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Opened 22 months ago
Closed 22 months ago
#10446 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2.1-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 0x00000002962bf000 (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 0x00000002952b3000 (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 0x00000002942a7000 (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 0x000000029329b000 (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 0x000000029228f000 (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 0x0000000291283000 (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 0x0000000290277000 (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 0x000000028f26b000 (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 0x000000028e25f000 (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 0x000000028d253000 (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 0x000000028c247000 (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 0x00000001dbdc5000 (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":"2024-01-08 14:22:55.00 -0500","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 14.2.1 (23C71)","roots_installed":0,"name":"ChimeraX","incident_id":"EED58CCD-2C98-4ED5-ADD0-815CF88D9A12"}
{
"uptime" : 730000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 88308,
"osVersion" : {
"train" : "macOS 14.2.1",
"build" : "23C71",
"releaseType" : "User"
},
"captureTime" : "2024-01-08 14:22:50.2654 -0500",
"codeSigningMonitor" : 1,
"incident" : "EED58CCD-2C98-4ED5-ADD0-815CF88D9A12",
"pid" : 75645,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-01-08 11:51:47.1182 -0500",
"procStartAbsTime" : 17340648365482,
"procExitAbsTime" : 17558163227509,
"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":"4009FAF6-E9AB-50BF-9F04-0B89775FDB68","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "99DA3F3A-511F-2832-8536-7AEDB6E711CB",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 11363,
"sleepWakeUUID" : "B41793A7-447C-4392-97B2-81835EC9CF7E",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 105553653137384\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600020000000-600040000000 [512.0M] rw-\/rwx SM=PRV ",
"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":75645},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 105553653137384\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600020000000-600040000000 [512.0M] rw-\/rwx SM=PRV ",
"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":6532705549},{"value":5100731416},{"value":14653896621418052622},{"value":0},{"value":6160720120},{"value":4503198375180363156},{"value":4503198382573073812},{"value":78},{"value":0},{"value":49},{"value":17},{"value":10888413184},{"value":0},{"value":328},{"value":8135078720},{"value":0},{"value":11},{"value":7983616000,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":7983616224,"symbolLocation":224,"symbol":"_main_thread"},{"value":4773626496},{"value":1},{"value":32769},{"value":32768},{"value":7983622472,"symbolLocation":0,"symbol":"_NSConcreteStackBlock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6532521152},"cpsr":{"value":1073745920},"fp":{"value":5100731216},"sp":{"value":5100731184},"esr":{"value":1442840704,"description":" Address size 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===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
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
> open /Users/TEST/Desktop/EMD/emd_12243.map
Opened emd_12243.map as #1, grid size 400,400,400, pixel 1.05, shown at level
0.00713, step 2, values float32
> volume #1 step 1
> volume #1 level 0.01363
> open 7BOH
7boh title:
Complete Bacterial 30S ribosomal subunit assembly complex state E
(+RbfA)(Consensus Refinement) [more info...]
Chain information for 7boh #2
---
Chain | Description | UniProt
A | RNA (1527-MER) |
B | 30S ribosomal protein S2 | RS2_ECOLI 1-241
C | 30S ribosomal protein S3 | RS3_ECOLI 1-233
D | 30S ribosomal protein S4 | RS4_ECOLI 1-206
E | 30S ribosomal protein S5 | RS5_ECOLI 1-167
F | 30S ribosomal protein S6 | RS6_ECOLI 1-135
