![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18172 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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
Current thread 0x00007ff854668dc0 (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":"2025-07-09 20:16:03.00 +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 15.5 (24F74)","roots_installed":0,"name":"ChimeraX","incident_id":"1233F5C6-E920-4908-A3F9-B9E920EF74AD"}
{
"uptime" : 68000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 8281,
"osVersion" : {
"train" : "macOS 15.5",
"build" : "24F74",
"releaseType" : "User"
},
"captureTime" : "2025-07-09 20:15:51.6220 +0200",
"codeSigningMonitor" : 0,
"incident" : "1233F5C6-E920-4908-A3F9-B9E920EF74AD",
"pid" : 15953,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-09 12:10:21.5032 +0200",
"procStartAbsTime" : 39251862114148,
"procExitAbsTime" : 68336787749392,
"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":"5475C0C3-039C-53E8-89A6-F12B7B37AE6A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "69F1B9D9-604E-01D5-03EF-91F38D4674EF",
"lowPowerMode" : 1,
"appleIntelligenceStatus" : {"reasons":["deviceNotCapable"],"state":"unavailable"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"bootSessionUUID" : "12440AD3-49D6-4A7D-A03E-AF9DF17E927C",
"wakeTime" : 1524,
"bridgeVersion" : {"build":"22P5072","train":"9.5"},
"sleepWakeUUID" : "82BF8090-2AC5-4D3E-8007-061852577DB2",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4368773096\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104663000-104664000 [ 4K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":15953},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4368773096\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104663000-104664000 [ 4K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=60.9G written=1.3G(2%) resident=0K(0%) swapped_out=1.3G(2%) unallocated=59.7G(98%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 1176K 69 \nCG raster data 8K 1 \nColorSync 296K 38 \nCoreAnimation 2304K 188 \nCoreGraphics 16K 3 \nCoreUI image data 6368K 59 \nFoundation 104K 5 \nIOKit 23.3M 3 \nKernel Alloc Once 8K 1 \nMALLOC 58.6G 576 \nMALLOC guard page 72K 18 \nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 144K 36 \nStack 168.8M 37 \nStack Guard 56.0M 1 \nVM_ALLOCATE 2.1G 425 \nVM_ALLOCATE (reserved) 64.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 48.9M 1111 \n__DATA_CONST 115.2M 963 \n__DATA_DIRTY 2590K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 194.2M 152 \n__OBJC_RO 61.3M 1 \n__OBJC_RW 2395K 2 \n__TEXT 1.4G 1113 \n__TEXT (graphics) 4240K 13 \n__TPRO_CONST 16 2 \ndyld private memory 2836K 25 \nmapped file 314.7M 80 \nshared memory 3512K 27 \n=========== ======= ======= \nTOTAL 63.1G 5307 \nTOTAL, minus reserved VM space 63.1G 5307 \n",
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"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "d417de97e23772ee386c549338e5524c795fb03d",
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}
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Laba/Data/YBEY/coIP/IP structure/ybey-
> ko-s27-ip/collection-2-session.cxs" format session
Opened cryosparc_P7_J156_002_volume_map.mrc as #1, grid size 150,150,150,
pixel 4.06, shown at level 0.657, step 1, values float32
Opened cryosparc_P7_J156_002_volume_map.mrc z flip as #4, grid size
150,150,150, pixel 4.06, shown at level 0.733, step 1, values float32
Opened cryosparc_P7_J156_002_volume_mask_refine.mrc as #5, grid size
150,150,150, pixel 4.06, shown at level 0.0126, step 1, values float32
Opened mask-lsu-molmap-5ool-15-0c0709.mrc as #6, grid size 150,150,150, pixel
4.06, shown at level 0.0709, step 1, values float32
Opened cryosparc_P7_J159_mask.mrc as #7, grid size 150,150,150, pixel 4.06,
shown at level 1, step 1, values float32
Opened cryosparc_P7_J160_mask.mrc as #8, grid size 150,150,150, pixel 4.06,
shown at level 1, step 1, values float32
Opened mask-lsu-erased.mrc as #9, grid size 150,150,150, pixel 4.06, shown at
level 0.955, step 1, values float32
Opened cryosparc_P7_J161_class_01_00054_volume.mrc as #11, grid size
128,128,128, pixel 4.76, shown at level 1.45, step 1, values float32
Opened cryosparc_P7_J161_class_00_00054_volume.mrc as #12, grid size
128,128,128, pixel 4.76, shown at level 1.17, step 1, values float32
Opened cryosparc_P7_J163_mask.mrc as #13, grid size 150,150,150, pixel 4.06,
shown at level 1, step 1, values float32
Opened mask-ssu-erased.mrc as #10, grid size 150,150,150, pixel 4.06, shown at
level 1.01, step 1, values float32
Opened cryosparc_P7_J166_mask.mrc as #15, grid size 150,150,150, pixel 4.06,
shown at level 1, step 1, values float32
Opened cryosparc_P7_J164_class_01_00054_volume.mrc as #16, grid size
128,128,128, pixel 4.76, shown at level 0.931, step 1, values float32
Opened cryosparc_P7_J164_class_00_00054_volume.mrc as #17, grid size
128,128,128, pixel 4.76, shown at level 1.28, step 1, values float32
Opened cryosparc_P7_J167_class_01_00054_volume.mrc as #14, grid size
128,128,128, pixel 4.76, shown at level 1.54, step 1, values float32
Opened cryosparc_P7_J167_class_00_00054_volume.mrc as #18, grid size
128,128,128, pixel 4.76, shown at level 1.56, step 1, values float32
Opened cryosparc_P7_J171_002_volume_map.mrc as #19, grid size 150,150,150,
