Opened 21 months ago

Closed 21 months ago

#14660 closed defect (duplicate)

Crash in garbage collection

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

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-97-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007fdd8ee4f700 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 324 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 622 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1392 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007fde00aac740 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/ctypes/__init__.py", line 512 in cast
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/numpy/core/_internal.py", line 282 in data_as
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 333 in pointer
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 208 in get_prop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1887 in _update_graphics_if_needed
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/view.py", line 294 in check_for_drawing_change
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 76 in draw_new_frame
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 50 in display
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/toolbar/providers.py", line 38 in _file_save
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/toolbar/providers.py", line 56 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/toolbar/__init__.py", line 37 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 165 in callback
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, PIL._webp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 57)
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/zm/PCS4/ggp19/PCS4gpp19_c995c.result/PCS4gpp19_c995c/PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
> format pdb

Chain information for
PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
  

> preset "molecular surfaces" "atomic coloring (transparent)"

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> color cornflower blue

> preset "molecular surfaces" "atomic coloring (transparent)"

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> set bgColor white

> ui tool show "Side View"

> view

> movie record

> turn y 2 180

> wait 180

> movie encode /home/zm/Desktop/movie1.mp4

Movie saved to /home/zm/Desktop/movie1.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /home/zm/Desktop/movie2.mp4

Movie saved to /home/zm/Desktop/movie2.mp4  
  

> save /home/zm/Desktop/image1.png supersample 3

> save /home/zm/Desktop/image2.png supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode /home/zm/Desktop/movie3.mp4

Movie saved to /home/zm/Desktop/movie3.mp4  
  

> save /home/zm/Desktop/image1.png supersample 3

> save /home/zm/PCS4/ggp19/gpp19-1.tif width 1251 height 803 supersample 3
> transparentBackground true

> surface hidePatches

> save /home/zm/PCS4/ggp19/gpp19-2.tif width 1251 height 803 supersample 3

> preset "molecular surfaces" "atomic coloring (transparent)"

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> save /home/zm/PCS4/ggp19/gpp19-1.tif width 1251 height 803 supersample 3

> surface hidePatches

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for
PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface #1.1: minimum, -10.19, mean 1.74, maximum 12.17  
To also show corresponding color key, enter the above coulombic command and
add key true  

> surface hidePatches

> save /home/zm/PCS4/ggp19/gpp19-2.tif width 1251 height 803 supersample 3

> preset "molecular surfaces" "atomic coloring (transparent)"

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> save /home/zm/PCS4/ggp19/gpp19-1.tif width 1251 height 803 supersample 3

> coulombic

Coulombic values for
PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface #1.1: minimum, -10.19, mean 1.74, maximum 12.17  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for
PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface #1.1: minimum, -10.19, mean 1.74, maximum 12.17  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for
PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface #1.1: minimum, -10.19, mean 1.74, maximum 12.17  
To also show corresponding color key, enter the above coulombic command and
add key true  

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting full

> lighting flat

> view

> ui tool show "Side View"

> view

> view orient

> view

> ui tool show "Side View"

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting simple

> lighting shadows true

> lighting flat

> select up

Nothing selected  

> ui mousemode right select

> select /A:135@CB

1 atom, 1 residue, 1 model selected  

> select clear

> coulombic protein key true

Coulombic values for
PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface #1.1: minimum, -10.19, mean 1.74, maximum 12.17  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right "color key"

> ui mousemode right select

> coulombic protein key true

Coulombic values for
PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface #1.1: minimum, -10.19, mean 1.74, maximum 12.17  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right "color key"

> key red:-10 white:0

> key red:-10 white:0 white:

> ui mousemode right select

> coulombic protein key true

Coulombic values for
PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface #1.1: minimum, -10.19, mean 1.74, maximum 12.17  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right "color key"