G | 30S ribosomal protein S7 | RS7_ECOLI 1-179
H | 30S ribosomal protein S8 | RS8_ECOLI 1-130
I | 30S ribosomal protein S9 | RS9_ECOLI 1-130
J | 30S ribosomal protein S10 | RS10_ECOLI 1-103
K | 30S ribosomal protein S11 | RS11_ECOLI 1-129
L | 30S ribosomal protein S12 | RS12_ECOLI 1-124
M | 30S ribosomal protein S13 | RS13_ECOLI 1-118
N | 30S ribosomal protein S14 | RS14_ECOLI 1-101
O | 30S ribosomal protein S15 | RS15_ECOLI 1-89
P | 30S ribosomal protein S16 | RS16_ECOLI 1-82
Q | 30S ribosomal protein S17 | RS17_ECOLI 1-84
R | 30S ribosomal protein S18 | RS18_ECOLI 1-75
S | 30S ribosomal protein S19 | RS19_ECOLI 1-92
T | 30S ribosomal protein S20 | RS20_ECOLI 1-87
V | 30S ribosome-binding factor | RBFA_ECOLI 1-133
Non-standard residues in 7boh #2
---
MG — magnesium ion
ZN — zinc ion
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 51997 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> set bgColor black
> set bgColor white
> lighting flat
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting simple
> color #1 #b2b2b2cc models
> sequence chain #2/V
Alignment identifier is 2/V
> select /V:84-104
173 atoms, 176 bonds, 21 residues, 1 model selected
> select /V:6-84
614 atoms, 619 bonds, 79 residues, 1 model selected
> select /V:78-104
225 atoms, 229 bonds, 27 residues, 1 model selected
> select /V
783 atoms, 792 bonds, 99 residues, 1 model selected
> ui tool show "Color Zone"
> color zone #1 near sel distance 4
> select add #2
52154 atoms, 56194 bonds, 1667 pseudobonds, 4129 residues, 4 models selected
> select subtract #2
Nothing selected
> volume #1 level 0.01493
> volume #1 level 0.01601
> open /Users/TEST/Desktop/cryosparc_P37_J127_009_volume_map.mrc
Opened cryosparc_P37_J127_009_volume_map.mrc as #3, grid size 384,384,384,
pixel 0.855, shown at level 0.0889, step 2, values float32
> open /Users/TEST/Desktop/cryosparc_P37_J130_007_volume_map.mrc
Opened cryosparc_P37_J130_007_volume_map.mrc as #4, grid size 384,384,384,
pixel 0.855, shown at level 0.0922, step 2, values float32
> volume #4 color #929292
> Volume flip#3
Unknown command: Volume flip#3
> Volume flip #3
Unknown command: Volume flip #3
> Flip volume#3
Unknown command: Flip volume#3
> flip volume#3
Unknown command: flip volume#3
> volume flip#3
Expected a density maps specifier or a keyword
> volume flip #3
Opened cryosparc_P37_J127_009_volume_map.mrc z flip as #5, grid size
384,384,384, pixel 0.855, shown at step 1, values float32
> ui mousemode right select
> select #5
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.4933,-0.77976,0.38553,144.83,0.70356,0.6183,0.35031,-116.89,-0.51153,0.098429,0.85361,95.286
> view matrix models
> #5,0.54346,-0.51885,0.65988,52.265,-0.0768,0.75207,0.65459,-53.281,-0.83592,-0.40642,0.36887,305.74
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.54346,-0.51885,0.65988,92.871,-0.0768,0.75207,0.65459,-2.5794,-0.83592,-0.40642,0.36887,356.62
> fitmap #2 inMap #5
Fit molecule 7boh (#2) to map cryosparc_P37_J127_009_volume_map.mrc z flip
(#5) using 52154 atoms
average map value = 0.1072, steps = 172
shifted from previous position = 6.88
rotated from previous position = 15.1 degrees
atoms outside contour = 25183, contour level = 0.088917
Position of 7boh (#2) relative to cryosparc_P37_J127_009_volume_map.mrc z flip
(#5) coordinates:
Matrix rotation and translation
0.67315578 -0.23783323 -0.70021187 220.00709757
-0.42476837 0.65073060 -0.62938185 246.63226221
0.60533720 0.72109988 0.33701903 -184.55574865
Axis 0.71543201 -0.69162846 -0.09903087
Axis point 0.00000000 410.98082186 169.39766307
Rotation angle (degrees) 70.70374472
Shift along axis 5.09894631
> ui mousemode right select
> select clear
> volume #5 color darkgrey
> volume #5 color #a9a9a9a3
> volume #5 color #a9a9a9e6
> volume #5 level 0.1057
> volume #5 level 0.8
> volume #5 level 0.08
Drag select of 18 residues, 48 shapes, 5 cryosparc_P37_J127_009_volume_map.mrc
z flip
> ui mousemode right select
> select clear
> ui mousemode right "translate selected models"
> fitmap #2 inMap #5
Fit molecule 7boh (#2) to map cryosparc_P37_J127_009_volume_map.mrc z flip
