![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17774 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.7-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001eb574f40 (most recent call first):
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/serialize.py", line 70 in msgpack_deserialize
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 708 in restore
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 1004 in open
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core_formats/__init__.py", line 26 in open
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 435 in remember_data_format
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 465 in collated_open
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 194 in provider_open
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 119 in cmd_open
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1918 in _open_dropped_file
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 240 in event
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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"captureTime" : "2025-05-22 14:25:24.5071 -0400",
"codeSigningMonitor" : 1,
"incident" : "10036566-1767-449A-BB40-03D9410F99AD",
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"procLaunch" : "2025-05-22 14:05:57.0733 -0400",
"procStartAbsTime" : 30585340994552,
"procExitAbsTime" : 30613359468301,
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"codeSigningTeamID" : "LWV8X224YF",
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"sleepWakeUUID" : "6BACF95F-2226-452B-963C-3998578A2ED3",
"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":72592},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 4343578455\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102e5c000-102e60000 [ 16K] r-x\/r-x SM=COW \/opt\/sbgrid\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/OPT env DH17_6 fab with each protomer.cxs"
Opened cryosparc_P36_J75_006_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 1.1, shown at level 0.134, step 2, values float32
Log from Thu May 22 01:20:32 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/OPT env DH17_6 fab_glycan fitting.cxs"
Opened cryosparc_P36_J75_006_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 1.1, shown at level 0.12, step 2, values float32
Log from Wed May 21 18:28:54 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/OPT env DH17_6 fab.cxs"
Opened cryosparc_P36_J75_006_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 1.1, shown at level 0.1, step 2, values float32
Log from Tue May 20 13:58:06 2025 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
> remotecontrol rest start port 55786
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
REST server started on host 127.0.0.1 port 55786
Visit http://127.0.0.1:55786/cmdline.html for CLI interface
> open "/Users/rk387/Documents/Experiments/Cryo-EM/Data
> Processing/OPT_HIVenv_DH17-6/RealSpaceRefine_8/Unshielded HIV env OPT with
> DH17_6 Fab_real_space_refined_006-coot-19_real_space_refined_008.pdb"
Chain information for Unshielded HIV env OPT with DH17_6
Fab_real_space_refined_006-coot-19_real_space_refined_008.pdb #1
---
Chain | Description
A G | No description available
B C | No description available
D | No description available
E | No description available
H | No description available
P | No description available
> open "/Users/rk387/Documents/Experiments/Cryo-EM/Data
> Processing/OPT_HIVenv_DH17-6/cryosparc_P36_J75_006_volume_map_sharp.mrc"
Opened cryosparc_P36_J75_006_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 1.1, shown at level 0.0664, step 2, values float32
> surface dust #2 size 11
> hide atoms
> show cartoons
> set bgColor white
> transparency 50
> volume #2 level 0.1
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/OPT env DH17_6 fab.cxs" includeMaps true
> select /B
995 atoms, 1019 bonds, 1 pseudobond, 124 residues, 2 models selected
> select /P
1616 atoms, 1655 bonds, 211 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /P
Alignment identifier is 1/P
> color sel cyan
> select /H
1750 atoms, 1800 bonds, 230 residues, 1 model selected
> color sel blue
> ui tool show "Model Panel"
> color #1 #942193ff
> color #1 #941751ff
> color #1 #942193ff
> color sel blue
> select /P
1616 atoms, 1655 bonds, 211 residues, 1 model selected
> color sel cyan
> color zone #2 near sel & #1 distance 6.6
> select add #1
18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 2 models selected
> color zone #2 near sel & #1 distance 6.6
> hide #!2 models
> show #!2 models
> hide #!1 models
> volume #2 level 0.13
> volume #2 level 0.12
> color #2 #929292ff models
> color #2 darkgrey models
> color #2 silver models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
[Repeated 1 time(s)]
> color #1 darkgrey
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
[Repeated 2 time(s)]
> transparency 50
> show #!1 models
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select /P
1616 atoms, 1655 bonds, 211 residues, 1 model selected
> color sel cyan
> select /H
1750 atoms, 1800 bonds, 230 residues, 1 model selected
> color sel blue
> select add #1
18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 2 models selected
> color zone #2 near sel & #1 distance 6.6
> hide #!2 models
> show #!2 models
> hide #!1 models
> volume #2 level 0.1
> save "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/OPT env DH17_6 fab.cxs" includeMaps true
——— End of log from Tue May 20 13:58:06 2025 ———