pixel 4.06, shown at level 1.85, step 1, values float32
Opened cryosparc_P7_J172_002_volume_map.mrc as #20, grid size 150,150,150,
pixel 4.06, shown at level 1.24, step 1, values float32
Opened cryosparc_P7_J173_002_volume_map.mrc as #21, grid size 150,150,150,
pixel 4.06, shown at level 1.21, step 2, values float32
Opened cryosparc_P7_J174_002_volume_map.mrc as #22, grid size 150,150,150,
pixel 4.06, shown at level 0.681, step 1, values float32
Opened cryosparc_P7_J175_class_02_00067_volume.mrc as #23, grid size
128,128,128, pixel 4.76, shown at level 1.45, step 1, values float32
Opened cryosparc_P7_J175_class_01_00067_volume.mrc as #24, grid size
128,128,128, pixel 4.76, shown at level 1.49, step 1, values float32
Opened cryosparc_P7_J175_class_00_00067_volume.mrc as #25, grid size
128,128,128, pixel 4.76, shown at level 2.41, step 1, values float32
Opened mask-16s-immature-erased.mrc as #26, grid size 150,150,150, pixel 4.06,
shown at level 0.318, step 1, values float32
Opened cryosparc_P7_J177_mask.mrc as #28, grid size 150,150,150, pixel 4.06,
shown at level 1, step 1, values float32
Opened cryosparc_P7_J178_class_02_00068_volume.mrc as #39, grid size
128,128,128, pixel 4.76, shown at level 1.17, step 1, values float32
Opened cryosparc_P7_J178_class_01_00068_volume.mrc as #40, grid size
128,128,128, pixel 4.76, shown at level 1.04, step 1, values float32
Opened cryosparc_P7_J178_class_00_00068_volume.mrc as #41, grid size
128,128,128, pixel 4.76, shown at level 1.42, step 1, values float32
Opened cryosparc_P7_J189_class_01_00042_volume.mrc as #27, grid size
128,128,128, pixel 4.76, shown at level 0.181, step 1, values float32
Opened cryosparc_P7_J189_class_00_00042_volume.mrc as #42, grid size
128,128,128, pixel 4.76, shown at level 0.199, step 1, values float32
Opened mask-malsu1-molmap-5ool.mrc as #43, grid size 150,150,150, pixel 4.06,
shown at level 0.0346, step 1, values float32
Opened cryosparc_P7_J193_mask.mrc as #44, grid size 150,150,150, pixel 4.06,
shown at level 1, step 1, values float32
Opened cryosparc_P7_J185_005_volume_map.mrc as #46, grid size 600,600,600,
pixel 1.02, shown at level 0.0519, step 4, values float32
Opened cryosparc_P7_J194_class_02_00039_volume.mrc as #47, grid size
150,150,150, pixel 4.06, shown at level 1.86, step 1, values float32
Opened cryosparc_P7_J194_class_01_00039_volume.mrc as #48, grid size
150,150,150, pixel 4.06, shown at level 1.82, step 1, values float32
Opened cryosparc_P7_J194_class_00_00039_volume.mrc as #49, grid size
150,150,150, pixel 4.06, shown at level 1.85, step 1, values float32
Opened cryosparc_P7_J190_002_volume_map.mrc as #50, grid size 600,600,600,
pixel 1.02, shown at level 0.0294, step 4, values float32
Opened cryosparc_P7_J191_005_volume_map.mrc as #51, grid size 600,600,600,
pixel 1.02, shown at level 0.0275, step 4, values float32
Opened mask-a-trna-molmap-7qi5.mrc as #53, grid size 300,300,300, pixel 2.03,
shown at level 0.031, step 1, values float32
Opened cryosparc_P7_J196_mask.mrc as #54, grid size 300,300,300, pixel 2.03,
shown at level 1, step 2, values float32
Opened cryosparc_P7_J197_class_02_00032_volume.mrc as #55, grid size
160,160,160, pixel 3.81, shown at level 0.365, step 1, values float32
Opened cryosparc_P7_J197_class_01_00032_volume.mrc as #56, grid size
160,160,160, pixel 3.81, shown at level 0.391, step 1, values float32
Opened cryosparc_P7_J197_class_00_00032_volume.mrc as #57, grid size
160,160,160, pixel 3.81, shown at level 0.4, step 1, values float32
Opened cryosparc_P7_J198_005_volume_map.mrc as #58, grid size 600,600,600,
pixel 1.02, shown at level 0.0478, step 2, values float32
Opened mask-p-trna-molmap-7qi5.mrc as #60, grid size 160,160,160, pixel 3.81,
shown at level 0.031, step 1, values float32
Opened cryosparc_P7_J202_mask.mrc as #62, grid size 160,160,160, pixel 3.81,
shown at level 1, step 1, values float32
Opened cryosparc_P7_J199_004_volume_map.mrc as #63, grid size 600,600,600,
pixel 1.02, shown at level 0.081, step 2, values float32
Opened cryosparc_P7_J203_class_02_00030_volume.mrc as #64, grid size
160,160,160, pixel 3.81, shown at level 0.415, step 1, values float32
Opened cryosparc_P7_J203_class_01_00030_volume.mrc as #65, grid size
160,160,160, pixel 3.81, shown at level 0.458, step 1, values float32
Opened cryosparc_P7_J203_class_00_00030_volume.mrc as #66, grid size
160,160,160, pixel 3.81, shown at level 1.12, step 1, values float32
Opened cryosparc_P7_J200_005_volume_map.mrc as #67, grid size 600,600,600,
pixel 1.02, shown at level 0.0665, step 2, values float32
Opened cryosparc_P7_J187_006_volume_map.mrc as #68, grid size 600,600,600,
pixel 1.02, shown at level 0.0234, step 4, values float32
Opened cryosparc_P7_J188_004_volume_map.mrc as #69, grid size 600,600,600,
pixel 1.02, shown at level 0.0324, step 4, values float32
Opened mask-s27-flag-erased.mrc as #70, grid size 600,600,600, pixel 1.02,
shown at level 0.00762, step 1, values float32
Opened cryosparc_P7_J211_mask.mrc as #72, grid size 600,600,600, pixel 1.02,
shown at level 1, step 4, values float32
Opened cryosparc_P7_J213_class_02_00031_volume.mrc as #71, grid size
160,160,160, pixel 3.81, shown at level 0.317, step 1, values float32
Opened cryosparc_P7_J213_class_01_00031_volume.mrc as #73, grid size
160,160,160, pixel 3.81, shown at level 0.379, step 1, values float32
