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Opened 3 years ago
Closed 3 years ago
#8780 closed defect (can't reproduce)
Unsupported scale factor (0.000000) detected on Display0
| 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-13.2.1-arm64-arm-64bit
ChimeraX Version: 1.6.dev202303282212 (2023-03-28 22:12:57 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000002ab40b000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002aa3ff000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002a93f3000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002a83e7000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002a73db000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000293a7f000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000292a73000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000291a67000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000290a5b000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028fa4f000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028ea43000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001f99c0140 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 284 in event_loop
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX_Daily.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":"2023-04-04 14:11:28.00 +0200","app_version":"1.6.0","slice_uuid":"a5992708-d5b4-36ec-ac0a-e525f6105b56","build_version":"1.6.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.2.1 (22D68)","roots_installed":0,"name":"ChimeraX","incident_id":"B9C59D67-659C-43F8-A00B-9166BC0378EC"}
{
"uptime" : 120000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 5341,
"osVersion" : {
"train" : "macOS 13.2.1",
"build" : "22D68",
"releaseType" : "User"
},
"captureTime" : "2023-04-04 14:11:22.6266 +0200",
"incident" : "B9C59D67-659C-43F8-A00B-9166BC0378EC",
"pid" : 88472,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-03-31 12:19:09.6891 +0200",
"procStartAbsTime" : 1913243947093,
"procExitAbsTime" : 2935930722868,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"9273870C-30DB-5EED-A912-2D90B281157B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "8860AA8B-6057-CF38-87BA-6AF1B2794A88",
"throttleTimeout" : 2147483647,
"wakeTime" : 15733,
"sleepWakeUUID" : "D7610D38-024F-4387-8DCC-34F07E7974EB",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 105553518919656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600018000000-600020000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
"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: 105553518919656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600018000000-600020000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
"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":1361991,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6950360653},{"value":6096767688},{"value":2687450676206892235},{"value":0},{"value":6096765576},{"value":1651576759626310740},{"value":1651576751178720532},{"value":78},{"value":0},{"value":49},{"value":4370807984},{"value":0},{"value":0},{"value":328},{"value":8564913880},{"value":0},{"value":11},{"value":8482718016,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8482718240,"symbolLocation":224,"symbol":"_main_thread"},{"value":4669585600},{"value":1},{"value":32769},{"value":32768},{"value":8482724448,"symbolLocation":0,"symbol":"_NSConcreteStackBlock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6950182124},"cpsr":{"value":1073745920},"fp":{"value":6096767488},"sp":{"value":6096767456},"esr":{"value":1442840704,"description":" Address size 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===== Log before crash start =====
UCSF ChimeraX version: 1.6.dev202303282212 (2023-03-28)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/panos/Documents/mounts/mntemstorage/emstorage2/panos/Datasets/OpuA/OpuA_1E3D1_low_salt_50mM/merged_bPD32s3-5_bPD33s1-2/Class3D/job048/run_it030_class002.mrc
> format mrc
Opened run_it030_class002.mrc as #1, grid size 128,128,128, pixel 2.04, shown
at level 0.0391, step 1, values float32
> volume #1 level 0.00769
> open
> /Users/panos/Documents/mounts/mntemstorage/emstorage2/panos/Datasets/OpuA/OpuA_1E3D1_low_salt_50mM/merged_bPD32s3-5_bPD33s1-2/MaskCreate/job055/mask.mrc
Opened mask.mrc as #2, grid size 128,128,128, pixel 2.04, shown at level 1,
step 1, values float32
> volume #2 level 1
> volume #2
> volume #2 style mesh
> open
> /Users/panos/Documents/mounts/mntemstorage/emstorage2/panos/Datasets/OpuA/OpuA_1D1_APO/all_combined_Hendirk/Class3D/job033/run_it025_class025_handness.mrc
> format mrc
Opened run_it025_class025_handness.mrc as #3, grid size 128,128,128, pixel
2.02, shown at level 0.04, step 1, values float32
> select add #3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.49821,-0.77784,0.38307,107.62,0.86622,0.42713,-0.25929,-10.663,0.038066,0.461,0.88658,-44.912
