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Opened 102 minutes ago
#19820 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-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
Thread 0x000000031b7f7000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031a7eb000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003197df000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003187d3000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003177c7000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003167bb000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003157af000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003147a3000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000313797000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031278b000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031177f000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001f6decf40 (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":"2026-02-07 09:55:41.00 +0800","app_version":"1.6.1","slice_uuid":"a5992708-d5b4-36ec-ac0a-e525f6105b56","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 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"BA8A4251-5F9C-455F-A8F4-87455D4F2946"}
{
"uptime" : 480000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 8111,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2026-02-07 09:55:35.5100 +0800",
"codeSigningMonitor" : 1,
"incident" : "BA8A4251-5F9C-455F-A8F4-87455D4F2946",
"pid" : 15775,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-02-06 15:24:37.8067 +0800",
"procStartAbsTime" : 11031532554178,
"procExitAbsTime" : 11544796300308,
"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":"09BF9554-559A-58EB-B179-228514084143","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "80084792-CB22-7A1F-C008-6006ED674C51",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 1,
"sleepWakeUUID" : "FDBB287A-9E74-4274-A14F-127A66061D84",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4299915240\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1004b8000-1004bc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":15775},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4299915240\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1004b8000-1004bc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"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" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6693894221},{"value":5100567576},{"value":12220302368683796090},{"value":0},{"value":6166937688},{"value":13735687325005326864},{"value":13735687325899941200},{"value":78},{"value":0},{"value":49},{"value":18},{"value":4552916992},{"value":0},{"value":328},{"value":8611882216},{"value":0},{"value":11},{"value":8436764480,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8436764704,"symbolLocation":224,"symbol":"_main_thread"},{"value":4547450960},{"value":1},{"value":8421377},{"value":32768},{"value":8436770952,"symbolLocation":0,"symbol":"_NSConcreteStackBlock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6693706784},"cpsr":{"value":1073745920},"fp":{"value":5100567376},"sp":{"value":5100567344},"esr":{"value":1442840704,"description":" Address size 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===== 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: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Registration
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.
jigaoyuan@163.ocm is subscribed to the ChimeraX announcements list
> open "/Users/jigaoyuan/Desktop/SH folder/Draw/SH-NCP 1-1 multibody.cxs"
> format session
Opened J166 deepEMhancer map.mrc as #1, grid size 400,400,400, pixel 0.809,
shown at level 0.01, step 1, values float32
Opened multibody_local_refine J163_J217_J230 SH-1.mrc as #9, grid size
400,400,400, pixel 0.809, shown at level 0.9, step 1, values float32
Opened volume maximum as #13, grid size 400,400,400, pixel 0.809, shown at
level 0.000457, step 1, values float32
opened ChimeraX session
> show #!2 models
> hide #!9 models
> show #!9 models
> hide #!2 models
> ui tool show "Segment Map"
Segmenting multibody_local_refine J163_J217_J230 SH-1.mrc, density threshold
0.900106
Only showing 100 of 531 regions.