(#5) using 52154 atoms
average map value = 0.1072, steps = 60
shifted from previous position = 0.00785
rotated from previous position = 0.00599 degrees
atoms outside contour = 22210, contour level = 0.08
Position of 7boh (#2) relative to cryosparc_P37_J127_009_volume_map.mrc z flip
(#5) coordinates:
Matrix rotation and translation
0.67321205 -0.23775232 -0.70018525 219.97767516
-0.42479011 0.65071717 -0.62938106 246.63894830
0.60525937 0.72113868 0.33707581 -184.56527011
Axis 0.71546537 -0.69158590 -0.09908708
Axis point 0.00000000 410.96888656 169.40982950
Rotation angle (degrees) 70.70072116
Shift along axis 5.10242367
> volume flip #4
Opened cryosparc_P37_J130_007_volume_map.mrc z flip as #6, grid size
384,384,384, pixel 0.855, shown at step 1, values float32
> ui mousemode right select
> select #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,58.857,0,1,0,32.855,0,0,1,40.286
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.49673,0.53209,-0.68567,168.71,-0.071775,-0.76213,-0.64343,455.64,-0.86493,0.36882,-0.34038,349.95
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.49673,0.53209,-0.68567,161.56,-0.071775,-0.76213,-0.64343,456.91,-0.86493,0.36882,-0.34038,344.48
> fitmap #2 inMap #6
Fit molecule 7boh (#2) to map cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) using 52154 atoms
average map value = 0.1092, steps = 148
shifted from previous position = 13.8
rotated from previous position = 4.92 degrees
atoms outside contour = 25285, contour level = 0.092213
Position of 7boh (#2) relative to cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) coordinates:
Matrix rotation and translation
0.68529294 -0.24480885 -0.68588790 216.20271485
0.37897532 -0.68436668 0.62291248 97.43482379
-0.62189331 -0.68681211 -0.37621514 517.29154942
Axis -0.90195504 -0.04407052 0.42957526
Axis point 0.00000000 164.45628448 286.65330045
Rotation angle (degrees) 133.44393362
Shift along axis 22.91651852
> volume #6 level 0.089
> volume #6 level 0.08
> volume #6 color #929292d7
> volume #6 color #929292cc
> view matrix models
> #6,0.49673,0.53209,-0.68567,153.81,-0.071775,-0.76213,-0.64343,434.01,-0.86493,0.36882,-0.34038,352.92
> undo
> ui mousemode right select
> select clear
> fitmap #2 inMap #6
Fit molecule 7boh (#2) to map cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) using 52154 atoms
average map value = 0.1092, steps = 48
shifted from previous position = 0.00906
rotated from previous position = 0.00769 degrees
atoms outside contour = 21358, contour level = 0.08
Position of 7boh (#2) relative to cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) coordinates:
Matrix rotation and translation
0.68536512 -0.24470339 -0.68585341 216.16552790
0.37897767 -0.68438745 0.62288823 97.44035501
-0.62181233 -0.68682899 -0.37631817 517.29721270
Axis -0.90198033 -0.04410402 0.42951871
Axis point 0.00000000 164.44866357 286.63938718
Rotation angle (degrees) 133.44597052
Shift along axis 22.91426777
Drag select of 417 residues, 488 shapes, 6
cryosparc_P37_J130_007_volume_map.mrc z flip
> select clear
> volume #6 level 0.09
> select /V
783 atoms, 792 bonds, 99 residues, 1 model selected
> color zone #6 near sel distance 5.13
> color zone #6 near sel distance 5
> color zone #6 near sel distance 5.5
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.96853,-0.012704,0.24858,-34.336,0.060076,0.9811,-0.18393,34.798,-0.24154,0.19307,0.95099,17.402
> view matrix models
> #2,0.96815,-0.012668,0.25004,-34.581,0.06066,0.98083,-0.18518,35.009,-0.2429,0.19445,0.95036,17.501
> ui mousemode right select
> select clear
> fitmap #2 inMap #6
Fit molecule 7boh (#2) to map cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) using 52154 atoms
average map value = 0.1092, steps = 44
shifted from previous position = 0.0361
rotated from previous position = 0.16 degrees
atoms outside contour = 24622, contour level = 0.09
Position of 7boh (#2) relative to cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) coordinates:
Matrix rotation and translation
0.68538534 -0.24467747 -0.68584246 216.16016140
0.37902882 -0.68433422 0.62291559 97.41975345
