![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9511 closed defect (limitation)
Crash saving session including maps
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
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 0x0000000204bc0600 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-08-02 19:13:51.00 -0400","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.6 (21G115)","incident_id":"5BBF3C54-C57B-4F6B-A3F9-5249E0A6DDF5","name":"ChimeraX"}
{
"uptime" : 2800000,
"procLaunch" : "2023-07-31 11:01:27.0369 -0400",
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"procStartAbsTime" : 66563758337866,
"coalitionID" : 266612,
"osVersion" : {
"train" : "macOS 12.6",
"build" : "21G115",
"releaseType" : "User"
},
"captureTime" : "2023-08-02 19:13:43.8995 -0400",
"incident" : "5BBF3C54-C57B-4F6B-A3F9-5249E0A6DDF5",
"bug_type" : "309",
"pid" : 84180,
"procExitAbsTime" : 68773045392335,
"translated" : true,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"97DBD241-47B6-59D7-A3AA-B6EAA8D8A648","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "5E8DCD59-6021-BB99-0D36-3E49E42E18EB",
"wakeTime" : 33204,
"sleepWakeUUID" : "14DDADEF-90B8-4091-8622-5882CC12336D",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140722747883496\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc91664000-7ffc91ca0000 [ 6384K] r-x\/r-x SM=COW ...t_id=7e09f5c3",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140722747883496\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc91664000-7ffc91ca0000 [ 6384K] r-x\/r-x SM=COW ...t_id=7e09f5c3",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/Models/Model Building-NEW/State2-ssDNA-conf.1-CT/State2-Protein-
> and-DNA-model-ssDNA-conf.1-coot-1.pdb"
Chain information for State2-Protein-and-DNA-model-ssDNA-conf.1-coot-1.pdb #1
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
X | No description available
Y | No description available
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/Models/Model Building-NEW/State3-ssDNA-conf.2-CT/Protein-and-DNA-
> model-ssDNA-conf.2-coot-0.pdb"
Summary of feedback from opening /Users/ben/Library/CloudStorage/GoogleDrive-
ballwein@gmail.com/My Drive/Grad School/Thesis Work/EM Data
Processing/20221108-CMG-reaction/Models/Model Building-NEW/State3-ssDNA-
conf.2-CT/Protein-and-DNA-model-ssDNA-conf.2-coot-0.pdb
---
warning | PDB SEQRES record for chain 6 is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for Protein-and-DNA-model-ssDNA-conf.2-coot-0.pdb #2
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
X | No description available
Y | No description available
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/Models/Model Building-NEW/State2-ssDNA-conf.1-CT/State2-composite-
> map-ssDNA-conf.1.mrc"
Opened State2-composite-map-ssDNA-conf.1.mrc as #3, grid size 448,448,448,
pixel 0.826, shown at level 0.396, step 2, values float32
> volume #3 step 1
> volume #3 level 1.235
> hide atoms
> show cartoons
> hide #!3 models
> ui autostart false Log
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui mousemode right zoom
> lighting soft
> rename #2 State3-Protein-and-DNA-model-ssDNA-conf.2-coot-0.pdb
> rename #2 id #4
> rename #4 id #2
> rename #2 id #4
> rename #3 id #2
> rename #4 id #3
> color #1 #a9f3a8ff
> color #3 #f3b3dfff
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> nucleotides slab
> style nucleic stick
Changed 2845 atom styles
> select nucleic-acid
2845 atoms, 3192 bonds, 137 residues, 2 models selected
> style sel stick
Changed 2845 atom styles
> style sel stick
Changed 2845 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 2845 atom styles
> show sel atoms
> nucleotides sel fill
> style nucleic & sel stick
Changed 2845 atom styles
> nucleotides sel tube/slab shape box
> align #3 toAtoms #1
Unequal number of atoms to pair, 48514 and 48564
> show sel surfaces
> select add #3
49947 atoms, 51100 bonds, 62 pseudobonds, 6033 residues, 9 models selected