opened ChimeraX session
> transparency 0
> transparency 50
> ui tool show "Model Panel"
> show #!1 models
> select subtract #1
Nothing selected
> select ::name="BMA"::name="MAN"::name="NAG"
1991 atoms, 2066 bonds, 148 residues, 1 model selected
> show sel atoms
> color sel red
> color zone #2 near sel & #1 distance 6.6
> transparency 0
> transparency 50
> volume #2 level 0.12
> select add #1
18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 2 models selected
> select subtract #1
Nothing selected
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select /A
3938 atoms, 4049 bonds, 2 pseudobonds, 477 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A /G
Alignment identifier is 1
> select /A,G:168
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /A,G:168-171
80 atoms, 78 bonds, 8 residues, 1 model selected
> select /A,G:167
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /A,G:167-177
210 atoms, 214 bonds, 22 residues, 1 model selected
> select /A,G:172
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /A,G:172-177
114 atoms, 118 bonds, 12 residues, 1 model selected
> select add #1
18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 2 models selected
> select subtract #1
Nothing selected
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/rk387/Desktop/movie1.mp4
Movie saved to /Users/rk387/Desktop/movie1.mp4
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/OPT env DH17_6 fab_glycan fitting.cxs" includeMaps true
> hide #!2 models
> show #!2 models
> volume #2 level 0.2
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> volume #2 level 0.12
> hide #!2 models
> show #!2 models
> hide #!1 models
> volume #2 level 0.2027
[Repeated 1 time(s)]
> show #!1 models
> volume #2 level 0.1344
> volume #2 level 0.174
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> volume #2 level 0.1056
> volume #2 level 0.12
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save /Users/rk387/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/rk387/Desktop/movie2.mp4
Movie saved to /Users/rk387/Desktop/movie2.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/rk387/Desktop/movie3.mp4
Movie saved to /Users/rk387/Desktop/movie3.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/rk387/Desktop/movie4.mp4
Movie saved to /Users/rk387/Desktop/movie4.mp4
> save "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/OPT env DH17_6 fab_glycan fitting.cxs" includeMaps true
——— End of log from Wed May 21 18:28:54 2025 ———
opened ChimeraX session
> volume #2 level 0.1584
> color zone #2 near #1 distance 6.6
> transparency 0
> transparency 50
> volume #2 level 0.134
> color zone #2 near #1 distance 6.6
> transparency 0
> transparency 50
> transparency 0
> ui tool show "Model Panel"
> hide #!2 models
> hide atoms
> show surfaces
[Repeated 1 time(s)]
> select ::name="BMA"::name="MAN"::name="NAG"
1991 atoms, 2066 bonds, 148 residues, 1 model selected
> show sel surfaces
> select add #1
18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 29 models selected
> select subtract #1
35 models selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show cartoons
> transparency #1.2-36 50
> select ::name="BMA"::name="MAN"::name="NAG"
1991 atoms, 2066 bonds, 148 residues, 1 model selected
> select ::name="BMA"::name="MAN"::name="NAG"
1991 atoms, 2066 bonds, 148 residues, 1 model selected
> show sel atoms
> select add #1
18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 29 models selected
> select subtract #1
35 models selected
> transparency #1.2-36 0
> transparency #1.2-36 50
> transparency #1.2-36 0
> transparency #1.2-36 50
> transparency #1.2-36 0
> transparency #1.2-36 50
> show #!2 models
> hide #!2 models
> transparency #1.2-36 0
> lighting shadows false
> lighting shadows true
> lighting shadows false
> select /C
995 atoms, 1019 bonds, 1 pseudobond, 124 residues, 2 models selected
> select /A
3938 atoms, 4049 bonds, 2 pseudobonds, 477 residues, 2 models selected
> color (#!1 & sel) light sea green
> color (#!1 & sel) forest green
> select /B
995 atoms, 1019 bonds, 1 pseudobond, 124 residues, 2 models selected
> color (#!1 & sel) purple
> select /C
995 atoms, 1019 bonds, 1 pseudobond, 124 residues, 2 models selected
> color (#!1 & sel) forest green
> select /E
952 atoms, 976 bonds, 1 pseudobond, 118 residues, 2 models selected
> color (#!1 & sel) gray
> select /G
3949 atoms, 4063 bonds, 1 pseudobond, 478 residues, 2 models selected
> color (#!1 & sel) purple
> select /E
952 atoms, 976 bonds, 1 pseudobond, 118 residues, 2 models selected
> color (#!1 & sel) orange
> select /H
1750 atoms, 1800 bonds, 230 residues, 1 model selected
> select /G
3949 atoms, 4063 bonds, 1 pseudobond, 478 residues, 2 models selected
> select /H
1750 atoms, 1800 bonds, 230 residues, 1 model selected
> select /D
3950 atoms, 4062 bonds, 1 pseudobond, 477 residues, 2 models selected
> color (#!1 & sel) orange
> select add #1
18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 4 models selected
> select subtract #1
35 models selected
> select /A
3938 atoms, 4049 bonds, 2 pseudobonds, 477 residues, 2 models selected
> color (#!1 & sel) light gray
> select /B
995 atoms, 1019 bonds, 1 pseudobond, 124 residues, 2 models selected
> color (#!1 & sel) dark gray
> color (#!1 & sel) dim gray
> color (#!1 & sel) gray
> select /C
995 atoms, 1019 bonds, 1 pseudobond, 124 residues, 2 models selected
> color (#!1 & sel) light gray
> select /D