Showing 100 of 531 region surfaces
9425 watershed regions, grouped to 531 regions
Showing multibody_local_refine J163_J217_J230 SH-1.seg - 531 regions, 100
surfaces
> close #3
> volume gaussian #9 sDev 2
Opened multibody_local_refine J163_J217_J230 SH-1.mrc gaussian as #3, grid
size 400,400,400, pixel 0.809, shown at step 1, values float32
Segmenting multibody_local_refine J163_J217_J230 SH-1.mrc gaussian, density
threshold 0.680690
Showing 57 region surfaces
331 watershed regions, grouped to 57 regions
Showing multibody_local_refine J163_J217_J230 SH-1 gaussian.seg - 57 regions,
57 surfaces
> hide #!4 models
> volume #3 level 0.4101
Segmenting multibody_local_refine J163_J217_J230 SH-1.mrc gaussian, density
threshold 0.410088
Showing 57 region surfaces
342 watershed regions, grouped to 57 regions
Showing multibody_local_refine J163_J217_J230 SH-1 gaussian.seg - 57 regions,
57 surfaces
> ui mousemode right select
> select #4.3
1 model selected
> select add #4.22
2 models selected
> select add #4.27
3 models selected
Segmenting multibody_local_refine J163_J217_J230 SH-1.mrc gaussian, density
threshold 0.410088
Showing 57 region surfaces
342 watershed regions, grouped to 57 regions
Showing multibody_local_refine J163_J217_J230 SH-1 gaussian.seg - 57 regions,
57 surfaces
Segmenting multibody_local_refine J163_J217_J230 SH-1.mrc gaussian, density
threshold 0.410088
Showing 143 region surfaces
342 watershed regions, grouped to 143 regions
Showing multibody_local_refine J163_J217_J230 SH-1 gaussian.seg - 143 regions,
143 surfaces
> show #!9 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> volume #9 level 0.5404
> volume #9 level 0.7
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> select #4.86
1 model selected
> select add #4.51
2 models selected
> select add #4.2
3 models selected
> select add #4.50
4 models selected
> select add #4.92
5 models selected
> select add #4.47
6 models selected
> select add #4.41
7 models selected
> hide #!9 models
> select subtract #4.2
6 models selected
> select add #4.2
7 models selected
> select #4.2
1 model selected
> select #4.2
1 model selected
> select clear
> select #4.86
1 model selected
> select add #4.43
2 models selected
> select add #4.41
3 models selected
> select add #4.2
4 models selected
> select add #4.51
5 models selected
Segmenting multibody_local_refine J163_J217_J230 SH-1.mrc gaussian, density
threshold 0.410088
Showing 143 region surfaces
342 watershed regions, grouped to 143 regions
Showing multibody_local_refine J163_J217_J230 SH-1 gaussian.seg - 143 regions,
143 surfaces
> select #4.86
1 model selected
> select add #4.2
2 models selected
> select add #4.27
3 models selected
> select add #4.41
4 models selected
> select add #4.51
5 models selected
> select add #4.44
6 models selected
Grouped 6 regions
> select add #4.43
2 models selected
Grouped 2 regions
> select add #4.47
2 models selected
> select add #4.50
3 models selected
> select add #4.92
4 models selected
> select add #4.88
5 models selected
Grouped 5 regions
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!9 models
> show cartoons
> hide atoms
> show #!9 models
> hide #!9 models
> show #!9 models
> select clear
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!4 models
> select add #4.58
1 model selected
> select add #4.136
2 models selected
> select add #4.22
3 models selected
> select add #4.93
4 models selected
> select add #4.29
5 models selected
> select add #4.80
6 models selected
Grouped 6 regions
Grouped 1 regions
> hide #!9 models
> hide #!2 models
> select add #4.81
2 models selected
Grouped 2 regions
> select add #4.106
2 models selected
> select add #4.1
3 models selected
> select add #4.133
4 models selected
Grouped 4 regions
> select add #4.116
2 models selected
> select add #4.129
3 models selected
Grouped 3 regions
> select clear
> select #4.1
1 model selected
> select add #4.111
2 models selected
> select add #4.2
3 models selected
Grouped 3 regions
> show #!2 models
> select #4.95
1 model selected
> select clear
> select #4.95
1 model selected
Grouped 1 regions
> select add #4.1
2 models selected
Grouped 2 regions
> select #4.19
1 model selected
> select add #4.4
2 models selected
> select add #4.5
3 models selected
Grouped 3 regions
Drag select of 454, 118 of 21144 triangles
> select clear
> select #4.2
1 model selected
> select #4.11
1 model selected
> select add #4.2
2 models selected
Grouped 2 regions
> select clear
> select add #4.2
1 model selected
> select add #4.1
2 models selected
Grouped 2 regions
Drag select of 454, 550 of 21144 triangles, 442, 308 of 17300 triangles, 390,
497 of 18268 triangles, 56, 235 of 15444 triangles, 19, 624 of 13592
triangles, 92, 19 of 8988 triangles, 28, 322 of 9360 triangles, 385, 251 of
8144 triangles, 491, 1999 of 235380 triangles, 9 residues
> select clear
> select #4.1
1 model selected
> select #4.63
1 model selected
> select clear
> select #4.1
1 model selected
Saving 1 regions to mrc file...