> select add #1
97078 atoms, 99038 bonds, 125 pseudobonds, 11933 residues, 12 models selected
> show sel surfaces
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> select subtract #1
48514 atoms, 49492 bonds, 62 pseudobonds, 5964 residues, 33 models selected
> select subtract #3
15 models selected
> show #!1 models
> show #!3 models
> graphics silhouettes true
> lighting soft
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!3 models
> morph #3 #1
Computed 51 frame morph #4
> coordset #4 1,51
> view #4 clip false
> color #!4 bychain
> nucleotides #!4 tube/slab shape box
> movie record
> movie encode /Users/ben/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/ben/Desktop/movie.mp4
> morph #1 #3
Computed 51 frame morph #5
> coordset #5 1,51
> hide #!4 models
> nucleotides #!5 tube/slab shape box
> color #!5 bychain
> lighting soft
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting soft
> view #5 clip false
> morph #1 #3 #1
Computed 51 frame morph #6
> coordset #6 1,51
> hide #!5 models
> show #!5 models
> hide #!5 models
> close #6
> show #!5 models
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/Models/Model Building-NEW/State2-ssDNA-conf.1-CT/State2-Protein-
> and-DNA-model-ssDNA-conf.1-coot-1.pdb"
Chain information for State2-Protein-and-DNA-model-ssDNA-conf.1-coot-1.pdb #6
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
X | No description available
Y | No description available
> show #!5-6 cartoons
> hide #!5-6 atoms
> morph #1 #3 #6
Computed 101 frame morph #7
> coordset #7 1,101
> hide #!5 models
> nucleotides #!7 tube/slab shape box
> color #!7 bychain
> movie record
> movie encode /Users/ben/Desktop/movie.mp4 framerate 25.0
Error processing trigger "new frame":
Movie encoding failed because no images were recorded.
> movie record
> movie encode /Users/ben/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/ben/Desktop/movie.mp4
> movie record
> movie encode /Users/ben/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/ben/Desktop/movie.mp4
> movie record
> movie encode /Users/ben/Desktop/movie.mp4 framerate 25.0
Error processing trigger "new frame":
Movie encoding failed because no images were recorded.
> movie record
> movie encode /Users/ben/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/ben/Desktop/movie.mp4
> hide #!7 models
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/Density Modification/J1171_denmod_map.ccp4"
Opened J1171_denmod_map.ccp4 as #8, grid size 247,215,219, pixel 0.826, shown
at level 4.35, step 1, values float32
> volume #8 level 1.2
> surface dust #8 size 8.26
> view #8 clip false
> graphics silhouettes false
> lighting soft
> hide #!8 models
> show #!8 models
> color #8 #a2a7ffff models
> color #8 #f8a4ffff models
> set bgColor white
> close #8
> show #!7 models
> hide #!7 models
> set bgColor black
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 surfaces
> show #!3 models
> hide #!1,3 surfaces
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!7 models
> view #7 clip false
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!7 models
> movie record
> movie encode /Users/ben/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/ben/Desktop/movie.mp4
> show #!1 models
> hide #!5 models
> color #!1 bychain
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!4 models
> view #4 clip false
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!3 models
> show #!2 models
> show #!6 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> close #6
> rainbow #!1
> color #!1 bychain
> show #!7 models
> hide #!1 models
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data
> Processing/20230103-ssDNA-T15/Maps/cryosparc_P37_J1186_004_volume_map.mrc"
Opened cryosparc_P37_J1186_004_volume_map.mrc as #6, grid size 192,192,192,
pixel 1.65, shown at level 0.88, step 1, values float32
> view #6 clip false
Must specify one map, got 0