Opened cryosparc_P7_J213_class_00_00031_volume.mrc as #74, grid size
160,160,160, pixel 3.81, shown at level 0.327, step 1, values float32
Opened mask-.mrc as #75, grid size 600,600,600, pixel 1.02, shown at level
0.0588, step 2, values float32
Opened cryosparc_P7_J214_004_volume_map.mrc as #77, grid size 600,600,600,
pixel 1.02, shown at level 0.061, step 4, values float32
Opened cryosparc_P7_J216_mask.mrc as #78, grid size 600,600,600, pixel 1.02,
shown at level 1, step 4, values float32
Opened cryosparc_P7_J216_mask.mrc as #79, grid size 600,600,600, pixel 1.02,
shown at level 1, step 4, values float32
Opened cryosparc_P7_J216_mask.mrc as #80, grid size 600,600,600, pixel 1.02,
shown at level 1, step 4, values float32
Opened cryosparc_P7_J217_class_02_00020_volume.mrc as #76, grid size
256,256,256, pixel 2.38, shown at level 0.168, step 1, values float32
Opened cryosparc_P7_J217_class_01_00020_volume.mrc as #81, grid size
256,256,256, pixel 2.38, shown at level 0.187, step 1, values float32
Opened cryosparc_P7_J217_class_00_00020_volume.mrc as #82, grid size
256,256,256, pixel 2.38, shown at level 0.156, step 1, values float32
Opened mask_smaller.mrc as #83, grid size 180,180,180, pixel 2.54, shown at
level 1, step 1, values float32
Opened mask_larger.mrc as #84, grid size 180,180,180, pixel 2.54, shown at
level 1, step 1, values float32
Opened run_class001.mrc as #85, grid size 540,540,540, pixel 0.846, shown at
level 0.00448, step 4, values float32
Opened mask-16s-interface-small-from-vivek.mrc as #90, grid size 600,600,600,
pixel 1.02, shown at level 1, step 1, values float32
Opened mask-16s-interface-large-from-vivek.mrc as #91, grid size 600,600,600,
pixel 1.02, shown at level 1, step 1, values float32
Opened cryosparc_P7_J240_class_02_00039_volume.mrc as #86, grid size
256,256,256, pixel 2.38, shown at level 0.236, step 1, values float32
Opened cryosparc_P7_J240_class_01_00039_volume.mrc as #87, grid size
256,256,256, pixel 2.38, shown at level 0.215, step 1, values float32
Opened cryosparc_P7_J240_class_00_00039_volume.mrc as #88, grid size
256,256,256, pixel 2.38, shown at level 0.211, step 1, values float32
Opened cryosparc_P7_J242_class_02_00038_volume.mrc as #89, grid size
256,256,256, pixel 2.38, shown at level 0.167, step 1, values float32
Opened cryosparc_P7_J242_class_01_00038_volume.mrc as #92, grid size
256,256,256, pixel 2.38, shown at level 0.159, step 1, values float32
Opened cryosparc_P7_J242_class_00_00038_volume.mrc as #93, grid size
256,256,256, pixel 2.38, shown at level 0.161, step 1, values float32
Opened cryosparc_P7_J243_class_02_00037_volume.mrc as #94, grid size
256,256,256, pixel 2.38, shown at level 0.235, step 1, values float32
Opened cryosparc_P7_J243_class_00_00037_volume.mrc as #95, grid size
256,256,256, pixel 2.38, shown at level 0.243, step 1, values float32
Opened cryosparc_P7_J244_class_01_00055_volume.mrc as #96, grid size
256,256,256, pixel 2.38, shown at level 0.221, step 1, values float32
Opened cryosparc_P7_J244_class_00_00055_volume.mrc as #97, grid size
256,256,256, pixel 2.38, shown at level 0.123, step 1, values float32
Opened cryosparc_P7_J245_class_05_00025_volume.mrc as #98, grid size
256,256,256, pixel 2.38, shown at level 0.233, step 1, values float32
Opened cryosparc_P7_J245_class_04_00025_volume.mrc as #99, grid size
256,256,256, pixel 2.38, shown at level 0.243, step 1, values float32
Opened cryosparc_P7_J245_class_03_00025_volume.mrc as #100, grid size
256,256,256, pixel 2.38, shown at level 0.236, step 1, values float32
Opened cryosparc_P7_J245_class_02_00025_volume.mrc as #101, grid size
256,256,256, pixel 2.38, shown at level 0.305, step 1, values float32
Opened cryosparc_P7_J245_class_01_00025_volume.mrc as #102, grid size
256,256,256, pixel 2.38, shown at level 0.294, step 1, values float32
Opened cryosparc_P7_J245_class_00_00025_volume.mrc as #103, grid size
256,256,256, pixel 2.38, shown at level 0.276, step 1, values float32
Opened cryosparc_P7_J248_002_volume_map.mrc as #104, grid size 600,600,600,
pixel 1.02, shown at level 0.0408, step 1, values float32
Opened cryosparc_P7_J246_005_volume_map.mrc as #105, grid size 600,600,600,
pixel 1.02, shown at level 0.0536, step 4, values float32
Opened backproject.mrc as #106, grid size 128,128,128, pixel 4.76, shown at
level 0.172, step 1, values float32
Opened vol_000.mrc as #107, grid size 128,128,128, pixel 4.76, shown at level
0.067, step 1, values float32
Opened vol_001.mrc as #108, grid size 128,128,128, pixel 4.76, shown at level
0.0561, step 1, values float32
Opened vol_002.mrc as #109, grid size 128,128,128, pixel 4.76, shown at level
0.134, step 1, values float32
Opened vol_003.mrc as #110, grid size 128,128,128, pixel 4.76, shown at level
0.117, step 1, values float32
Opened vol_004.mrc as #111, grid size 128,128,128, pixel 4.76, shown at level
0.11, step 1, values float32
Opened vol_005.mrc as #112, grid size 128,128,128, pixel 4.76, shown at level
0.0933, step 1, values float32
Opened vol_006.mrc as #113, grid size 128,128,128, pixel 4.76, shown at level
0.0926, step 1, values float32
Opened vol_007.mrc as #114, grid size 128,128,128, pixel 4.76, shown at level
0.13, step 1, values float32
Opened vol_008.mrc as #115, grid size 128,128,128, pixel 4.76, shown at level