> key colorTreatment distinct

> key colorTreatment blended

> key borderWidth 3.0

> key borderWidth 4.0

> key borderWidth 3.0

> key border false

> key fontSize 23

> key fontSize 22

> key fontSize 21

> key fontSize 20

> key fontSize 19

> key pos 0.69000,0.08000

> key pos 0.68000,0.08000

> key pos 0.67000,0.08000

> key size 0.26000,0.05000

> key size 0.25000,0.05000

> key fontSize 18

> key fontSize 17

> key fontSize 16

> key fontSize 15

> key fontSize 14

> key fontSize 13

> key fontSize 12

> key fontSize 11

> key fontSize 12

> key fontSize 13

> key fontSize 14

> key fontSize 15

> key fontSize 16

> key fontSize 17

> key tickLength 12.0

> key tickLength 14.0

> key tickLength 16.0

> key tickThickness 3.0

> key tickThickness 2.0

> key tickThickness 1.0

> key tickThickness 0.0

> key tickThickness 1.0

> key tickThickness 2.0

> key tickThickness 3.0

> key tickThickness 4.0

> ui mousemode right select

> ui mousemode right "color key"

> key bold true

> key labelSide right/bottom

> key labelSide left/top

> key labelSide right/bottom

> key numericLabelSpacing equal

> key labelOffset -1.0

> key labelOffset -2.0

> key labelOffset -3.0

> key labelOffset -4.0

> key labelOffset -5.0

> key labelOffset -4.0

> key labelOffset -3.0

> key justification left

> ui mousemode right select

> surface style solid

> surface style mesh

> surface style dot

> surface style solid

> ui tool show "Selection Inspector"

> graphics silhouettes depthJump 0.03

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting full

> lighting soft

> lighting simple

> lighting flat

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> graphics silhouettes false

> graphics silhouettes true

> save /home/zm/PCS4/ggp19/gpp19-3.tif width 1251 height 803 supersample 3

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> save /home/zm/PCS4/ggp19/gpp19-4.tif width 1251 height 803 supersample 3

> mlp

Map values for surface
"PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface": minimum -28.15, mean -3.896, maximum 22.66  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic protein key true

Coulombic values for
PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface #1.1: minimum, -10.19, mean 1.74, maximum 12.17  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right "color key"

> ui mousemode right select

> undo

> coulombic

Coulombic values for
PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface #1.1: minimum, -10.19, mean 1.74, maximum 12.17  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface
"PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface": minimum -28.15, mean -3.896, maximum 22.66  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic

Coulombic values for
PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface #1.1: minimum, -10.19, mean 1.74, maximum 12.17  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface
"PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface": minimum -28.15, mean -3.896, maximum 22.66  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic protein key true

Coulombic values for
PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface #1.1: minimum, -10.19, mean 1.74, maximum 12.17  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right "color key"

> mlp

Map values for surface
"PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface": minimum -28.15, mean -3.896, maximum 22.66  
To also show corresponding color key, enter the above mlp command and add key
true  

> ui mousemode right select

> coulombic

Coulombic values for
PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface #1.1: minimum, -10.19, mean 1.74, maximum 12.17  
To also show corresponding color key, enter the above coulombic command and
add key true  

> save /home/zm/PCS4/ggp19/gpp19-4.tif width 1251 height 803 supersample 3

> lighting full

> save /home/zm/PCS4/ggp19/gpp19-3.tif width 1251 height 803 supersample 3

> surface hidePatches

> coulombic protein key false

Coulombic values for
PCS4gpp19_c995c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface #1.1: minimum, -10.19, mean 1.74, maximum 12.17  

> surface hidePatches

> select clear

> hide #2 target m

> save /home/zm/PCS4/ggp19/gpp19-1.tif width 1251 height 803 supersample 3

> preset "molecular surfaces" "atomic coloring (transparent)"

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> save /home/zm/PCS4/ggp19/gpp19-2.tif width 1251 height 803 supersample 3

> surface style mesh

> surface style solid

> color bfactor

2421 atoms, 153 residues, 1 surfaces, atom bfactor range 43.9 to 98.9  

> save /home/zm/PCS4/ggp19/gpp19-5-bfactor.tif width 1251 height 803
> supersample 3

> hbonds reveal true

143 hydrogen bonds found  

> surface hidePatches #1

> hbonds reveal true

143 hydrogen bonds found  

> hbonds reveal true

143 hydrogen bonds found  

> ~hbonds

> interfaces ~solvent

0 buried areas:  

