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Opened 2 years ago
Closed 2 years ago
#9705 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| 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
Thread 0x00000003259ad000 (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 0x00000003249aa000 (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 0x00000003239a7000 (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 0x00000003229a4000 (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 0x00000003219a1000 (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 0x000000032099e000 (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 0x000000031f99b000 (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 0x000000031e998000 (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 0x000000031d995000 (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 0x000000031c992000 (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 0x000000031b98f000 (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 0x000000031a98c000 (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 0x0000000319989000 (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 0x0000000204a25280 (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":"2023-09-04 09:18:52.00 +0200","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 13.4 (22F66)","roots_installed":0,"name":"ChimeraX","incident_id":"ACA44488-D3F7-4068-9BEC-E8D9D49AF336"}
{
"uptime" : 190000,
"procRole" : "Background",
"version" : 2,
"userID" : 1197608630,
"deployVersion" : 210,
"modelCode" : "Mac14,9",
"coalitionID" : 21726,
"osVersion" : {
"train" : "macOS 13.4",
"build" : "22F66",
"releaseType" : "User"
},
"captureTime" : "2023-09-04 09:17:35.3625 +0200",
"incident" : "ACA44488-D3F7-4068-9BEC-E8D9D49AF336",
"pid" : 56774,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-09-01 14:34:41.9701 +0200",
"procStartAbsTime" : 4045640534165,
"procExitAbsTime" : 4566808230122,
"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":"B9F9C638-D31C-5FD4-A86B-35A3B758CD97","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "2F1583CC-662F-F391-31B1-BF000E50A7D5",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 1150,
"sleepWakeUUID" : "B1F3D080-454D-4211-85BC-8FEEB4C50CAE",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140723109740520\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffca6f7c000-7ffcb60b0000 [241.2M] r-x\/r-x SM=COW ...t_id=d9fabfe9",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140723109740520\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffca6f7c000-7ffcb60b0000 [241.2M] r-x\/r-x SM=COW ...t_id=d9fabfe9",
"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" : [{"triggered":true,"id":1855788,"threadState":{"flavor":"x86_THREAD_STATE","rbp":{"value":13236028312572121582},"r12":{"value":259},"rosetta":{"tmp2":{"value":140703558627816},"tmp1":{"value":140705970596220},"tmp0":{"value":18446744073709551615}},"rbx":{"value":8667681408,"symbolLocation":0,"symbol":"_main_thread"},"r8":{"value":11},"r15":{"value":22},"r10":{"value":8667681408,"symbolLocation":0,"symbol":"_main_thread"},"rdx":{"value":0},"rdi":{"value":13236028312572121582},"r9":{"value":13236028312572121582},"r13":{"value":4},"rflags":{"value":643},"rax":{"value":0},"rsp":{"value":4526256264},"r11":{"value":140703559498139,"symbolLocation":0,"symbol":"-[__NSCFArray 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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/rlinares/Desktop/p142_papier/p143/p143_AF_fit.pdb
> /Users/rlinares/Desktop/p142_papier/p143/p143_flexiblefit.pdb
Chain information for p143_AF_fit.pdb #1
---
Chain | Description
A | No description available
Chain information for p143_flexiblefit.pdb #2
---
Chain | Description
A | No description available
> open
> /Users/rlinares/Desktop/p142_papier/p143/Cartes_box200/mask_p143monomer_box200.mrc
> /Users/rlinares/Desktop/p142_papier/p143/Cartes_box200/p143_map.mrc
Opened mask_p143monomer_box200.mrc as #3.1, grid size 200,200,200, pixel 1.36,
shown at level 1, step 1, values float32
Opened p143_map.mrc as #3.2, grid size 200,200,200, pixel 1.36, shown at level
0.0245, step 1, values float32
> turn x 90
> turn y 90
> hide #2 models
> hide #1 models
> volume #3.2 level 0.01504
> show #1 models
> color bfactor #1 palette alphafold key true
> key alphafold :0 :50 :70 :90 :100 showTool true
> ui mousemode right "color key"
3981 atoms, 255 residues, atom bfactor range 31.6 to 89.4
> key numericLabelSpacing equal
> key labelColor default
> key labelColor black
> transparency #3 50
> ui mousemode right translate
> color #3 #ffb2b2ff models
> color #3 #ffffb2ff models
> color #3 white models
> color #3 #ffffff6d models
> graphics silhouettes true
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting simple
> lighting flat
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> open /Users/rlinares/Downloads/7zhj(1).cif
7zhj(1).cif title:
Tail tip of siphophage T5 : tip proteins [more info...]