Opened J166_midleHelicalDNA_Mask.mrc as #5, grid size 120,115,91, pixel 0.809,
shown at step 1, values float32
Wrote J166_midleHelicalDNA_Mask.mrc
> hide #!4 models
> select add #4
116 models selected
> select subtract #4
Nothing selected
> hide #!5 models
> show #!9 models
> hide #!9 models
> show #!5 models
> volume #5 level 0.4199
> volume #5 level 0.4
> volume resample #5 onGrid #9
Opened J166_midleHelicalDNA_Mask.mrc resampled as #6, grid size 400,400,400,
pixel 0.809, shown at step 1, values float32
> save "/Users/jigaoyuan/Downloads/J166_midleHelicalDNA_Mask OG.mrc" models #6
> hide #!6 models
> open /Users/jigaoyuan/Downloads/cryosparc_P32_J254_006_volume_map_sharp.mrc
Opened cryosparc_P32_J254_006_volume_map_sharp.mrc as #7, grid size
400,400,400, pixel 0.809, shown at level 0.429, step 2, values float32
> surface dust #7 size 8.09
> volume #7 level 1.053
Drag select of 15 residues, 7 cryosparc_P32_J254_006_volume_map_sharp.mrc
> select /J:135
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> volume #7 level 0.6492
> show #!9 models
> volume #9 level 0.8
> hide #!2 models
> hide #!7 models
> show #!7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> select #7
2 models selected
> select #7
2 models selected
> select clear
> volume #7 level 1.274
> volume #7 level 0.8329
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> volume #9 level 1.058
> show #!2 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> volume #7 level 0.5757
> hide #!9 models
> volume #7 level 0.5389
> volume #7 level 0.6859
> show #!9 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!7 models
> show #!7 models
> hide #!9 models
> volume #9 level 0.7
> show #!9 models
> hide #!9 models
> show #!9 models
> vop maximum #7 #9
Opened volume maximum as #8, grid size 400,400,400, pixel 0.809, shown at step
1, values float32
> surface dust #8 size 8.09
> volume #8 level 0.8
> volume #8 level 1.01
Drag select of 6 residues, 8 volume maximum
> select #8
2 models selected
> select clear
> volume #8 level 0.8786
> show #!13 models
> ui tool show "Surface Color"
> hide #!13 models
> close #4
> color sample #8.1 map #13 palette
> 2,#0fc6ce:3,#6fdde1:4,#cff3f5:5,#ebd2de:6,#c4799e:7,#9e1f5e
Map values for surface "surface": minimum 0, mean 2.621, maximum 20.64
> color sample #8.1 map #13 palette
> 1.5,#0fc6ce:2,#6fdde1:2.5,#cff3f5:3,#ebd2de:3.5,#c4799e:4,#9e1f5e
Map values for surface "surface": minimum 0, mean 2.621, maximum 20.64
> color sample #8.1 map #13 palette
> 2,#0fc6ce:3,#6fdde1:4,#cff3f5:5,#ebd2de:6,#c4799e:7,#9e1f5e
Map values for surface "surface": minimum 0, mean 2.621, maximum 20.64
> color sample #9.1 map #13 palette
> 2,#0fc6ce:2.5,#53d6dc:3,#98e6ea:3.5,#dcf6f8:4,#f1dfe8:4.5,#d59fba:5,#b95f8c
Map values for surface "surface": minimum 0, mean 2.215, maximum 28.6
> show #!9 models
> hide #!9 models
> color sample #9.1 map #13 palette
> 2,#0fc6ce:2.5,#53d6dc:3,#98e6ea:3.5,#dcf6f8:4,#f1dfe8:4.5,#d59fba:5,#b95f8c
Map values for surface "surface": minimum 0, mean 2.215, maximum 28.6
> color sample #9.1 map #13 palette
> 2,#0fc6ce:3,#6fdde1:4,#cff3f5:5,#ebd2de:6,#c4799e:7,#9e1f5e
Map values for surface "surface": minimum 0, mean 2.215, maximum 28.6
> show #!9 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
> volume #8 level 0.8
> volume #9 level 0.8
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 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
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> select clear
> hide #!2 models
> hide #!8 models