> color bypolymer

> color bychain

> color byhetero

> color bynucleotide

> open
> /home/zm/PCS4/gpp43/PCS4gpp43_44eb7.result/PCS4gpp43_44eb7/PCS4gpp43_44eb7_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb

Chain information for
PCS4gpp43_44eb7_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #3  
---  
Chain | Description  
A | No description available  
  

> close #2

> close #1

> lighting full

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting shadows true

> save /home/zm/PCS4/gpp43/PCS4gpp43_44eb7.result/PCS4gpp43_44eb7/gpp43-1.tif
> width 1251 height 803 supersample 3

> preset "molecular surfaces" "atomic coloring (transparent)"

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> color hot pink

> preset "molecular surfaces" "atomic coloring (transparent)"

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> save /home/zm/PCS4/gpp43/PCS4gpp43_44eb7.result/PCS4gpp43_44eb7/gpp43-2.tif
> width 1251 height 803 supersample 3

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for
PCS4gpp43_44eb7_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface #3.1: minimum, -12.50, mean -0.46, maximum 21.48  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface
"PCS4gpp43_44eb7_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface": minimum -26.52, mean -1.953, maximum 23.22  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic

Coulombic values for
PCS4gpp43_44eb7_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface #3.1: minimum, -12.50, mean -0.46, maximum 21.48  
To also show corresponding color key, enter the above coulombic command and
add key true  

> open
> /home/zm/PCS4/gpp43/PCS4gpp43_44eb7.result/PCS4gpp43_44eb7/PCS4gpp43_44eb7_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb

Chain information for
PCS4gpp43_44eb7_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
  

> close #3

> color hot pink

> ui tool show "Color Actions"

> color #bf5555ff

> color #c55858ff

> color #c56e6eff

> color #bf6a6aff

> color #bf6c6cff

> color #bf6b6bff

> color #c06c6cff

> color #c06969ff

> color #c26a6aff

> color #c26969ff

> color #c36a6aff

> color #c36d6dff

> color #c76f6fff

> color #c77474ff

> color #ce7878ff

> color #ce7979ff

> color #d07a7aff

> color #d07b7bff

> color #d57e7eff

> color #d57f7fff

> color #dc8383ff

> color #dc8888ff

> color #ef9393ff

> color #ef9797ff

> color #f39a9aff

> color #f3a3a3ff

> color #f9a7a7ff

> color #faa7a7ff

> color #fba8a8ff

> color #fba5a5ff

> color #fea8a8ff

> color #fea9a9ff

> color #feaeaeff

> color #ffaeaeff

> color #ffb3b3ff

> color #ffb4b4ff

> color #ffbdbdff

> color #fdbbbbff

> color #fdbdbdff

> color #fcbcbcff

> color #fcbfbfff

> color #fbbfbfff

> color #fbc1c1ff

> color #f9c0c0ff

> color #f9c3c3ff

> color #f8c2c2ff

> color #f8bfbfff

> color #f9c0c0ff

> color #f9b2b2ff

> color #fab3b3ff

> color #faacacff

> color #faababff

> color #faa8a8ff

> color #f9a8a8ff

> color #f9a7a7ff

> color #f8a6a6ff

> lighting full

> lighting shadows false

> lighting shadows true

> save /home/zm/PCS4/gpp43/PCS4gpp43_44eb7.result/PCS4gpp43_44eb7/gpp43-1.tif
> width 1251 height 803 supersample 3

> preset "molecular surfaces" "atomic coloring (transparent)"

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.6 (Core Profile) Mesa 21.2.6
OpenGL renderer: Mesa Intel(R) UHD Graphics 630 (CFL GT2)
OpenGL vendor: Intel

Python: 3.11.2
Locale: zh_CN.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:0
Manufacturer: Dell Inc.
Model: Precision 5540
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi       7.0Gi       2.5Gi       2.9Gi       5.8Gi       5.0Gi
	Swap:         2.0Gi       301Mi       1.7Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 630 (Mobile) [8086:3e9b]	
	DeviceName:  Onboard IGD	
	Subsystem: Dell UHD Graphics 630 (Mobile) [1028:0906]

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 21 months ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection

comment:2 by Eric Pettersen, 21 months ago

Resolution: → duplicate
Status: accepted → closed
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