0.15, step 1, values float32
Opened vol_009.mrc as #116, grid size 128,128,128, pixel 4.76, shown at level
0.171, step 1, values float32
Opened vol_010.mrc as #117, grid size 128,128,128, pixel 4.76, shown at level
0.189, step 1, values float32
Opened vol_011.mrc as #118, grid size 128,128,128, pixel 4.76, shown at level
0.092, step 1, values float32
Opened vol_012.mrc as #119, grid size 128,128,128, pixel 4.76, shown at level
0.123, step 1, values float32
Opened vol_013.mrc as #120, grid size 128,128,128, pixel 4.76, shown at level
0.113, step 1, values float32
Opened vol_014.mrc as #121, grid size 128,128,128, pixel 4.76, shown at level
0.115, step 1, values float32
Opened vol_015.mrc as #122, grid size 128,128,128, pixel 4.76, shown at level
0.08, step 1, values float32
Opened vol_016.mrc as #123, grid size 128,128,128, pixel 4.76, shown at level
0.0973, step 1, values float32
Opened vol_017.mrc as #124, grid size 128,128,128, pixel 4.76, shown at level
0.11, step 1, values float32
Opened vol_018.mrc as #125, grid size 128,128,128, pixel 4.76, shown at level
0.121, step 1, values float32
Opened vol_019.mrc as #126, grid size 128,128,128, pixel 4.76, shown at level
0.0882, step 1, values float32
Opened cryosparc_P7_J183_006_volume_map.mrc as #127, grid size 600,600,600,
pixel 1.02, shown at level 0.0257, step 4, values float32
Opened cryosparc_P7_J252_class_02_00037_volume.mrc as #128, grid size
256,256,256, pixel 2.38, shown at level 0.0766, step 1, values float32
Opened cryosparc_P7_J252_class_01_00037_volume.mrc as #129, grid size
256,256,256, pixel 2.38, shown at level 0.0659, step 1, values float32
Opened cryosparc_P7_J252_class_00_00037_volume.mrc as #130, grid size
256,256,256, pixel 2.38, shown at level 0.0662, step 1, values float32
Opened cryosparc_P7_J253_002_volume_map.mrc as #131, grid size 600,600,600,
pixel 1.02, shown at level 0.0464, step 2, values float32
opened ChimeraX session
> open /Users/dmitrii.shiriaev/Downloads/cryosparc_P7_J277_001_volume_map.mrc
Opened cryosparc_P7_J277_001_volume_map.mrc as #132, grid size 150,150,150,
pixel 4.06, shown at level 1.8, step 1, values float32
> select add #132
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #132,1,0,0,-16.234,0,1,0,-17.332,0,0,1,-236.74
> view matrix models
> #132,-0.9784,0.029452,-0.2046,735.79,-0.1108,-0.91031,0.39881,503.39,-0.17451,0.41287,0.89392,-273.1
> view matrix models
> #132,-0.9784,0.029452,-0.2046,660.66,-0.1108,-0.91031,0.39881,510.85,-0.17451,0.41287,0.89392,-288.1
> view matrix models
> #132,-0.96136,0.0058291,-0.27525,684.33,-0.11979,-0.90903,0.39914,513.51,-0.24788,0.41669,0.8746,-257.39
> view matrix models
> #132,-0.90584,0.19552,0.37581,400.11,-0.045402,-0.92682,0.37276,501.23,0.42119,0.3206,0.84842,-454.41
> view matrix models
> #132,-0.91767,0.17182,0.35827,417.31,-0.24356,-0.95565,-0.16554,749.22,0.31394,-0.23917,0.91882,-260.89
> view matrix models
> #132,-0.95996,0.09282,0.26433,486.8,-0.27538,-0.48597,-0.82946,819.66,0.051465,-0.86903,0.49207,165.68
> view matrix models
> #132,-0.99428,0.028444,-0.10295,634.66,0.088005,-0.32805,-0.94055,676.32,-0.060527,-0.94423,0.32367,281.9
> view matrix models
> #132,-0.76854,-0.07653,-0.63521,755.57,-0.30452,0.91691,0.25797,42.848,0.56269,0.39169,-0.72799,-31.936
> view matrix models
> #132,-0.88657,-0.19963,-0.41731,767.85,-0.32215,0.91383,0.24725,53.406,0.33199,0.35364,-0.87448,107.44
> view matrix models
> #132,-0.93418,-0.35561,-0.028984,712.27,-0.35182,0.90461,0.24064,68.864,-0.059356,0.235,-0.97018,313.07
> view matrix models
> #132,-0.92732,-0.36829,0.066567,683.88,-0.34236,0.90662,0.24662,63.013,-0.15118,0.20591,-0.96682,353.62
> view matrix models
> #132,-0.95986,0.17431,-0.21975,612.86,-0.26194,-0.27681,0.92454,197.8,0.10033,0.94498,0.31136,-371.09
> view matrix models
> #132,-0.86487,0.25761,-0.43085,619.2,-0.23035,0.55892,0.79659,-38.658,0.44602,0.78819,-0.42405,-212.21
> view matrix models
> #132,-0.76612,0.10849,-0.63348,695.39,0.10295,0.99364,0.045664,-58.456,0.6344,-0.030231,-0.77241,90.779
> view matrix models
> #132,-0.76612,0.10849,-0.63348,663.22,0.10295,0.99364,0.045664,-19.993,0.6344,-0.030231,-0.77241,357.59
> fitmap #132 inMap 3131
Invalid "inMap" argument: invalid density map specifier
> fitmap #132 inMap #131
Fit map cryosparc_P7_J277_001_volume_map.mrc in map
cryosparc_P7_J253_002_volume_map.mrc using 33750 points
correlation = 0.7771, correlation about mean = 0.2015, overlap = 8560
steps = 548, shift = 38.5, angle = 26.8 degrees
Position of cryosparc_P7_J277_001_volume_map.mrc (#132) relative to
cryosparc_P7_J253_002_volume_map.mrc (#131) coordinates:
Matrix rotation and translation
-0.94984629 -0.11179421 -0.29205158 712.99353485
-0.13484771 0.98904986 0.05997073 28.97589079
0.28214918 0.09634547 -0.95452051 478.36072136
Axis 0.06317104 -0.99719933 -0.04003641
Axis point 322.14913164 0.00000000 291.18880246
Rotation angle (degrees) 163.26732481
Shift along axis -3.00603830
> hide #!2 models
> view matrix models
> #132,-0.94985,-0.11179,-0.29205,654.04,-0.13485,0.98905,0.059971,41.883,0.28215,0.096345,-0.95452,320.47
> view matrix models
> #132,-0.94985,-0.11179,-0.29205,648.7,-0.13485,0.98905,0.059971,53.229,0.28215,0.096345,-0.95452,281.08
> view matrix models
> #132,-0.94985,-0.11179,-0.29205,637.8,-0.13485,0.98905,0.059971,78.636,0.28215,0.096345,-0.95452,216.35