Chain information for 7zhj(1).cif #5
---
Chain | Description | UniProt
A B C D E F | Tail tube protein | TUBE_BPT5 1-464
G H I | Minor tail protein | TAIL1_BPT5 1-298
J K L M N O P Q R S T U | L-shaped tail fiber protein p132 | FIBL2_BPT5 1-140
V W X Y Z a | Distal tail protein | DIT_BPT5 1-204
b c d | Probable baseplate hub protein | BPPB3_BPT5 1-949
e f g | Pore-forming tail tip protein pb2 | Q7Y5E2_BPT5 1-1219
> hide #!3.2 models
> hide #4 models
> hide #5 models
> show #5 models
> show #4 models
> hide #4 models
> show #2 models
> show #!3.2 models
> select add #5
74346 atoms, 75777 bonds, 9528 residues, 1 model selected
> hide #1 models
> hide #2 models
> hide #!3 models
> hide #!3.1 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> show #1 models
> show #2 models
> fitin map #5 #3.250
Unknown command: fitin map #5 #3.250
> fitinmap #5 #3.250
Unknown command: fitinmap #5 #3.250
> fitmap #5 #3.250
Missing required "in_map" argument
> fitmap #5 inMap #3.2
Fit molecule 7zhj(1).cif (#5) to map p143_map.mrc (#3.2) using 74346 atoms
average map value = -5.916e-05, steps = 204
shifted from previous position = 7.95
rotated from previous position = 13.1 degrees
atoms outside contour = 74120, contour level = 0.015036
Position of 7zhj(1).cif (#5) relative to p143_map.mrc (#3.2) coordinates:
Matrix rotation and translation
0.97427484 0.03701817 0.22230203 -40.23333919
-0.04114622 0.99905553 0.01396531 15.19506856
-0.22157510 -0.02275294 0.97487783 59.25025831
Axis -0.08119914 0.98159479 -0.17285358
Axis point 250.12648893 0.00000000 207.02962675
Rotation angle (degrees) 13.06756936
Shift along axis 7.94069343
> fitmap #5 inMap #3.2
Fit molecule 7zhj(1).cif (#5) to map p143_map.mrc (#3.2) using 74346 atoms
average map value = -5.912e-05, steps = 80
shifted from previous position = 0.0121
rotated from previous position = 0.00905 degrees
atoms outside contour = 74120, contour level = 0.015036
Position of 7zhj(1).cif (#5) relative to p143_map.mrc (#3.2) coordinates:
Matrix rotation and translation
0.97426543 0.03688920 0.22236470 -40.20313144
-0.04100736 0.99906174 0.01392967 15.17587928
-0.22164221 -0.02268979 0.97486404 59.25237659
Axis -0.08096759 0.98172292 -0.17223345
Axis point 250.05239899 0.00000000 206.84289544
Rotation angle (degrees) 13.06972163
Shift along axis 7.94841759
> fitmap #5 inMap #3.2
Fit molecule 7zhj(1).cif (#5) to map p143_map.mrc (#3.2) using 74346 atoms
average map value = -5.911e-05, steps = 64
shifted from previous position = 0.00142
rotated from previous position = 0.00086 degrees
atoms outside contour = 74120, contour level = 0.015036
Position of 7zhj(1).cif (#5) relative to p143_map.mrc (#3.2) coordinates:
Matrix rotation and translation
0.97426734 0.03687571 0.22235856 -40.19973278
-0.04099377 0.99906227 0.01393135 15.17357478
-0.22163632 -0.02268817 0.97486542 59.25108487
Axis -0.08097064 0.98173207 -0.17217983
Axis point 250.05480159 0.00000000 206.83092907
Rotation angle (degrees) 13.06923748
Shift along axis 7.94954171
> fitmap #5 inMap #3.2
Fit molecule 7zhj(1).cif (#5) to map p143_map.mrc (#3.2) using 74346 atoms
average map value = -5.916e-05, steps = 80
shifted from previous position = 0.0194
rotated from previous position = 0.00524 degrees
atoms outside contour = 74120, contour level = 0.015036
Position of 7zhj(1).cif (#5) relative to p143_map.mrc (#3.2) coordinates:
Matrix rotation and translation
0.97427557 0.03691185 0.22231651 -40.21249872
-0.04101203 0.99906261 0.01385310 15.17403842
-0.22159677 -0.02261439 0.97487613 59.22104120
Axis -0.08064930 0.98173187 -0.17233175
Axis point 249.95688838 0.00000000 206.92391673
Rotation angle (degrees) 13.06679563
Shift along axis 7.93428107
> show #!3.1 models
> hide #!3.2 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> show #!3.2 models
> hide #!3.1 models
> ui mousemode right "move picked models"
> view matrix models
> #5,0.97428,0.036912,0.22232,-29.135,-0.041012,0.99906,0.013853,-94.154,-0.2216,-0.022614,0.97488,-64.023