3950 atoms, 4062 bonds, 1 pseudobond, 477 residues, 2 models selected
> color (#!1 & sel) light sea green
> select /E
952 atoms, 976 bonds, 1 pseudobond, 118 residues, 2 models selected
> color (#!1 & sel) light sea green
> select /E
952 atoms, 976 bonds, 1 pseudobond, 118 residues, 2 models selected
> select /G
3949 atoms, 4063 bonds, 1 pseudobond, 478 residues, 2 models selected
> color (#!1 & sel) dark gray
> color (#!1 & sel) gray
> select add #1
18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 4 models selected
> select subtract #1
35 models selected
> select ::name="BMA"::name="MAN"::name="NAG"
1991 atoms, 2066 bonds, 148 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select /H
1750 atoms, 1800 bonds, 230 residues, 1 model selected
> color (#!1 & sel) forest green
> color (#!1 & sel) orange red
> select /P
1616 atoms, 1655 bonds, 211 residues, 1 model selected
> color (#!1 & sel) yellow
> turn x +90
> turn x -90
[Repeated 1 time(s)]
> turn x +90
> select add #1
18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 3 models selected
> select subtract #1
35 models selected
> save "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/OPT env DH17_6 fab with each protomer.cxs" includeMaps true
> save "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/Images/OPT env DH17_6 fab with each protomer_top.tif" width 840 height
> 696 supersample 3 transparentBackground true
> turn x +90
> turn x -90
[Repeated 1 time(s)]
> save "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/Images/OPT env DH17_6 fab with each protomer_side.tif" width 840 height
> 696 supersample 3 transparentBackground true
> turn y -90
> turn y +90
[Repeated 1 time(s)]
> turn y -90
> turn x -90
> turn x +90
[Repeated 1 time(s)]
> save "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/OPT env DH17_6 fab with each protomer.cxs" includeMaps true
——— End of log from Thu May 22 01:20:32 2025 ———
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain /H
Alignment identifier is 1/H
> select /H:250
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /H:142-250
792 atoms, 813 bonds, 109 residues, 1 model selected
> select /H:250
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /H:148-250
750 atoms, 769 bonds, 103 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain /P
Alignment identifier is 1/P
> select /P:231
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /P:121-231
854 atoms, 871 bonds, 111 residues, 1 model selected
> select /P:231
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /P:127-231
805 atoms, 822 bonds, 105 residues, 1 model selected
> select /P:129
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /P:129-231
787 atoms, 804 bonds, 103 residues, 1 model selected
> select /P:127
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /P:127-231
805 atoms, 822 bonds, 105 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> turn x +90
> save "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/Images/CE89_7_top.tif" width 936 height 696 supersample 3
> transparentBackground true
> turn x -90
> save "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/Images/CE89_7_side.tif" width 936 height 696 supersample 3
> transparentBackground true
> lighting simple
> save "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/Images/CE89_7_side.tif" width 936 height 696 supersample 3
> transparentBackground true
> turn x +90
> save "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/Images/CE89_7_top.tif" width 936 height 696 supersample 3
> transparentBackground true
> transparency sel 50
> transparency sel 0
> select /P:231
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /P:126-231
814 atoms, 831 bonds, 106 residues, 1 model selected
> select /P:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /P:21-125
802 atoms, 823 bonds, 105 residues, 1 model selected
> select /P:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /P:21-126
811 atoms, 832 bonds, 106 residues, 1 model selected
> ui tool show "Model Panel"
> select add #1
18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 3 models selected
> transparency sel 50
> turn x 990
> turn x +90
> hide sel surfaces
> turn x -90
> select subtract #1
35 models selected
> turn x +90
> turn x -90
> save "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/Images/CE89_7_side acrtoon.tif" width 840 height 696 supersample 3
> transparentBackground true
> turn x +90
> graphics silhouettes false
> graphics silhouettes true
> save "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/Images/CE89_7_top acrtoon.tif" width 840 height 696 supersample 3
> transparentBackground true
> open "/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23
> 2025/comparison of all natural Ab.cxs"
===== 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: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: MRX73LL/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 11881.1.1
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7 (23H124)
Kernel Version: Darwin 23.6.0
Time since boot: 48 days, 23 hours, 20 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
T27i-30:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
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: 1.1.1
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: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
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: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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