, shown at level 1.84, step 2, values float32  

> volume #1 step 1

> volume #1 style image

> volume #1 style surface

> volume #1 change image level 0,0 level 0.4644,0.8 level 2.38,1

> volume #1 level 0.3038

> volume #3 level 0.1362

> volume #3 level 0.01139

> ui tool show "Hide Dust"

> volume #2 level 0.05035

> surface dust #2 size 62.76

> surface dust #2 size 192.57

> volume #3 step 1

> volume #2 step 1

> volume #2 level 0.03839

> volume #2 level 0.006507

> volume #2 level 0.03042

> volume #2 level 0.07028

> surface dust #2 size 3345.7

> surface dust #2 size 3352.6

> surface dust #2 size 3366.5

> surface dust #2 size 4088.8 metric volume

> surface dust #2 size 61919 metric volume

> surface dust #2 size 60914 metric volume

> surface dust #2 size 59925 metric volume

> surface dust #2 size 58951 metric volume

> surface dust #2 size 6.7888e+07 metric volume

> surface dust #2 size 1000 metric "size rank"

> surface dust #2 size 6 metric "size rank"

> surface dust #2 size 2 metric "size rank"

> surface dust #2 size 3 metric "size rank"

> surface dust #2 size 6 metric "size rank"

> surface dust #3 size 3 metric "size rank"

> surface dust #3 size 971 metric "size rank"

> volume #3 level 0.04708

> volume #3 level 0.02354

> volume #3 level 0.01

> surface dust #3 size 4088.8 metric volume

> surface dust #3 size 3.8182e+05 metric volume

> ui tool show "Map Eraser"

> volume erase #3 center 1907.9,1731.8,1247.2 radius 2019.3 outside true

Opened Lam_102_ccRedo_corrected_crop_preproc__ribo-positive_seg.hdf copy as
#5, grid size 440,440,288, pixel 8.8, shown at step 1, values float32  

> volume erase #5 center 4194.4,1750.4,1312.7 radius 1231.3

> volume erase #5 center -128.6,1906.5,1460.1 radius 363.97

> volume erase #5 center -250.56,1673.6,473.39 radius 596.29

> volume erase #5 center -214.83,1061.8,1069.4 radius 596.29

> volume erase #5 center -193.58,2346.4,1828.1 radius 596.29

> volume erase #5 center -169.24,1843.8,2052.3 radius 596.29

> volume erase #5 center -319.65,1319.6,1897.4 radius 596.29

> volume erase #5 center -273.9,895.05,1625.1 radius 596.29

> volume erase #5 center -324.16,772.62,1319 radius 596.29

> volume erase #5 center -287.7,1072,491.87 radius 596.29

> volume erase #5 center -374.25,2202.6,901.04 radius 596.29

> volume erase #5 center -248.02,2707.1,1354 radius 596.29

> volume erase #5 center -233.82,2654,1042.7 radius 596.29

> volume erase #5 center -273.68,2251.1,490.92 radius 596.29

> volume erase #5 center -277.67,1685.3,1028.2 radius 596.29

> volume erase #5 center -283.03,1486.4,1346.5 radius 596.29

> volume erase #5 center -300.4,2060.1,1165.2 radius 596.29

> volume erase #5 center 1675.5,3918.5,967.72 radius 336.86

> volume erase #5 center 1646.3,3839,1303.1 radius 336.86

> volume erase #5 center 1961.9,3733,878.1 radius 336.86

> volume erase #5 center 2249.1,3739.4,960.13 radius 336.86

> volume erase #5 center 1904.8,3827.1,1529.5 radius 336.86

> volume erase #5 center 1548.1,132.7,1771 radius 336.86

> volume erase #5 center 1669.9,242.51,2123.6 radius 336.86

> surface dust #3 size 7601.6 metric volume

> surface dust #3 size 9.8535e+05 metric volume

> surface dust #3 size 1.1909e+07 metric volume

> surface dust #3 size 3.4044e+09 metric volume

> surface dust #3 size 69667 metric volume

> surface dust #5 size 15496 metric volume

> surface dust #5 size 61919 metric volume

> volume #5 level 0.005

Can only have one displayed volume when erasing  

> volume erase #2 center 2619.9,1820.1,1416.7 radius 1928.3 outside true

Opened Lam_102_ccRedo_corrected_crop_preproc__mt-positive_seg.hdf copy as #6,
grid size 440,440,288, pixel 8.8, shown at step 1, values float32  