-0.62175887 -0.68689127 -0.37629283 517.29428287
Axis -0.90198394 -0.04413045 0.42950840
Axis point 0.00000000 164.44598994 286.63791018
Rotation angle (degrees) 133.44207273
Shift along axis 22.91006921
Drag select of 46 residues, 33 shapes, 6 cryosparc_P37_J130_007_volume_map.mrc
z flip
> select clear
> ui mousemode right translate
> fitmap #2 inMap #6
Fit molecule 7boh (#2) to map cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) using 52154 atoms
average map value = 0.1092, steps = 48
shifted from previous position = 0.0175
rotated from previous position = 0.00505 degrees
atoms outside contour = 24610, contour level = 0.09
Position of 7boh (#2) relative to cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) coordinates:
Matrix rotation and translation
0.68533362 -0.24474155 -0.68587127 216.17412593
0.37901688 -0.68434110 0.62291530 97.42157257
-0.62182315 -0.68686158 -0.37624079 517.29503805
Axis -0.90196716 -0.04410621 0.42954614
Axis point 0.00000000 164.44948982 286.64636235
Rotation angle (degrees) 133.44233126
Shift along axis 22.92323105
> volume #6 level 0.04764
> volume #6 level 0.08199
> volume #5 level 0.08872
> volume #6 level 0.08886
No atoms selected for color zoning
> volume #6 level 0.09229
> select /V
783 atoms, 792 bonds, 99 residues, 1 model selected
> select /V
783 atoms, 792 bonds, 99 residues, 1 model selected
> select /V
783 atoms, 792 bonds, 99 residues, 1 model selected
> select add #2
52154 atoms, 56194 bonds, 1667 pseudobonds, 4129 residues, 4 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> volume #6 level 0.1014
> select /V:6-8
22 atoms, 22 bonds, 3 residues, 1 model selected
> select /V
783 atoms, 792 bonds, 99 residues, 1 model selected
> select add #2
52154 atoms, 56194 bonds, 1667 pseudobonds, 4129 residues, 4 models selected
> select subtract #2
Nothing selected
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
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
> open 7BOH
7boh title:
Complete Bacterial 30S ribosomal subunit assembly complex state E
(+RbfA)(Consensus Refinement) [more info...]
Chain information for 7boh #1
---
Chain | Description | UniProt
A | RNA (1527-MER) |
B | 30S ribosomal protein S2 | RS2_ECOLI 1-241
C | 30S ribosomal protein S3 | RS3_ECOLI 1-233
D | 30S ribosomal protein S4 | RS4_ECOLI 1-206
E | 30S ribosomal protein S5 | RS5_ECOLI 1-167
F | 30S ribosomal protein S6 | RS6_ECOLI 1-135
G | 30S ribosomal protein S7 | RS7_ECOLI 1-179
H | 30S ribosomal protein S8 | RS8_ECOLI 1-130
I | 30S ribosomal protein S9 | RS9_ECOLI 1-130
J | 30S ribosomal protein S10 | RS10_ECOLI 1-103
K | 30S ribosomal protein S11 | RS11_ECOLI 1-129
L | 30S ribosomal protein S12 | RS12_ECOLI 1-124
M | 30S ribosomal protein S13 | RS13_ECOLI 1-118
N | 30S ribosomal protein S14 | RS14_ECOLI 1-101
O | 30S ribosomal protein S15 | RS15_ECOLI 1-89
P | 30S ribosomal protein S16 | RS16_ECOLI 1-82
Q | 30S ribosomal protein S17 | RS17_ECOLI 1-84
R | 30S ribosomal protein S18 | RS18_ECOLI 1-75
S | 30S ribosomal protein S19 | RS19_ECOLI 1-92
T | 30S ribosomal protein S20 | RS20_ECOLI 1-87
V | 30S ribosome-binding factor | RBFA_ECOLI 1-133
Non-standard residues in 7boh #1
---
MG — magnesium ion
ZN — zinc ion
> sequence chain #1/V
Alignment identifier is 1/V
> select /V:104
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /V:101-104
29 atoms, 28 bonds, 4 residues, 1 model selected
> select add #1
52154 atoms, 56194 bonds, 1667 pseudobonds, 4129 residues, 4 models selected
> select subtract #1
Nothing selected
OpenGL version: 4.1 Metal - 88
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
Model Number: MKGP3LL/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 19 days, 21 hours, 41 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
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
DELL U2415:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 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-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
Change History (2)
comment:1 by , 22 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 22 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Hi Songzhe,
--Eric