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.97428,0.036912,0.22232,-30.135,-0.041012,0.99906,0.013853,-81.743,-0.2216,-0.022614,0.97488,-56.104
> fitmap #5 inMap #3.2
Fit molecule 7zhj(1).cif (#5) to map p143_map.mrc (#3.2) using 74346 atoms
average map value = 0.004884, steps = 460
shifted from previous position = 114
rotated from previous position = 24.4 degrees
atoms outside contour = 62783, contour level = 0.015036
Position of 7zhj(1).cif (#5) relative to p143_map.mrc (#3.2) coordinates:
Matrix rotation and translation
0.79707552 0.17904412 0.57672681 -161.56622262
-0.20567972 0.97842531 -0.01948761 -40.36204889
-0.56777325 -0.10308791 0.81670461 148.95265937
Axis -0.06907272 0.94561537 -0.31786872
Axis point 114.40803191 0.00000000 329.30371724
Rotation angle (degrees) 37.24046536
Shift along axis -74.35454670
> view matrix models
> #5,0.79708,0.17904,0.57673,-161,-0.20568,0.97843,-0.019488,-43.171,-0.56777,-0.10309,0.8167,144.04
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.96226,0.26648,-0.05509,-93.698,-0.26897,0.96214,-0.044061,-19.624,0.041263,0.057216,0.99751,-72.258
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.96226,0.26648,-0.05509,-91.163,-0.26897,0.96214,-0.044061,-14.109,0.041263,0.057216,0.99751,-126.71
> fitmap #5 inMap #3.2
Fit molecule 7zhj(1).cif (#5) to map p143_map.mrc (#3.2) using 74346 atoms
average map value = 0.01629, steps = 352
shifted from previous position = 43
rotated from previous position = 14.3 degrees
atoms outside contour = 43749, contour level = 0.015036
Position of 7zhj(1).cif (#5) relative to p143_map.mrc (#3.2) coordinates:
Matrix rotation and translation
0.99934057 0.02175343 -0.02907263 -90.75244437
-0.02327652 0.99831678 -0.05312076 -78.81777772
0.02786813 0.05376244 0.99816480 -125.16904318
Axis 0.82723654 -0.44070043 -0.34851519
Axis point 0.00000000 2254.73809000 -1527.94261998
Rotation angle (degrees) 3.70403387
Shift along axis 3.28460370
> fitmap #5 inMap #3.2
Fit molecule 7zhj(1).cif (#5) to map p143_map.mrc (#3.2) using 74346 atoms
average map value = 0.01629, steps = 144
shifted from previous position = 0.00899
rotated from previous position = 0.00769 degrees
atoms outside contour = 43748, contour level = 0.015036
Position of 7zhj(1).cif (#5) relative to p143_map.mrc (#3.2) coordinates:
Matrix rotation and translation
0.99934437 0.02175097 -0.02894341 -90.78307278
-0.02326612 0.99831893 -0.05308488 -78.82815505
0.02774010 0.05372348 0.99817046 -125.13328168
Axis 0.82780804 -0.43932012 -0.34890067
Axis point 0.00000000 2256.70651611 -1530.43284215
Rotation angle (degrees) 3.69887762
Shift along axis 3.13892188
> hide #5 models
> ui tool show "Side View"
> show #5 models
> hide #!3.2 models
> select #5.b-d
Expected an objects specifier or a keyword
> select #5.b-d
Expected an objects specifier or a keyword
> select #5/b-d
22731 atoms, 23226 bonds, 2847 residues, 1 model selected
> color #5/b-d yelloz
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #5/b-d yellow
> show sel cartoons
> hide sel atoms
> color #5/V-W-X-Y-Z-a orange
> color #5/V,W,X,Y,Z,a orange
> select #5/V,W,X,Y,Z,a, b, c, d
32391 atoms, 33120 bonds, 4071 residues, 1 model selected
> invert selection
Unknown command: invert selection
> select ~sel
47891 atoms, 48645 bonds, 5967 residues, 9 models selected
> hide #2 models
> hide #1 models
> hide #!3 models
> select #5/V,W,X,Y,Z,a, b, c, d
32391 atoms, 33120 bonds, 4071 residues, 1 model selected
> show #2 models
> hide #2 models
> select ~sel
47891 atoms, 48645 bonds, 5967 residues, 9 models selected
> show #!3.2 models
> hide #!3.2 models
> show #4 models
> show #!3.2 models
> select clear
> hide #!3 models
> hide #4 models
> hide #!3.2 models
> select #5/V,W,X,Y,Z,a, b, c, d
32391 atoms, 33120 bonds, 4071 residues, 1 model selected
> select ~sel
47891 atoms, 48645 bonds, 5967 residues, 9 models selected
> show #!3.2 models
> hide #!3.2 models
> show #4 models
> hide #4 models
> show #4 models
> select clear
> show #!3.2 models
> select #5/V,W,X,Y,Z,a, b, c, d