> volume erase #2 center 2619.9,1820.1,1416.7 radius 1928.3 outside true

Opened Lam_102_ccRedo_corrected_crop_preproc__mt-positive_seg.hdf copy as #7,
grid size 440,440,288, pixel 8.8, shown at step 1, values float32  

> close #6

> surface dust #2 size 3 metric "size rank"

> surface dust #2 size 10 metric "size rank"

> surface dust #7 size 7 metric "size rank"

> surface dust #7 size 9

> surface dust #7 size 52.8

> surface dust #7 size 305.06

> surface dust #7 size 434.19

> surface dust #7 size 681.47 metric volume

> surface dust #7 size 4088.8 metric volume

> surface dust #7 size 66982 metric volume

> surface dust #7 size 3.132e+05 metric volume

> surface dust #7 size 464.64 metric area

> surface dust #7 size 63528 metric area

> surface dust #7 size 1.9466e+06 metric area

> surface dust #7 size 1000 metric "area rank"

> surface dust #7 size 6 metric "area rank"

> surface dust #7 size 1 metric "area rank"

> volume #1 level 0.04373

> surface dust #1 size 82.73

> surface dust #1 size 253.85

> surface dust #1 size 498.52

> surface dust #1 size 5063.9

> surface dust #1 size 4084.9

> surface dust #1 size 4076.5

> surface dust #1 size 4059.6

> surface dust #1 size 4051.2

> surface dust #1 size 4042.8

> surface dust #1 size 4017.8

> surface dust #1 size 3992.8

> surface dust #1 size 3984.6

> surface dust #1 size 3959.9

> surface dust #1 size 3932.6

> surface dust #1 size 3924.5

> surface dust #1 size 3897.5

> surface dust #1 size 3870.6

> surface dust #1 size 3862.6

> surface dust #1 size 3836

> surface dust #1 size 3809.6

> surface dust #1 size 1000 metric "size rank"

> surface dust #1 size 6 metric "size rank"

> surface dust #1 size 2 metric "size rank"

> surface dust #1 size 3 metric "size rank"

> surface dust #1 size 1 metric "size rank"

> volume #1 step 4

> volume #1 step 16

> volume #1 step 8

> volume #1 step 2

> volume #1 level 0.1202

> close #1

> open C:/Users/rnwok/Documents/Tomo-
> Processing/20230419-CP01_TEM4/Lam_10/corrected_tomos-v6/crop/segmentations/Lam_102_ccRedo_corrected_crop_preproc__actin-
> positive_seg.hdf

Opened Lam_102_ccRedo_corrected_crop_preproc__actin-positive_seg.hdf as #1,
grid size 440,440,288, pixel 8.8, shown at level 0.304, step 2, values float32  

> volume #1 level 0.1617

> volume #1 step 1

> volume #1 level 0.1328

> volume #1 level 0.0401

> volume #1 level 0.01694

> surface dust #1 size 73.21

> surface dust #1 size 710.04

> volume #1 level 0.008256

> volume #1 step 8

> volume #1 step 2

> surface dust #1 size 4088.8 metric volume

> surface dust #1 size 1.8095e+09 metric volume

> volume erase #1 center 2009,2082.5,1448.7 radius 1852.8 outside true

Opened Lam_102_ccRedo_corrected_crop_preproc__actin-positive_seg.hdf copy as
#6, grid size 440,440,288, pixel 8.8, shown at step 1, values float32  