> volume flip #132
Opened cryosparc_P7_J277_001_volume_map.mrc z flip as #133, grid size
150,150,150, pixel 4.06, shown at step 1, values float32
> select add #133
4 models selected
> select subtract #132
2 models selected
> view matrix models
> #133,-0.98608,-0.1604,-0.04374,593.73,-0.14475,0.95772,-0.24864,181.92,0.081772,-0.23885,-0.96761,397.26
> view matrix models
> #133,-0.76395,0.24129,0.59847,200.89,-0.53703,0.27645,-0.79698,696.2,-0.35775,-0.93025,-0.081612,513.86
> view matrix models
> #133,-0.53914,0.61551,0.57486,9.6589,-0.79305,-0.14123,-0.59255,859.6,-0.28353,-0.77537,0.56428,250.49
> view matrix models
> #133,-0.32583,0.94517,0.021909,-9.269,-0.92495,-0.32348,0.19958,733.38,0.19573,0.044766,0.97964,-299.85
> view matrix models
> #133,-0.66934,0.74236,-0.029782,191.25,-0.7378,-0.66887,-0.090895,861.72,-0.087398,-0.038866,0.99542,-178.11
> view matrix models
> #133,-0.81721,0.49531,0.29467,227.4,-0.43885,-0.86621,0.23893,723.06,0.37359,0.065938,0.92525,-353.42
> view matrix models
> #133,-0.83514,0.39244,0.3854,239.98,-0.26626,-0.90155,0.34105,643.74,0.4813,0.18221,0.85741,-408.56
> view matrix models
> #133,-0.99355,0.087137,-0.072524,526.1,-0.075064,-0.02623,0.99683,107.39,0.084959,0.99585,0.032602,-287.28
> view matrix models
> #133,-0.99038,-0.13812,0.0088621,572.85,-0.12242,0.90406,0.40949,-0.49375,-0.06457,0.40447,-0.91227,228.34
> view matrix models
> #133,-0.98621,-0.1593,0.044905,567.62,-0.14521,0.96301,0.22698,41.944,-0.079401,0.21733,-0.97286,310.66
> view matrix models
> #133,-0.87678,-0.39814,0.26971,539.49,-0.32959,0.90592,0.26586,113.73,-0.35018,0.14421,-0.92551,415.52
> view matrix models
> #133,-0.90032,-0.38126,0.20994,559.82,-0.267,0.86474,0.42536,58.328,-0.34372,0.32691,-0.88034,342.05
> view matrix models
> #133,-0.90032,-0.38126,0.20994,570.68,-0.267,0.86474,0.42536,-18.728,-0.34372,0.32691,-0.88034,558.03
> fitmap #133 inMap #131
Fit map cryosparc_P7_J277_001_volume_map.mrc z flip in map
cryosparc_P7_J253_002_volume_map.mrc using 33750 points
correlation = 0.8951, correlation about mean = 0.3851, overlap = 1.159e+04
steps = 644, shift = 67.8, angle = 39.4 degrees
Position of cryosparc_P7_J277_001_volume_map.mrc z flip (#133) relative to
cryosparc_P7_J253_002_volume_map.mrc (#131) coordinates:
Matrix rotation and translation
-0.98415313 -0.05660863 -0.16804198 672.64626914
-0.05370647 0.99831944 -0.02176908 21.62154561
0.16899189 -0.01239915 -0.98553943 552.04748398
Axis 0.02778938 -0.99957674 0.00860724
Axis point 313.17953004 0.00000000 304.68118915
Rotation angle (degrees) 170.29425047
Shift along axis 1.83163013
> select subtract #133
Nothing selected
> hide #!131 models
> show #!68 models
> color #68 #d0bc6dd6 models
> volume #68 level 0.04908
> volume #133 level 0.6908
> hide #!68 models
> show #!19 models
> volume #19 level 0.8611
> volume #133 level 1.305
Must specify one map, got 0
> fitmap #133 inMap #19
Fit map cryosparc_P7_J277_001_volume_map.mrc z flip in map
cryosparc_P7_J171_002_volume_map.mrc using 41518 points
correlation = 0.9544, correlation about mean = 0.7823, overlap = 5.318e+05
steps = 52, shift = 4.56, angle = 0.459 degrees
Position of cryosparc_P7_J277_001_volume_map.mrc z flip (#133) relative to
cryosparc_P7_J171_002_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
-0.98355160 -0.06456502 -0.16869387 679.54031276
-0.06152925 0.99783637 -0.02316712 24.86525566
0.16982466 -0.01240644 -0.98539618 550.75433240
Axis 0.03177025 -0.99945501 0.00896293
Axis point 316.66578643 0.00000000 304.48179078
Rotation angle (degrees) 170.24988048
Shift along axis 1.67383542
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> volume #133 level 1.367
> volume #133 level 1.428
> volume #133 level 1.459
> volume #133 level 1.52
> volume #133 level 1.551
> volume #133 level 1.582
> volume #133 level 1.674
> volume #133 level 1.704
> volume #133 level 1.735
> volume #133 level 1.766
> volume #133 level 1.735
> volume #133 level 1.674
> volume #133 level 1.643
> volume #133 level 1.582
> volume #133 level 1.52
> volume #133 level 1.489
> volume #133 level 1.459
> volume #133 level 1.428
> volume #133 level 1.305
> volume #133 level 1.244
> volume #133 level 1.213
> volume #133 level 1.152
> volume #133 level 1.09
> volume #133 level 1.059
> volume #133 level 0.8137
> volume #133 level 0.7829
> volume #133 level 0.7522
> volume #133 level 0.7215
> volume #133 level 0.6908
> volume #133 level 0.7215
> volume #133 level 0.7522
> volume #133 level 0.7829
> volume #19 level 0.5749
> hide #!133 models
> show #!133 models
> hide #!133 models
> show #!133 models
> hide #!19 models
> show #!29 models
> hide #!29 models
> color #133 #b2b2b2e2 models
> color #133 #92bf7ee2 models
> color #133 #92bf7edc models
> color #133 #92bf7edb models
> show #!29 models
> color #133 #7bc7bcdb models
> color #133 #7bc7bce6 models
> color #133 #8be1d5e6 models
> color #133 #8be1d5af models
> color #133 #8be1d5b0 models
> hide #!29 models
> show #!30 models
> hide #!30 models
> show #!31 models
> hide #!31 models
> show #!32 models
> hide #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!34 models
> show #!35 models
> show #!36 models
> hide #!35 models
> hide #!36 models
> show #!37 models
> hide #!37 models
> show #!38 models
> hide #!38 models
> show #!52 models