> fitmap #6 inMap #2
Fit map cryosparc_P37_J1186_004_volume_map.mrc in map State2-composite-map-
ssDNA-conf.1.mrc using 70710 points
correlation = 0.02191, correlation about mean = 0.0005065, overlap = 3623
steps = 60, shift = 2.41, angle = 1.05 degrees
Position of cryosparc_P37_J1186_004_volume_map.mrc (#6) relative to
State2-composite-map-ssDNA-conf.1.mrc (#2) coordinates:
Matrix rotation and translation
0.99984352 0.00441790 0.01712935 -2.73168958
-0.00433589 0.99997897 -0.00482212 3.40130991
-0.01715029 0.00474709 0.99984165 3.17174316
Axis 0.26109025 0.93530015 -0.23884200
Axis point 207.02842200 0.00000000 187.43707829
Rotation angle (degrees) 1.05003132
Shift along axis 1.71048269
> show #!2 models
> select add #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.99984,0.0044179,0.017129,2.4532,-0.0043359,0.99998,-0.0048221,36.099,-0.01715,0.0047471,0.99984,34.408
> view matrix models
> #6,0.99984,0.0044179,0.017129,2.2068,-0.0043359,0.99998,-0.0048221,30.22,-0.01715,0.0047471,0.99984,31.847
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.99982,-0.015082,0.011457,6.0527,0.014078,0.99643,0.083193,13.838,-0.012671,-0.083017,0.99647,44.907
> fitmap #6 inMap #2
Fit map cryosparc_P37_J1186_004_volume_map.mrc in map State2-composite-map-
ssDNA-conf.1.mrc using 70710 points
correlation = 0.04464, correlation about mean = 0.01502, overlap = 1.029e+04
steps = 72, shift = 1.71, angle = 2.27 degrees
Position of cryosparc_P37_J1186_004_volume_map.mrc (#6) relative to
State2-composite-map-ssDNA-conf.1.mrc (#2) coordinates:
Matrix rotation and translation
0.99936355 -0.02301927 -0.02725075 12.89966060
0.02527985 0.99599622 0.08574644 13.10365671
0.02516783 -0.08638076 0.99594424 40.54146978
Axis -0.92391693 -0.28136408 0.25925233
Axis point 0.00000000 489.94099490 -113.22443911
Rotation angle (degrees) 5.34489668
Shift along axis -5.09464238
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.99936,-0.023019,-0.027251,35.045,0.02528,0.996,0.085746,11.037,0.025168,-0.086381,0.99594,35.901
> fitmap #6 inMap #2
Fit map cryosparc_P37_J1186_004_volume_map.mrc in map State2-composite-map-
ssDNA-conf.1.mrc using 70710 points
correlation = 0.6082, correlation about mean = 0.4079, overlap = 2.413e+05
steps = 96, shift = 0.94, angle = 5.48 degrees
Position of cryosparc_P37_J1186_004_volume_map.mrc (#6) relative to
State2-composite-map-ssDNA-conf.1.mrc (#2) coordinates:
Matrix rotation and translation
0.99993979 -0.01078503 -0.00202036 28.26595694
0.01077417 0.99992786 -0.00530861 26.83639602
0.00207747 0.00528652 0.99998386 23.80889650
Axis 0.43477884 -0.16815756 0.88469791
Axis point -2931.06092995 1474.56504051 0.00000000
Rotation angle (degrees) 0.69813758
Shift along axis 28.84037816
> select subtract #6
Nothing selected
> ui mousemode right zoom
> hide #!2 models
> transparency #6.1 50
> hide #!7 models
> show #!1 models
> volume #6 level 0.5307
> close #1-7
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-reaction/CMG-
> EM-Data/State3/State3-Models/State3-Protein-model-ssDNA-conf.2-coot-12.pdb"
Summary of feedback from opening /Users/ben/Library/CloudStorage/GoogleDrive-
ballwein@gmail.com/My Drive/Grad School/Thesis Work/EM Data
Processing/20221108-CMG-reaction/CMG-EM-
Data/State3/State3-Models/State3-Protein-model-ssDNA-conf.2-coot-12.pdb
---
warning | PDB SEQRES record for chain 6 is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for State3-Protein-model-ssDNA-conf.2-coot-12.pdb #1
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
X | No description available
Y | No description available
> show cartoons
> hide atoms
> open emdb-10227
'emdb-10227' has no suffix
> open emdb:10227
Opened emdb 10227 as #2, grid size 360,360,360, pixel 1.05, shown at level
0.0111, step 2, values float32
> volume #2 step 1
> open pdb:6skl
6skl title:
Cryo-EM structure of the CMG Fork Protection Complex at a replication fork -
Conformation 1 [more info...]