> surface dust #6 size 18164 metric volume

> surface dust #6 size 1.2387e+07 metric volume

> volume erase #6 center 2070.4,2190.8,-1025.5 radius 1816

> volume erase #6 center 4986.7,1940.4,1074.2 radius 1816

> volume erase #6 center 1953.2,2019.1,3849.5 radius 1816

> volume erase #6 center 2690.8,3144.4,3273.3 radius 1060.9

> volume erase #6 center 1698.1,3133.5,3151.2 radius 1060.9

> volume erase #6 center 798.51,2510.9,3254 radius 1060.9

> volume erase #6 center 807.57,1434.2,3320.6 radius 1060.9

> volume erase #6 center 1724.7,1117.3,3141.9 radius 1060.9

> volume erase #6 center 2882.1,1166.6,3048.7 radius 1060.9

> volume erase #6 center 3412.8,1912.1,2763.2 radius 1060.9

> volume erase #6 center 2909.5,1004,-111.45 radius 1060.9

> volume #6 level 0.01984

> volume erase #6 center 557.33,1763,1652.1 radius 1060.9

> volume erase #6 center 1053.9,3231,1350.8 radius 1060.9

> volume #6 level 0.01405

> volume #6 level 0.005

> volume #6 level 0.015

> volume #6 level 0.01

> volume #6 level 0.0125

> volume #6 level 0.008686

> surface dust #6 size 2.9598e+07 metric volume

> close #1

> close #3

> close #2

> open C:/Users/rnwok/Documents/Tomo-
> Processing/20230419-CP01_TEM4/Lam_10/corrected_tomos-v6/crop/Lam_102_ccRedo_corrected_crop-
> segment.mrc

Opened Lam_102_ccRedo_corrected_crop-segment.mrc as #1, grid size 420,422,266,
pixel 8.8,8.8,8.8, shown at level 1, step 2, values int8  

> volume #1

> volume #1 level 0.5667

> volume #1 level 0.2574

> volume #1 step 1

> surface dust #1 size 4088.8 metric volume

> surface dust #1 size 6.1388e+05 metric volume

> surface dust #1 size 6.0391e+05 metric volume

> surface dust #1 size 5.941e+05 metric volume

> surface dust #1 size 2.7082e+08 metric volume

> surface dust #1 size 1.384e+08 metric volume

> surface dust #1 size 1000 metric "size rank"

> surface dust #1 size 6 metric "size rank"

> surface dust #1 size 8 metric "size rank"

> ui tool show "Map Eraser"

> volume erase #1 center 2215,1786.2,593.64 radius 406.35

Opened Lam_102_ccRedo_corrected_crop-segment.mrc copy as #3, grid size
420,422,266, pixel 8.8,8.8,8.8, shown at step 1, values int8  

> surface dust #1 size 6 metric "size rank"

> surface dust #3 size 3 metric "size rank"

> surface dust #3 size 8 metric "size rank"

> volume erase #3 center 2232.2,2166.6,943.84 radius 404.78

> volume erase #3 center 2538.9,3327.2,766.08 radius 404.78

> volume erase #3 center 2582.4,3512.6,1675 radius 404.78

> volume erase #3 center 2609.4,3047.3,1964.8 radius 404.78

> volume erase #3 center 2488.6,2376.6,2034.5 radius 404.78

> volume erase #3 center 2392.4,1684.4,2045.6 radius 404.78

> volume erase #3 center 2349.3,2529.2,503.12 radius 404.78

> volume erase #3 center 2135.9,1228.2,720.21 radius 404.78

> volume erase #3 center 2089,936.69,1631 radius 404.78

> volume erase #3 center 2223.8,1466.3,1128.9 radius 404.78

> volume erase #3 center 2235.1,717.06,2138.1 radius 321.23

> volume erase #3 center 1884.4,306.94,1645.4 radius 321.23

> volume erase #3 center 1874,337.48,1459.9 radius 321.23

> volume erase #3 center 2068.3,309.89,1433 radius 321.23

> volume erase #3 center 2355.2,2835.4,1632.2 radius 321.23

> volume erase #3 center 2411.1,3251,1542.6 radius 321.23

> volume erase #3 center 2439.3,3456.8,1327.1 radius 321.23

> volume erase #3 center 2441.1,3318.9,478.85 radius 321.23

> volume erase #3 center 2351.1,3009.7,1736.8 radius 321.23

> volume erase #3 center 2300,2643,1277.6 radius 321.23

> volume erase #3 center 2334.3,1814.4,903.02 radius 321.23

> close #1

> volume #3 step 2

> volume #3 step 1

> volume #3 level 0.1

> volume #3 level 0.001

> volume #3 level 1

> ui tool show "Map Eraser"

Can only have one displayed volume when erasing  

> volume erase #5 center 3396.6,877.06,355.59 radius 574.99

> volume erase #5 center 3172.2,6.5555,1071 radius 574.99

> volume erase #5 center 3116.8,327.98,1690.8 radius 640.82

> volume erase #5 center 3321.4,2379.8,2802 radius 640.82

> save C:/Users/rnwok/Documents/Tomo-Processing/Chimera-
> models/04192023-Lam_102-ccRedo-crop.cxs

> open C:/Users/rnwok/Documents/Tomo-
> Processing/20230419-CP01_TEM4/Lam_10/corrected_tomos-v6/crop/Lam_102_ccRedo_corrected_crop.mrc