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.49821,-0.77784,0.38307,119.66,0.86622,0.42713,-0.25929,-4.0738,0.038066,0.461,0.88658,-51.899
> view matrix models
> #3,0.49821,-0.77784,0.38307,119.98,0.86622,0.42713,-0.25929,-4.7239,0.038066,0.461,0.88658,-52.438
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.69522,-0.5086,0.50793,45.842,0.71862,0.50731,-0.47562,33.412,-0.015776,0.69567,0.71819,-51.208
> open
> /Users/panos/Documents/mounts/mntemstorage/emstorage2/panos/Datasets/OpuA/OpuA_1D1_APO/all_combined_Hendirk/Class3D/job033/run_it025_class002.mrc
Opened run_it025_class002.mrc as #4, grid size 128,128,128, pixel 2.02, shown
at level 0.04, step 1, values float32
> close #3
> select add #4
2 models selected
> view matrix models
> #4,-0.92824,-0.35351,-0.11579,305.48,0.25447,-0.83049,0.49552,119.93,-0.27133,0.43049,0.86085,1.9883
> view matrix models
> #4,-0.96636,-0.17784,0.18577,249.84,0.25678,-0.7072,0.65873,83.512,0.014233,0.68428,0.72908,-47.647
> view matrix models
> #4,-0.28774,-0.7326,0.61685,171.84,0.82277,0.14054,0.55072,-76.022,-0.49015,0.66599,0.56232,41.372
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.28774,-0.7326,0.61685,191.87,0.82277,0.14054,0.55072,-65.285,-0.49015,0.66599,0.56232,31.465
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.37375,-0.59795,0.70906,174.79,0.63653,0.39068,0.66498,-86.098,-0.67464,0.69988,0.23459,94.258
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.37375,-0.59795,0.70906,163.44,0.63653,0.39068,0.66498,-78.051,-0.67464,0.69988,0.23459,94.639
> select add #2
4 models selected
> select subtract #2
2 models selected
> select add #1
4 models selected
> fitmap #1 inMap #4
Fit map run_it030_class002.mrc in map run_it025_class002.mrc using 55001
points
correlation = 0.9663, correlation about mean = 0.8706, overlap = 78.78
steps = 100, shift = 11.6, angle = 19.4 degrees
Position of run_it030_class002.mrc (#1) relative to run_it025_class002.mrc
(#4) coordinates:
Matrix rotation and translation
-0.60976844 0.45907432 -0.64609072 236.30879674
-0.63600414 0.20301780 0.74450151 89.90316127
0.47294944 0.86488990 0.16817932 -68.37840695
Axis 0.07666431 -0.71261396 -0.69735495
Axis point 145.84229098 0.00000000 2.17233558
Rotation angle (degrees) 128.26398836
Shift along axis 1.73422495
> volume #1 level 0.007044
> volume #4 level 0.007099
> hide #!2 models
> color #1 #99afc1ff models
> color #4 #f7d3bdff models
> color #4 #dcae9cff models
> color #1 #8798a4ff models
> color #1 #71a3a4ff models
> color #1 #4e75a4ff models
> color #1 #6fa7ebff models
> color #1 #70a1ebff models
> color #1 #79b6ebff models
> open
> /Users/panos/Documents/mounts/mntemstorage/emstorage2/panos/Datasets/OpuA/OpuA_1E3D1_low_salt_100mM/bPD1s4/Refine3D/job026/run_class001.mrc
Opened run_class001.mrc as #3, grid size 128,128,128, pixel 2.04, shown at
level 0.041, step 1, values float32
> select subtract #1
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.63373,-0.64938,-0.42036,354.88,-0.62514,0.10985,0.77274,127.68,-0.45562,0.75249,-0.47557,148.42
> undo
> select subtract #4
Nothing selected
> select add #3
2 models selected
> view matrix models
> #3,-0.54263,-0.83975,-0.01916,288.49,0.81852,-0.53375,0.21246,83.665,-0.18864,0.099603,0.97698,11.083
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.54263,-0.83975,-0.01916,307.03,0.81852,-0.53375,0.21246,87.536,-0.18864,0.099603,0.97698,13.804
> volume flip #3 axis z
Opened run_class001.mrc z flip as #5, grid size 128,128,128, pixel 2.04, shown
at step 1, values float32
> select subtract #3
Nothing selected
> select add #5
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.58907,-0.7947,0.14645,283.99,0.58664,-0.29593,0.75385,9.3194,-0.55574,0.52998,0.64052,43.874
> view matrix models
> #5,-0.63038,-0.58558,0.50962,212,0.741,-0.25825,0.61986,4.901,-0.23137,0.76837,0.59671,-18.556
> view matrix models
> #5,-0.37097,-0.82251,0.43112,224.52,0.89611,-0.19525,0.39858,8.8258,-0.24365,0.53419,0.80949,-14.876
> select add #4
4 models selected
> fitmap #4 inMap #5
Fit map run_it025_class002.mrc in map run_class001.mrc z flip using 59777
points
correlation = 0.953, correlation about mean = 0.8193, overlap = 80.46
steps = 172, shift = 10.3, angle = 31.8 degrees
Position of run_it025_class002.mrc (#4) relative to run_class001.mrc z flip
(#5) coordinates:
Matrix rotation and translation
0.57082706 0.80513071 0.16100001 -74.17374813
-0.38977045 0.43830003 -0.80992104 224.26687940
-0.72265861 0.39957180 0.56400967 102.15244539
Axis 0.63121991 0.46117091 -0.62360469
Axis point 0.00000000 35.27501724 256.47683633
Rotation angle (degrees) 73.34737889
Shift along axis -7.09732960
> select add #3
6 models selected
> select subtract #3
4 models selected
> select add #1
6 models selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 3 maps.