Chain information for 6skl #3
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST
3 | DNA replication licensing factor MCM3 | MCM3_YEAST
4 | DNA replication licensing factor MCM4 | MCM4_YEAST
5 | Minichromosome maintenance protein 5 | MCM5_YEAST
6 | DNA replication licensing factor MCM6 | MCM6_YEAST
7 | DNA replication licensing factor MCM7 | MCM7_YEAST
A | DNA replication complex GINS protein PSF1 | PSF1_YEAST
B | DNA replication complex GINS protein PSF2 | PSF2_YEAST
C | DNA replication complex GINS protein PSF3 | PSF3_YEAST
D | DNA replication complex GINS protein SLD5 | SLD5_YEAST
E | Cell division control protein 45 | CDC45_YEAST
F G H | DNA polymerase alpha-binding protein | CTF4_YEAST
I | DNA fork, leading-strand template |
J | DNA fork, lagging-strand template |
X | Topoisomerase 1-associated factor 1 | TOF1_YEAST
Y | Chromosome segregation in meiosis protein 3 | CSM3_YEAST
Non-standard residues in 6skl #3
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
ZN — zinc ion
> show cartoons
> hide atoms
> hide #!1 models
> volume #2 level 0.01251
> transparency 50
> show #!1 models
> view #1 clip false
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!1 models
> view #3 clip false
> select #3/I:49
32 atoms, 33 bonds, 1 residue, 1 model selected
> select up
1192 atoms, 1279 bonds, 37 residues, 1 model selected
> select up
118220 atoms, 119405 bonds, 7321 residues, 1 model selected
> select down
1192 atoms, 1279 bonds, 37 residues, 1 model selected
> show sel atoms
> nucleotides sel stubs
> nucleotides sel tube/slab shape box
> select clear
> select #2
4 models selected
> hide #!2 models
> select #3/7:363
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 20 atom styles
> select clear
> show #!2 models
> volume #2 level 0.02158
> volume #2 level 0.02363
> hide #!3 models
> hide #!2 models
> show #!1 models
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-reaction/CMG-
> EM-Data/State3/State3-Maps/State3_denmod_map-(C-tier).mrc"
Opened State3_denmod_map-(C-tier).mrc as #4, grid size 448,448,448, pixel
0.826, shown at level 0.504, step 2, values float32
> volume #4 level 1.25
> volume #4 step 1
> hide #!1 models
> view #4 clip false
> surface dust #4 size 8.26
> ui tool show "Segment Map"
Segmenting State3_denmod_map-(C-tier).mrc, density threshold 1.250051
Only showing 60 of 985 regions.
Showing 60 of 985 region surfaces
6810 watershed regions, grouped to 985 regions
Showing State3_denmod_map-(C-tier).seg - 985 regions, 60 surfaces
> hide #!4 models
> show #!1 models
> hide #!5 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!4 models
> molmap #1 4
Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 4 as #6, grid size
155,135,141, pixel 1.33, shown at level 0.0965, step 1, values float32
> hide #!6 models
> hide #!5 models
> hide #!1 models
> show #!6 models
> molmap #1 4 onGrid #4
Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 4 as #6, grid size
448,448,448, pixel 0.826, shown at level 0.0966, step 1, values float32
> close #5
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!4 models
> show #!6 models
> molmap #1 3 onGrid #4
Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #5, grid size
448,448,448, pixel 0.826, shown at level 0.111, step 1, values float32
> molmap #1 2 onGrid #4
Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 2 as #5, grid size
448,448,448, pixel 0.826, shown at level 0.19, step 1, values float32
> molmap #1 1 onGrid #4
Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 1 as #5, grid size
448,448,448, pixel 0.826, shown at level 0.773, step 1, values float32
> volume #5 step 2
> volume #5 step 4
> volume #5 step 16
> volume #5 step 1
> molmap #1 3 onGrid #4
Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #5, grid size
448,448,448, pixel 0.826, shown at level 0.111, step 1, values float32
> hide #!5 models
> show #!5 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> hide #!5 models
> show #!5 models
> show #!1 models
> select #1/2
5222 atoms, 5310 bonds, 6 pseudobonds, 657 residues, 3 models selected
> hide #!5 models
> molmap #1/2 3 onGrid #4
Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #6, grid size
448,448,448, pixel 0.826, shown at level 0.109, step 1, values float32
> hide #!6 models
> molmap #1/2:469-865 3 onGrid #4
Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #7, grid size
448,448,448, pixel 0.826, shown at level 0.11, step 1, values float32
> close #6
> close #5
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> molmap #1/3:338-739 3 onGrid #4
Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #5, grid size