Opened Lam_102_ccRedo_corrected_crop.mrc as #1, grid size 420,422,266, pixel
8.8, shown at level 0.164, step 2, values float32  

> volume #1 style image region 0,0,132,419,421,132 step 1 showOutlineBox true

> select #1

3 models selected  

> volume #5 region 0,0,0,439,439,287

> volume #1 level -0.8308,0 level 0.1498,0.8 level 0.8438,1

> volume #1 level -0.8308,0 level -0.3871,0.9385 level 0.8438,1

> volume #1 level -0.8308,0 level -0.3871,0.9385 level 0.382,0.7692

> volume #1 level -0.8308,0 level -0.3871,0.9385 level 0.3012,0.6

> volume #1 level -0.8308,0 level -0.3582,0.9385 level 0.3012,0.6

> volume #1 level -0.8308,0 level -0.5199,0.6308 level 0.3012,0.6

> volume #1 level -1.887,0 level -0.5199,0.6308 level 0.3012,0.6

> volume #1 level -1.887,0 level 0.1729,0.9692 level 0.3012,0.6

> volume #1 level -1.887,0 level 0.1729,0.9692 level 0.2665,0.9692

> volume #1 level -1.887,0 level 0.144,0.8462 level 0.2665,0.9692

> volume #1 level -1.887,0 level 0.144,0.8462 level 0.203,0.9692

> volume #1 level -1.887,0 level 0.144,0.8462 level 0.1337,0.9538

> volume #1 region 0,0,0,419,421,265 step 2

> volume #1 region 0,0,0,419,421,265 step 2 maximumIntensityProjection true

> volume #1 maximumIntensityProjection false

> volume #1 style surface

> volume #1 style image region 0,0,132,419,421,132 step 1

> volume #1 region 0,0,172,419,421,172

> volume #1 region 0,0,154,419,421,154

> volume #1 region 0,0,0,419,421,265 step 2

> volume #1 style surface region 0,0,0,419,421,265 step 2

> vop scale #1 shift -1 factor -1

Opened Lam_102_ccRedo_corrected_crop.mrc scaled as #2, grid size 420,422,266,
pixel 8.8, shown at step 1, values float32  

> select #1

3 models selected  

> ~select #1

Nothing selected  

> volume #2 level 1.938

> volume #2 level 1.813

> vop gaussian #2 sd 15

Opened Lam_102_ccRedo_corrected_crop.mrc scaled gaussian as #4, grid size
420,422,266, pixel 8.8, shown at step 1, values float32  

> volume #4 level 1.635

> lighting soft

> volume #4 style image region 0,0,132,419,421,132 step 1

> volume #4 color #b2b2b2 color #b3ffff color #b3ffff

> volume #4 level 1.305,0 level 1.588,0.6308 level 1.884,1

> color #4.1 #b2b2b2 transparency 0

> color #4.2 #b2b2b2 models transparency 0

> volume #4 level 0.692,0.01538 level 1.588,0.6308 level 1.884,1

> volume #4 level 0.692,0.01538 level 1.81,0.9385 level 1.884,1

> volume #4 level 0.692,0.01538 level 1.81,0.9385 level 1.85,0.6615

> volume #4 level 0.692,0.01538 level 1.547,0.5846 level 1.85,0.6615

> set bgColor white

> set bgColor black

> lighting simple

> lighting full

> lighting soft

> volume #4 level 0.692,0.01538 level 1.547,0.5846 level 1.783,0.6615

> volume #4 level 0.692,0.01538 level 1.587,0.8615 level 1.783,0.6615

> volume #4 level 0.692,0.01538 level 1.587,0.8615 level 1.746,1

> volume #4 level 0.692,0.01538 level 1.35,0.4769 level 1.746,1

> select #4.2

1 model selected  

> volume #4 region 0,0,158,419,421,158

> ui tool show "Fit to Segments"

Density map not found or not selected  

> volume #!3-4 step 1

> volume #!3-4 region all imageMode "full region"

> volume unzone #!3-4

> mousemode rightMode "crop volume"

> volume #4 region 0,0,0,419,259,265

> volume #4 region 0,0,0,419,421,265

> ui mousemode right "translate selected models"