> hide #!52 models
> show #!45 models
> hide #!45 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!19 models
> combine #133
No structures specified
> vop add #133
Opened cryosparc_P7_J277_001_volume_map.mrc z flip resampled as #134, grid
size 150,150,150, pixel 4.06, shown at step 1, values float32
> select add #134
2 models selected
> view matrix models
> #134,-0.93264,0.35963,0.028994,475.37,-0.29947,-0.81644,0.49371,496.94,0.20123,0.45177,0.86914,-155.06
> color #134 #b2ffffc5 models
> color #134 #b2ffffc4 models
> view matrix models
> #134,-0.93264,0.35963,0.028994,473.88,-0.29947,-0.81644,0.49371,662.61,0.20123,0.45177,0.86914,34.895
> volume #19 level 0.783
> view matrix models
> #134,-0.92275,-0.37604,-0.084366,728.88,-0.29023,0.82207,-0.48986,454.63,0.25356,-0.42753,-0.86771,806.02
> view matrix models
> #134,-0.95276,-0.28386,-0.10802,717.18,0.24508,-0.50846,-0.82547,794.32,0.1794,-0.81295,0.55401,521.28
> hide #!134 models
> show #!133 models
> select subtract #134
Nothing selected
> show #!3 models
> show #!29 models
> hide #!29 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> show #!134 models
> hide #!134 models
> show #!133 models
> volume #133 level 0.5986
> show #!2 models
> volume #19 level 0.4448
> hide #!2 models
> hide #!3 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> volume #19 level 0.3667
> show #!133 models
> hide #!133 models
> volume #19 level 0.809
> show #!133 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> show #!133 models
> volume #19 level 0.4968
> hide #!133 models
> show #!133 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> show #!133 models
> show #!2 models
> volume #134 level 0.9672
> volume #133 level 0.9058
> volume #133 level 0.6294
> volume #133 level 0.5372
> show #!3 models
> show #!29 models
> hide #!29 models
> show #!59 models
> open /Users/dmitrii.shiriaev/Downloads/cryosparc_P7_J280_map.mrc
Opened cryosparc_P7_J280_map.mrc as #135, grid size 128,128,128, pixel 4.76,
shown at level 2.1, step 1, values float32
> fitmap #135 inMap #19
Fit map cryosparc_P7_J280_map.mrc in map cryosparc_P7_J171_002_volume_map.mrc
using 20971 points
correlation = 0.6897, correlation about mean = 0.2323, overlap = 2.192e+05
steps = 148, shift = 18, angle = 23.3 degrees
Position of cryosparc_P7_J280_map.mrc (#135) relative to
cryosparc_P7_J171_002_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.91926652 0.14626098 0.36545422 -128.89016958
-0.15894189 0.98727685 0.00467877 38.58795569
-0.36012017 -0.06238702 0.93081755 134.76673598
Axis -0.08489308 0.91844506 -0.38633126
Axis point 287.90562574 0.00000000 417.60671571
Rotation angle (degrees) 23.26606926
Shift along axis -5.68180199
> fitmap #135 inMap #19
Fit map cryosparc_P7_J280_map.mrc in map cryosparc_P7_J171_002_volume_map.mrc
using 20971 points
correlation = 0.6897, correlation about mean = 0.2324, overlap = 2.192e+05
steps = 64, shift = 0.0248, angle = 0.0567 degrees
Position of cryosparc_P7_J280_map.mrc (#135) relative to
cryosparc_P7_J171_002_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.91893345 0.14702829 0.36598359 -129.18776556
-0.15967763 0.98715962 0.00435189 38.96468655
-0.36064437 -0.06243849 0.93061113 135.01394355
Axis -0.08438150 0.91800584 -0.38748554
Axis point 287.86893170 0.00000000 418.05329833
Rotation angle (degrees) 23.31365279
Shift along axis -5.64508376
> select add #135
2 models selected
> view matrix models
> #135,0.91893,0.14703,0.36598,-220.48,-0.15968,0.98716,0.0043519,37.687,-0.36064,-0.062438,0.93061,-106.61
> view matrix models
> #135,0.78532,-0.06657,-0.6155,167.61,0.093066,-0.97021,0.22368,472.94,-0.61205,-0.23294,-0.75573,509.05
> view matrix models
> #135,0.78532,-0.06657,-0.6155,304.88,0.093066,-0.97021,0.22368,480.97,-0.61205,-0.23294,-0.75573,741.1
> view matrix models
> #135,0.78532,-0.06657,-0.6155,286.08,0.093066,-0.97021,0.22368,498.09,-0.61205,-0.23294,-0.75573,766.26
> view matrix models
> #135,0.78844,-0.10315,-0.6064,293.17,0.061286,-0.96776,0.2443,499.83,-0.61205,-0.22978,-0.7567,765.63
> view matrix models
> #135,0.99071,-0.024048,-0.13383,76.084,-0.01786,-0.99872,0.047249,588.36,-0.13479,-0.04442,-0.98988,652.35
> view matrix models
> #135,0.99071,-0.024048,-0.13383,62.591,-0.01786,-0.99872,0.047249,593.97,-0.13479,-0.04442,-0.98988,657.04
> fitmap #135 inMap #19
Fit map cryosparc_P7_J280_map.mrc in map cryosparc_P7_J171_002_volume_map.mrc
using 20971 points
correlation = 0.953, correlation about mean = 0.7095, overlap = 3.922e+05
steps = 60, shift = 7.94, angle = 6.24 degrees
Position of cryosparc_P7_J280_map.mrc (#135) relative to
cryosparc_P7_J171_002_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.98405605 0.06240571 -0.16655082 41.74872208
0.05949021 -0.99797657 -0.02244203 595.73817087
-0.16761433 0.01217607 -0.98577743 650.07555665
Axis 0.99600573 0.03059848 -0.08388279
Axis point 0.00000000 294.38999861 329.39392473
Rotation angle (degrees) 179.00423720
Shift along axis 5.28049882
> open /Users/dmitrii.shiriaev/Downloads/cryosparc_P7_J281_002_volume_map.mrc
Opened cryosparc_P7_J281_002_volume_map.mrc as #136, grid size 600,600,600,
pixel 1.02, shown at level 0.0555, step 4, values float32
> fitmap #136 inMap #19
Fit map cryosparc_P7_J281_002_volume_map.mrc in map
cryosparc_P7_J171_002_volume_map.mrc using 33738 points