448,448,448, pixel 0.826, shown at level 0.111, step 1, values float32
> molmap #1/4:501-836 3 onGrid #4
Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #6, grid size
448,448,448, pixel 0.826, shown at level 0.11, step 1, values float32
> molmap #1/4:340-694 3 onGrid #4
Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #8, grid size
448,448,448, pixel 0.826, shown at level 0.107, step 1, values float32
> molmap #1/5:500-835 3 onGrid #4
Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #9, grid size
448,448,448, pixel 0.826, shown at level 0.109, step 1, values float32
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> close #8
> close #9
> molmap #1/5:340-694 3 onGrid #4
Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #8, grid size
448,448,448, pixel 0.826, shown at level 0.11, step 1, values float32
> molmap #1/6:500-835 3 onGrid #4
Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #9, grid size
448,448,448, pixel 0.826, shown at level 0.111, step 1, values float32
> molmap #1/7:409-730 3 onGrid #4
Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #10, grid size
448,448,448, pixel 0.826, shown at level 0.112, step 1, values float32
> hide #!1 models
> select #5
2 models selected
> select #8
2 models selected
> select #5
2 models selected
> select #8
2 models selected
> select #7
2 models selected
> select #8
2 models selected
> select #10
2 models selected
> show #!1 models
No segmentation chosen
> ui tool show "DICOM Browser"
> vop add #5,8,10
Opened volume sum as #11, grid size 448,448,448, pixel 0.826, shown at step 1,
values float32
> rename #11 Mcm7,3,5
> vop add #6,7,9
Opened volume sum as #12, grid size 448,448,448, pixel 0.826, shown at step 1,
values float32
> rename #12 Mcm4,6,2
> save "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-reaction/CMG-
> EM-Data/State3/State3-Masks/State3-Mcm7-3-5-mask.mrc" models #11
> save "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-reaction/CMG-
> EM-Data/State3/State3-Masks/State3-Mcm4-6-2-mask.mrc" models #12
> volume #11 level 0.05216
> lighting soft
> show #!4 models
> hide #!12 models
> hide #!11 models
> hide #!4 models
> show #!11 models
> show #!12 models
> save "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/ChimeraX Sessions/20221108-reaction-session-4.cxs" includeMaps true
===== Log before crash end =====
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 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: MacBookPro18,3
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 10
L2 Cache: 20 MB
Memory: 16 GB
Software:
System Software Overview:
System Version: macOS 12.6 (21G115)
Kernel Version: Darwin 21.6.0
Time since boot: 50 days 14:25
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
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
ASUS PB287Q:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 60.00Hz
Mirror: Off
Online: Yes
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-PhenixUI: 1.1.13
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: 2022.9.26
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 , 2 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash saving session including maps |
comment:2 by , 2 years ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
Looks like you were saving a session when ChimeraX crashed. Sorry about that. The stack trace shows it was in a system call _io_FileIO_write. It also says ChimeraX was using 49 Gbytes on this Mac that only has 16 Gbytes of physical memory. I'd guess it crashed writing the file because too much memory was used. It isn't clear why so much memory was being used. But saving the session including the many Gbytes of maps you had open I think makes a copy of that session file in memory so that might have doubled your memory use. It is also strange that you are running the Intel Mac ChimeraX 1.6.1. But ChimeraX 1.6.1 is distributed as a universal build including M1 and Intel versions, so I don't see how you could be using the Intel version unless you deliberately installed the Intel only version. Running the Intel version on an M1 Mac is likely to be a little less stable.
I think the only recommendation is that when looking at a lot of large maps and trying to save all those maps in a very large session file you probably need a computer with more memory. Usually it doesn't crash in these circumstances, but just issues an error message and keeps running. But once you are low on memory, any code that fails to allocate memory could crash and probably a small memory allocation failed that was not protected.
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Reported by Ben Allwein