> open /Users/jigaoyuan/Downloads/cryosparc_P32_J163_005_volume_map_sharp.mrc
Opened cryosparc_P32_J163_005_volume_map_sharp.mrc as #4, grid size
400,400,400, pixel 0.809, shown at level 0.461, step 2, values float32
> surface dust #4 size 8.09
> open /Users/jigaoyuan/Downloads/cryosparc_P32_J250_006_volume_map_sharp.mrc
> /Users/jigaoyuan/Downloads/cryosparc_P32_J251_005_volume_map_sharp.mrc
Opened cryosparc_P32_J250_006_volume_map_sharp.mrc as #10.1, grid size
800,800,800, pixel 0.405, shown at step 1, values float32
Opened cryosparc_P32_J251_005_volume_map_sharp.mrc as #10.2, grid size
800,800,800, pixel 0.405, shown at step 1, values float32
> volume #10.2 level -0.004035,0 level 0.01877,0.8 level 0.1741,1
> volume #10.2 level -0.004035,0 level 0.008376,0.9231 level 0.1741,1
> volume #10.2 level -0.004035,0 level 0.008376,0.9231 level 0.1741,0.9846
> volume #10.2 level -0.01916,0.04615 level 0.008376,0.9231 level
> 0.1741,0.9846
> volume #10.1 region 0,0,0,799,799,799 step 4
> volume #10.2 region 0,0,0,799,799,799 step 4
> surface dust #4 size 8.09
> surface dust #10.1 size 4.05
> surface dust #10.2 size 4.05
> volume #10.1 step 2
> volume #10.2 step 2
> volume #10.2 level 0.01297
> volume #10.1 change image level -0.003462,0 level 0.0168,0.8 level 0.1102,1
> volume #10.1 level 0.01238
> hide #!4 models
> volume #10.2 level 0.1
> hide #!10.1 models
> volume #10.2 level 0.05
> volume #10.2 level 0.02
> volume #10.2 level 0.03
> volume #10.2 level 0.01
> volume #10.2 level 0.015
> volume #10.2 level 0.018
> show #!2 models
> show #!1 models
> hide #!10.2 models
> show #!4 models
> hide #!1 models
> volume #4 level 0.7
> show #!10.2 models
> hide #!10.2 models
> show #!10.2 models
> hide #!10.2 models
> show #!10.2 models
> hide #!4 models
> volume #10.1 level 0.018
> show #!10.1 models
> volume resample #10.1 onGrid #4
Opened cryosparc_P32_J250_006_volume_map_sharp.mrc resampled as #11, grid size
400,400,400, pixel 0.809, shown at step 1, values float32
> volume resample #10.2 onGrid #4
Opened cryosparc_P32_J251_005_volume_map_sharp.mrc resampled as #12, grid size
400,400,400, pixel 0.809, shown at step 1, values float32
> surface dust #11 size 8.09
> surface dust #12 size 8.09
> vop maximum #4 #10.1 #10.2
Opened volume maximum as #14, grid size 402,402,402, pixel 0.809, shown at
step 1, values float32
> surface dust #11 size 8.09
> surface dust #12 size 8.09
> surface dust #14 size 8.09
> hide #!11 models
> hide #!12 models
> close #14
> vop maximum #4 #11 #12
Opened volume maximum as #14, grid size 400,400,400, pixel 0.809, shown at
step 1, values float32
> surface dust #14 size 8.09
> volume #14 level 0.9443
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> volume #14 level 0.7
> volume #14 level 0.8
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> volume #14 level 0.6872
> close #10-14#10.1-2
> show #!9 models
QPainter::begin: Paint device returned engine == 0, type: 3
===== 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 M2
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 Air
Model Identifier: Mac14,2
Model Number: Z15S0007VCH/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 9天21小时46分钟
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U2723QX:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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-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-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
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