> view matrix models #4.2,1,0,0,-421.1,0,1,0,-40.775,0,0,1,2579.5

> volume #4 region 0,0,132,419,421,132 step 1

> volume #3 region 0,0,0,419,421,265

> volume #4 region 0,0,188,419,421,188

> ui mousemode right "translate selected models"

> view matrix models #4.2,1,0,0,-496.27,0,1,0,-308.42,0,0,1,2602.8

> ~select #4.2

Nothing selected  

> hide #4.2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #3 style image region 0,0,132,419,421,132 step 1 showOutlineBox true

> volume #3 region 0,0,0,419,421,265 step 1

> volume #3 style surface region 0,0,0,419,421,265 step 1

> hide #!4 models

> hide #!3 models

> show #!3 models

> volume #2 style image region 0,0,132,419,421,132 step 1

> close #4

> volume #2 level 1.112,0 level 2.285,0.8 level 3.274,1

> volume #2 level 1.112,0 level 1.709,0.8154 level 3.274,1

> volume #2 level 0.4709,0 level 1.709,0.8154 level 3.274,1

> volume #2 level 0.4709,0 level 2.1,0.7538 level 3.274,1

> volume #2 level 0.4709,0 level 3.273,0.9231 level 3.274,1

> volume #2 level 0.4709,0 level 3.268,0.9231 level 3.274,1

> volume #2 level 0.4709,0 level 3.262,0.9231 level 3.274,1

> volume #2 level 0.4709,0 level 3.252,0.9231 level 3.274,1

> volume #2 level 0.4709,0 level 3.241,0.9231 level 3.274,1

> volume #2 level 0.4709,0 level 3.235,0.9231 level 3.274,1

> volume #2 level 0.4709,0 level 3.224,0.9231 level 3.274,1

> volume #2 level 0.4709,0 level 3.213,0.9231 level 3.274,1

> volume #2 level 0.4709,0 level 3.208,0.9231 level 3.274,1

> volume #2 level 0.4709,0 level 3.208,0.9077 level 3.274,1

> volume #2 level 0.4709,0 level 3.203,0.9077 level 3.274,1

> volume #2 level 0.4709,0 level 3.197,0.8923 level 3.274,1

> volume #2 level 0.4709,0 level 3.192,0.8923 level 3.274,1

> volume #2 level 0.4709,0 level 3.192,0.8769 level 3.274,1

> volume #2 level 0.4709,0 level 3.186,0.8769 level 3.274,1

> volume #2 level 0.4709,0 level 3.181,0.8769 level 3.274,1

> volume #2 level 0.4709,0 level 3.175,0.8769 level 3.274,1

> volume #2 level 0.4709,0 level 3.175,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 3.165,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 3.154,0.8462 level 3.274,1