32391 atoms, 33120 bonds, 4071 residues, 1 model selected
> select #5/A-U
41169 atoms, 41865 bonds, 5352 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #5/V,W,X,Y,Z,a, b, c, d
32391 atoms, 33120 bonds, 4071 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select clear
> ui tool show "Color Zone"
> ui tool show "Surface Color"
> show #2 models
> show #1 models
> hide #2 models
> show #2 models
> hide #2 models
> transparency #3 30
> transparency #3 70
> show #!3.1 models
> hide #!3.1 models
> select #5/e,f,g
786 atoms, 792 bonds, 105 residues, 1 model selected
> color #5/e,f,g red
> hide sel atoms
> show sel cartoons
> select clear
> save /Users/rlinares/Desktop/p142_papier/230901.cxs
> color zone #3.2 near #5 range 5
Expected a keyword
> color zone #3.2 near #5 distance 5
> transparency #3 70
> hide #4 models
> show #4 models
> hide #5 models
> transparency #3 50
> show #5 models
> hide #5 models
> save img22.tiff width 2000 height 2000 supersample 3 transparentBackground
> true
> hide #4 models
> show #4 models
> hide #!3.2 models
> show #!3.2 models
> hide #1 models
> save img22.tiff width 2000 height 2000 supersample 3 transparentBackground
> true
> show #!3.1 models
> hide #!3.1 models
> show #1 models
> save img23.tiff width 2000 height 2000 supersample 3 transparentBackground
> true
> hide #1 models
> show #2 models
> color #2 #00ceebff
> color #2 #0000ebff
> color #2 blue
> transparency #3 70
> save img24.tiff width 2000 height 2000 supersample 3 transparentBackground
> true
> color #2 blue
> background white
Unknown command: background white
> set background white
Expected a keyword
> bgColor white
Unknown command: bgColor white
> set bgColor white
> transparency #3 50
> hide #2 models
> save img22.tiff width 2000 height 2000 supersample 3 transparentBackground
> true
> show #2 models
> save img23.tiff width 2000 height 2000 supersample 3 transparentBackground
> true
> show #1 models
> hide #2 models
> save img24.tiff width 2000 height 2000 supersample 3 transparentBackground
> true
> turn x 90
> color zone #3.2 near #5 distance 5
> transparency #3 50
> save img25.tiff width 2000 height 2000 supersample 3 transparentBackground
> true
> show #2 models
> hide #1 models
> color zone #3.2 near #5 distance 5
> transparency #3 50
> save img26.tiff width 2000 height 2000 supersample 3 transparentBackground
> true
> turn x 180
> color zone #3.2 near #5 distance 5
> transparency #3 50
> save img27.tiff width 2000 height 2000 supersample 3 transparentBackground
> true
> show #1 models
> hide #2 models
> color zone #3.2 near #5 distance 5
> transparency #3 50
> save img28.tiff width 2000 height 2000 supersample 3 transparentBackground
> true
> turn x 180
> turn x 90
> color zone #3.2 near #5 distance 5
> transparency #3 70
> transparency #3 30
> hide #1 models
> save tip_p143_side.tiff width 2000 height 2000 supersample 3
> transparentBackground true
> color zone #3.2 near #5 distance 5
> transparency #3 80
> transparency #3 20
> save tip_p143_side.tiff width 2000 height 2000 supersample 3
> transparentBackground true
> save tip_p143_side.tiff width 1200 height 1200 supersample 3
> transparentBackground true
> save tip_p143_side.tiff width 1400 height 1400 supersample 3
> transparentBackground true
> show #2 models
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
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 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: Mac
Model Identifier: Mac14,9
Model Number: Z17G00197FN/A
Chip: Unknown
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4 (22F66)
Kernel Version: Darwin 22.5.0
Time since boot: 9 days, 9 hours, 56 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
EV3285:
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
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 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: 2022.9.26
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
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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