correlation = 0.6799, correlation about mean = 0.222, overlap = 8724
steps = 132, shift = 18.5, angle = 21.3 degrees
Position of cryosparc_P7_J281_002_volume_map.mrc (#136) relative to
cryosparc_P7_J171_002_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.93265540 0.10504917 0.34513560 -114.38838945
-0.11885373 0.99272960 0.01901906 19.32033986
-0.34062839 -0.05875888 0.93836011 124.39918006
Axis -0.10719540 0.94513619 -0.30858828
Axis point 287.50960121 0.00000000 389.97366638
Rotation angle (degrees) 21.27138053
Shift along axis -7.86586748
> fitmap #136 inMap #19
Fit map cryosparc_P7_J281_002_volume_map.mrc in map
cryosparc_P7_J171_002_volume_map.mrc using 33738 points
correlation = 0.6799, correlation about mean = 0.2221, overlap = 8724
steps = 44, shift = 0.0216, angle = 0.0579 degrees
Position of cryosparc_P7_J281_002_volume_map.mrc (#136) relative to
cryosparc_P7_J171_002_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.93242901 0.10597733 0.34546338 -114.70007483
-0.11975036 0.99262777 0.01870726 19.73320009
-0.34093400 -0.05881256 0.93824575 124.54511808
Axis -0.10667266 0.94453058 -0.31061701
Axis point 287.42902770 0.00000000 390.64994489
Rotation angle (degrees) 21.30630227
Shift along axis -7.81185942
> select add #136
4 models selected
> select subtract #135
2 models selected
> view matrix models
> #136,0.92765,0.19841,0.31638,-131.65,-0.11315,0.9567,-0.26819,114.08,-0.35589,0.21299,0.90993,57.867
> view matrix models
> #136,0.92146,0.34793,0.17279,-130.66,-0.08562,0.61574,-0.78328,359.75,-0.37892,0.70697,0.59717,13.581
> view matrix models
> #136,0.87462,0.48397,0.028558,-115.16,-0.10044,0.2385,-0.96593,527.62,-0.4743,0.84195,0.25721,100.21
> view matrix models
> #136,0.83463,0.53877,-0.11457,-78.134,-0.080894,-0.085858,-0.99302,624.92,-0.54484,0.83807,-0.028076,204.51
> view matrix models
> #136,0.76277,0.49265,-0.4189,44.451,0.03009,-0.67412,-0.73801,691.31,-0.64597,0.55033,-0.52902,463.44
> view matrix models
> #136,0.77662,0.52122,-0.35383,13.195,-0.0016261,-0.56,-0.82849,693.28,-0.62997,0.64399,-0.43406,403.8
> view matrix models
> #136,0.75527,0.47047,-0.45631,63.974,0.050782,-0.73614,-0.67493,685.21,-0.65344,0.48658,-0.57988,499.04
> view matrix models
> #136,0.75527,0.47047,-0.45631,66.918,0.050782,-0.73614,-0.67493,706.9,-0.65344,0.48658,-0.57988,512.04
> fitmap #136 inMap #19
Fit map cryosparc_P7_J281_002_volume_map.mrc in map
cryosparc_P7_J171_002_volume_map.mrc using 33738 points
correlation = 0.9581, correlation about mean = 0.7413, overlap = 1.616e+04
steps = 188, shift = 20.1, angle = 49.8 degrees
Position of cryosparc_P7_J281_002_volume_map.mrc (#136) relative to
cryosparc_P7_J171_002_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.98355870 0.06394349 -0.16888901 42.14471756
0.06090406 -0.99787579 -0.02312139 595.49777858
-0.17000872 0.01245522 -0.98536384 650.69914706
Axis 0.99588088 0.03134346 -0.08508154
Axis point 0.00000000 294.16573558 329.81950638
Rotation angle (degrees) 178.97653503
Shift along axis 5.27359445
> hide #!133 models
> select subtract #136
Nothing selected
> hide #!135 models
> show #!68 models
> hide #!3 models
> hide #!2 models
> volume #136 level 0.03981
> volume #136 level 0.05455
> volume #68 level 0.04117
> show #!134 models
> hide #!134 models
> show #!133 models
> volume #133 level 1.336
> volume #136 level 0.03391
> hide #!133 models
> volume #68 level 0.03128
> volume #68 level 0.04809
> volume #136 step 1
> volume #136 level 0.04044
> volume #136 level 0.05023
> volume #136 level 0.06656
> open /Users/dmitrii.shiriaev/Downloads/cryosparc_P7_J281_007_volume_map.mrc
Opened cryosparc_P7_J281_007_volume_map.mrc as #137, grid size 600,600,600,
pixel 1.02, shown at level 0.0549, step 4, values float32
> hide #!59 models
> hide #!136 models
> color #137 #80f7e7ff models
> select add #137
2 models selected
> view matrix models #137,1,0,0,0.58023,0,1,0,-1.4263,0,0,1,1.9977
> view matrix models
> #137,0.99698,-0.020053,-0.074988,29.548,0.040097,0.96023,0.27632,-82.73,0.066465,-0.27849,0.95814,77.986
> view matrix models
> #137,0.98658,-0.016436,-0.16248,57.3,0.10562,0.82304,0.55807,-144.01,0.12455,-0.56774,0.81373,189.86
> fitmap #137 inMap #19
Fit map cryosparc_P7_J281_007_volume_map.mrc in map
cryosparc_P7_J171_002_volume_map.mrc using 33746 points
correlation = 0.6723, correlation about mean = 0.1571, overlap = 8752
steps = 132, shift = 4.79, angle = 24.3 degrees
Position of cryosparc_P7_J281_007_volume_map.mrc (#137) relative to
cryosparc_P7_J171_002_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.96536412 0.14460287 0.21716838 -102.51643518
-0.23467328 0.84499542 0.48053220 -26.56733063
-0.11401995 -0.51485217 0.84966269 231.16533007
Axis -0.89232632 0.29689844 -0.34000744
Axis point 0.00000000 397.77899411 186.68286528
Rotation angle (degrees) 33.90011972
Shift along axis 4.99238227
> view matrix models
> #137,0.87587,0.21705,0.43098,-163.7,-0.16382,0.97383,-0.15752,107.33,-0.45389,0.067364,0.88851,139.76
> view matrix models
> #137,0.87587,0.21705,0.43098,-157.63,-0.16382,0.97383,-0.15752,105.37,-0.45389,0.067364,0.88851,167.5
> view matrix models
> #137,0.87587,0.21705,0.43098,-159.27,-0.16382,0.97383,-0.15752,107.87,-0.45389,0.067364,0.88851,163.25
> view matrix models
> #137,0.63941,0.7613,0.10762,-158.99,0.75502,-0.59527,-0.27494,357.25,-0.14525,0.25705,-0.95542,575.97