> volume #2 level 0.4709,0 level 3.148,0.8308 level 3.274,1

> volume #2 level 0.4709,0 level 3.137,0.8308 level 3.274,1

> volume #2 level 0.4709,0 level 3.132,0.8154 level 3.274,1

> volume #2 level 0.4709,0 level 3.127,0.8154 level 3.274,1

> volume #2 level 0.4709,0 level 3.121,0.8154 level 3.274,1

> volume #2 level 0.4709,0 level 3.11,0.8154 level 3.274,1

> volume #2 level 0.4709,0 level 3.105,0.8154 level 3.274,1

> volume #2 level 0.4709,0 level 3.089,0.8 level 3.274,1

> volume #2 level 0.4709,0 level 3.061,0.8 level 3.274,1

> volume #2 level 0.4709,0 level 3.034,0.7846 level 3.274,1

> volume #2 level 0.4709,0 level 3.007,0.7846 level 3.274,1

> volume #2 level 0.4709,0 level 2.985,0.7846 level 3.274,1

> volume #2 level 0.4709,0 level 2.953,0.7846 level 3.274,1

> volume #2 level 0.4709,0 level 2.926,0.7846 level 3.274,1

> volume #2 level 0.4709,0 level 2.871,0.7846 level 3.274,1

> volume #2 level 0.4709,0 level 2.822,0.7846 level 3.274,1

> volume #2 level 0.4709,0 level 2.779,0.8 level 3.274,1

> volume #2 level 0.4709,0 level 2.746,0.8 level 3.274,1

> volume #2 level 0.4709,0 level 2.725,0.8 level 3.274,1

> volume #2 level 0.4709,0 level 2.714,0.8 level 3.274,1

> volume #2 level 0.4709,0 level 2.708,0.8 level 3.274,1

> volume #2 level 0.4709,0 level 2.692,0.8 level 3.274,1

> volume #2 level 0.4709,0 level 2.665,0.8 level 3.274,1

> volume #2 level 0.4709,0 level 2.659,0.8 level 3.274,1

> volume #2 level 0.4709,0 level 2.594,0.8154 level 3.274,1

> volume #2 level 0.4709,0 level 2.562,0.8154 level 3.274,1

> volume #2 level 0.4709,0 level 2.551,0.8154 level 3.274,1

> volume #2 level 0.4709,0 level 2.545,0.8154 level 3.274,1

> volume #2 level 0.4709,0 level 2.54,0.8154 level 3.274,1

> volume #2 level 0.4709,0 level 2.529,0.8154 level 3.274,1

> volume #2 level 0.4709,0 level 2.502,0.8308 level 3.274,1

> volume #2 level 0.4709,0 level 2.453,0.8462 level 3.274,1

> volume #2 level 0.4709,0 level 2.448,0.8462 level 3.274,1

> volume #2 level 0.4709,0 level 2.399,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.393,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.388,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.377,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.355,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.317,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.29,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.279,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.274,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.268,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.263,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.241,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.225,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.22,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.214,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.209,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.198,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.171,0.8615 level 3.274,1

> volume #2 level 0.4709,0 level 2.149,0.8769 level 3.274,1

> volume #2 level 0.4709,0 level 2.133,0.8923 level 3.274,1

> volume #2 level 0.4709,0 level 2.116,0.8923 level 3.274,1

> volume #2 level 0.4709,0 level 2.111,0.8923 level 3.274,1

> volume #2 level 0.4709,0 level 2.111,0.9077 level 3.274,1

> volume #2 level 0.4709,0 level 2.106,0.9077 level 3.274,1

> volume #2 level 0.4709,0 level 2.106,0.9231 level 3.274,1

> volume #2 level 0.4709,0 level 2.1,0.9231 level 3.274,1

> volume #2 level 0.4709,0 level 2.084,0.9538 level 3.274,1

> volume #2 level 0.4709,0 level 2.078,0.9692 level 3.274,1

> volume #2 level 0.4709,0 level 2.073,0.9692 level 3.274,1

> volume #2 level 0.4709,0 level 2.067,0.9846 level 3.274,1

> volume #2 level 0.4709,0 level 2.062,0.9846 level 3.274,1

> volume #2 level 0.4709,0 level 2.062,1 level 3.274,1

> volume #2 level 0.4709,0 level 2.057,1 level 3.274,1

> volume #2 level 0.4709,0 level 2.046,1 level 3.274,1

> volume #2 level 0.4709,0 level 2.035,1 level 3.274,1

> volume #2 level 0.4709,0 level 2.029,1 level 3.274,1

> volume #2 level 0.4709,0 level 2.024,1 level 3.274,1

> volume #2 level 0.4709,0 level 2.029,1 level 3.274,1

> volume #2 level 0.4709,0 level 2.029,0.9846 level 3.274,1

> volume #2 level 0.4709,0 level 2.035,0.9846 level 3.274,1

> volume #2 level 0.4709,0 level 2.035,0.9692 level 3.274,1

> volume #2 level 0.4709,0 level 2.035,0.9538 level 3.274,1

> volume #2 level 0.4709,0 level 2.04,0.9538 level 3.274,1

> volume #2 level 0.4709,0 level 2.04,0.9385 level 3.274,1

> volume #2 level 0.4709,0 level 2.04,0.9538 level 3.274,1

> volume #2 level 0.4709,0 level 2.035,0.9538 level 3.274,1

> volume #2 level 0.4709,0 level 2.035,0.9692 level 3.274,1

> volume #3 change image level 0,0 level 0.1,0.8 level 1,1

> ui mousemode right "translate selected models"

> hide #!3 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> show #!3 models

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,-518.97,0,1,0,-451.68,0,0,1,2483.5

> view matrix models #2,1,0,0,-488.63,0,1,0,-355.61,0,0,1,2475.8

> view matrix models #3,1,0,0,0.57217,0,1,0,-26.266,0,0,1,-75.702

> show #!5 models


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 536.67
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7D09
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 17,055,731,712
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11700KF @ 3.60GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Platform
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash using File→Open on Windows and/or in return statement

comment:2 by Eric Pettersen, 2 years ago

Resolution: → can't reproduce
Status: accepted → closed

1.3

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