> select subtract #5
4 models selected
> fitmap #1 inMap #4
Fit map run_it030_class002.mrc in map run_it025_class002.mrc using 56958
points
correlation = 0.9658, correlation about mean = 0.8777, overlap = 78.85
steps = 156, shift = 7.91, angle = 31.8 degrees
Position of run_it030_class002.mrc (#1) relative to run_it025_class002.mrc
(#4) coordinates:
Matrix rotation and translation
-0.60941047 0.45934539 -0.64623578 236.27236714
-0.63598926 0.20348640 0.74438629 89.87937470
0.47343060 0.86463582 0.16813199 -68.41216859
Axis 0.07654595 -0.71273393 -0.69724534
Axis point 145.83869646 0.00000000 2.20654411
Rotation angle (degrees) 128.23556245
Shift along axis 1.72567796
> volume #3 level 0.01422
> select add #5
6 models selected
> select subtract #4
4 models selected
> view matrix models
> #1,0.84539,0.53123,-0.055761,-42.425,-0.42905,0.73751,0.52153,41.911,0.31818,-0.41697,0.85141,29.686,#5,-0.37661,-0.8034,0.46121,218.76,0.88742,-0.17003,0.42846,2.7315,-0.2658,0.57065,0.77699,-12.026
> undo
> select subtract #1
2 models selected
> select subtract #5
Nothing selected
> select add #5
2 models selected
> hide #!3 models
> volume #3 level 0.06246
> volume #5 level 0.009296
> volume #5 level 0.01087
> color #5 #90d8ffff models
> color #5 #7bbadcff models
> color #5 #6da4c2ff models
> color #5 #6da5c3ff models
> color #5 #79b7d8ff models
> color #5 #71accbff models
> color #5 #63bacbff models
> volume #5 level 0.008705
> surface dust #5 size 20.4
> volume #5 level 0.008902
> volume #1 level 0.005752
> surface dust #5 size 20.4
> volume #1 level 0.005536
> select subtract #5
Nothing selected
> volume #1 level 0.006613
> volume #5 level 0.01067
> set bgColor white
> graphics silhouettes true
> graphics silhouettes true width 1
> save "/Users/panos/Google Drive/My Drive/OpuA/Chimera Sessions/OpuA_wt_SBD-
> whereabouts_Hendrik high salt_50mM and 100mM.cxs"
> color #5 #a7d4d5ff models
> surface dust #1 size 20.4
> surface dust #4 size 20.2
> surface dust #5 size 20.4
> volume #5 level 0.01008
> volume #1 level 0.05464
> volume #1 level 0.005967
> volume #5 level 0.00713
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!3 models
> hide #!1 models
> hide #!5 models
> volume #3 level 0.03824
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> volume #3 level 0.01481
> show #!5 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> hide #!3 models
> show #!5 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> select add #5
2 models selected
> show #!1 models
> view matrix models
> #5,-0.374,-0.8248,0.42406,226.12,0.89812,-0.20806,0.38741,11.782,-0.23131,0.52575,0.81859,-16.391
> undo
> turn #5 180
Expected an axis vector or a keyword
> turn x #5 180
Expected a number or a keyword
> view matrix models
> #5,-0.9765,-0.1022,0.18976,229.89,-0.19653,0.78365,-0.58929,133.31,-0.088483,-0.61273,-0.78532,328.06
> view matrix models
> #5,-0.97916,0.17487,0.10328,202.13,0.071833,0.77386,-0.62926,105.9,-0.18997,-0.60873,-0.7703,338.4
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.97916,0.17487,0.10328,221.86,0.071833,0.77386,-0.62926,113.23,-0.18997,-0.60873,-0.7703,331.03
> fitmap #5 inMap #1
Fit map run_class001.mrc z flip in map run_it030_class002.mrc using 64737
points
correlation = 0.9877, correlation about mean = 0.9634, overlap = 81.23
steps = 80, shift = 12.8, angle = 9.64 degrees
Position of run_class001.mrc z flip (#5) relative to run_it030_class002.mrc
(#1) coordinates:
Matrix rotation and translation
-0.91888403 -0.39204506 0.04419050 291.30513062
-0.38742287 0.87549683 -0.28880587 106.57800489
0.07453627 -0.28249951 -0.95636728 283.31685122
Axis 0.20124383 -0.96837214 0.14750024
Axis point 155.57913813 0.00000000 150.95597597
Rotation angle (degrees) 179.10222737
Shift along axis -2.79450444
> volume #5 level 0.00969
> hide #!5 models
> show #!5 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.dev202303282212 (2023-03-28)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
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: MacBookPro17,1
Model Number: Z11B000V6N/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 6 days, 21 hours, 48 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
SAMSUNG:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 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
ChimeraX-AddH: 2.2.3
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.20.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.dev202303282212
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.dev0
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
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-QScore: 1.0
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: 1.10.2
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-ToQuest: 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: 1.6.6
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: 6.1.0
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: 3.2.0
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
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: 6.2
traitlets: 5.9.0
typing-extensions: 4.5.0
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 , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Unsupported scale factor (0.000000) detected on Display0 |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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*Probably* the same as #8226. The user does have two displays.