> view matrix models
> #137,0.63941,0.7613,0.10762,-156.4,0.75502,-0.59527,-0.27494,338.75,-0.14525,0.25705,-0.95542,558.66
> fitmap #137 inMap #19
Fit map cryosparc_P7_J281_007_volume_map.mrc in map
cryosparc_P7_J171_002_volume_map.mrc using 33746 points
correlation = 0.9544, correlation about mean = 0.7326, overlap = 1.628e+04
steps = 200, shift = 7.84, angle = 50.4 degrees
Position of cryosparc_P7_J281_007_volume_map.mrc (#137) relative to
cryosparc_P7_J171_002_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.98348429 0.06479498 -0.16899826 42.01742065
0.06182005 -0.99782667 -0.02281133 595.05380761
-0.17010903 0.01198709 -0.98535240 650.87370964
Axis 0.99586208 0.03178804 -0.08513655
Axis point 0.00000000 293.99934022 329.84227071
Rotation angle (degrees) 178.99890551
Shift along axis 5.34600967
> select subtract #137
Nothing selected
> volume #137 level 0.04045
> volume #137 level 0.02394
> open /Users/dmitrii.shiriaev/Downloads/cryosparc_P7_J286_006_volume_map.mrc
Opened cryosparc_P7_J286_006_volume_map.mrc as #138, grid size 600,600,600,
pixel 1.02, shown at level 0.0562, step 4, values float32
> hide #!137 models
> hide #!68 models
> volume #138 level 0.03356
> volume #138 step 1
> volume #138 level 0.05774
> volume #138 level 0.0928
> show #!1 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!68 models
> volume #138 step 4
> volume #138 level 0.04971
> volume #138 level 0.03463
> show #!84 models
> show #!83 models
> hide #!84 models
> hide #!138 models
> show #!132 models
> hide #!132 models
> show #!134 models
> hide #!134 models
> show #!133 models
> hide #!83 models
> hide #!68 models
> show #!68 models
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> volume #133 level 1.059
> hide #!68 models
> show #!29 models
> volume #68 step 8
> volume #68 level 0.04019
> open
> /Users/dmitrii.shiriaev/Downloads/cryosparc_P7_J290_class_05_00030_volume.mrc
Opened cryosparc_P7_J290_class_05_00030_volume.mrc as #139, grid size
256,256,256, pixel 2.38, shown at level 0.202, step 1, values float32
> open
> /Users/dmitrii.shiriaev/Downloads/cryosparc_P7_J290_class_04_00030_volume.mrc
Opened cryosparc_P7_J290_class_04_00030_volume.mrc as #140, grid size
256,256,256, pixel 2.38, shown at level 0.223, step 1, values float32
> open
> /Users/dmitrii.shiriaev/Downloads/cryosparc_P7_J290_class_03_00030_volume.mrc
Opened cryosparc_P7_J290_class_03_00030_volume.mrc as #141, grid size
256,256,256, pixel 2.38, shown at level 0.205, step 1, values float32
> open
> /Users/dmitrii.shiriaev/Downloads/cryosparc_P7_J290_class_02_00030_volume.mrc
Opened cryosparc_P7_J290_class_02_00030_volume.mrc as #142, grid size
256,256,256, pixel 2.38, shown at level 0.217, step 1, values float32
> open
> /Users/dmitrii.shiriaev/Downloads/cryosparc_P7_J290_class_01_00030_volume.mrc
Opened cryosparc_P7_J290_class_01_00030_volume.mrc as #143, grid size
256,256,256, pixel 2.38, shown at level 0.219, step 1, values float32
> open
> /Users/dmitrii.shiriaev/Downloads/cryosparc_P7_J290_class_00_00030_volume.mrc
Opened cryosparc_P7_J290_class_00_00030_volume.mrc as #144, grid size
256,256,256, pixel 2.38, shown at level 0.223, step 1, values float32
> hide #!29 models
> show #!134 models
> hide #!133 models
> hide #!134 models
> volume #144 level 0.3132
> hide #!68 models
> volume #139 level 0.2426
> volume #139 level 0.2022
> volume #141 level 0.2594
> volume #143 color #f969ff
> volume #144 color #6dfe6f
> volume #144 level 0.1785
> volume #143 level 0.1966
> volume #142 level 0.1802
> volume #141 level 0.1792
> volume #141 level 0.4031
> volume #141 level 0.289
> volume #140 level 0.1474
> volume #139 color #6a5be6
> volume #139 level 0.1619
> volume #139 level 0.3031
> volume #140 level 0.2261
> volume #141 level 0.4031
> volume #142 level 0.2909
> volume #143 level 0.3325
> volume #144 level 0.2715
> volume #140 level 0.3561
> volume #144 level 0.3453
> volume #139 level 0.3717
> volume #144 level 0.371
> volume #143 level 0.3692
> volume #142 level 0.3178
> volume #141 level 0.4792
> volume #140 level 0.3835
> volume #139 level 0.4281
> show #!3 models
> volume #139 level 0.2829
> hide #!3 models
> show #!59 models
> volume #141 level 0.3059
> volume #139 level 0.2305
> volume #141 level 0.2679
> volume #140 level 0.1987
> volume #142 level 0.2306
> volume #143 level 0.2554
> volume #144 level 0.2587
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-7.0.3
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: en_US.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: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2,6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 64 GB
System Firmware Version: 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0)
OS Loader Version: 583~1350
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 2 days, 23 hours, 41 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-019
Option ROM Version: 113-D32207P1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
VG272U V:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 59.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 3107183DA4201
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 2,55
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 , 3 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Dima,
--Eric