![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 12 months ago
Last modified 12 months ago
#16239 closed defect
Crash moving window between displays — at Version 1
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.1.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000003a0037000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001e110dec0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix (total: 61)
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{
"uptime" : 590000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac13,1",
"coalitionID" : 4514,
"osVersion" : {
"train" : "macOS 14.1.1",
"build" : "23B81",
"releaseType" : "User"
},
"captureTime" : "2024-11-03 13:34:59.8362 -0500",
"codeSigningMonitor" : 1,
"incident" : "6C7B9328-3579-473D-A64F-3F6C86AF1DF7",
"pid" : 55834,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-10-31 16:43:03.6273 -0400",
"procStartAbsTime" : 8299836855688,
"procExitAbsTime" : 14336226395122,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"F5319B2A-99FE-5DFC-A089-2820E639FE6C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "216F332D-5F24-FDDF-13EF-8C5782DCD983",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4299603968\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10046c000-100470000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":55834},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4299603968\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10046c000-100470000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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"faultingThread" : 0,
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.8G resident=0K(0%) swapped_out_or_unallocated=1.8G(100%)\nWritable regions: Total=142.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=142.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG image 1776K 78 \nColorSync 800K 39 \nCoreAnimation 5152K 299 \nCoreGraphics 128K 8 \nCoreImage 32K 2 \nCoreServices 624K 2 \nCoreUI image data 5728K 48 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 139.0G 903 \nMALLOC guard page 384K 24 \nMach message 64K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 848K 53 \nStack 201.3M 54 \nStack Guard 56.0M 1 \nVM_ALLOCATE 3.3G 3061 \nVM_ALLOCATE (reserved) 128.0M 2 reserved VM address space (unallocated)\n__AUTH 2177K 398 \n__AUTH_CONST 31.8M 623 \n__CTF 824 1 \n__DATA 22.6M 777 \n__DATA_CONST 41.9M 784 \n__DATA_DIRTY 2022K 235 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 916.5M 156 \n__OBJC_RO 70.8M 1 \n__OBJC_RW 2156K 1 \n__TEXT 938.4M 801 \ndyld private memory 592K 6 \nmapped file 545.2M 87 \nshared memory 3760K 31 \n=========== ======= ======= \nTOTAL 145.2G 8494 \nTOTAL, minus reserved VM space 145.1G 8494 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "c3b4f3ffe3eb693eca765b5fc8f83ed3b1882cc1",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "645c2d2f9e69a025b0a37e29",
"factorPackIds" : {
},
"deploymentId" : 240000003
},
{
"rolloutId" : "64b21a7351cbb02ce3442e4e",
"factorPackIds" : {
"REMINDERS_GROCERY" : "65542c604a6560536bdb1d22"
},
"deploymentId" : 240000042
}
],
"experiments" : [
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Final-ver5_-10032024.cxs
Opened 0838-bottom.mrc as #16, grid size 240,240,240, pixel 4.3, shown at
level 0.0144, step 1, values float32
Opened Hpwt-L0.08-Global-Rod-no-MS.mrc as #113, grid size 240,240,240, pixel
4.3, shown at level 0.0151, step 1, values float32
Opened Disk.mrc gaussian as #312, grid size 250,250,250, pixel 4.3, shown at
level 0.0186, step 1, values float32
Opened IM-old-maps.mrc gaussian as #313, grid size 120,120,120, pixel 8.8,
shown at level 0.0702, step 1, values float32
Opened OM.mrc copy gaussian as #316, grid size 240,240,240, pixel 4.3, shown
at level 0.0323, step 1, values float32
Opened New_FliF.mrc gaussian as #479, grid size 256,256,256, pixel 2.1, shown
at level 0.0115, step 1, values float32
Opened New_FlhA.mrc gaussian as #481, grid size 256,256,256, pixel 2.1, shown
at level 0.00316, step 1, values float32
Opened PflBC13.mrc as #482, grid size 256,256,256, pixel 2.1, shown at level
0.00615, step 1, values float32
Opened New_IM_Bottom2.mrc as #483, grid size 256,256,256, pixel 2.1, shown at
level 0.0072, step 1, values float32
Opened New_IM_Bottom2.mrc gaussian as #484, grid size 256,256,256, pixel 2.1,
shown at level 0.0072, step 1, values float32
Opened PflB_C13.mrc as #507, grid size 256,256,256, pixel 2.1, shown at level
0.0015, step 1, values float32
Opened PflB_monomer.mrc as #508, grid size 256,256,256, pixel 2.1, shown at
level 0.00116, step 1, values float32
Opened Unknown-ring.mrc as #509, grid size 256,256,256, pixel 2.1, shown at
level 0.000608, step 1, values float32
Opened PflB_C13.mrc gaussian as #510, grid size 256,256,256, pixel 2.1, shown
at level 0.00108, step 1, values float32
Opened PflB_monomer.mrc gaussian as #511, grid size 256,256,256, pixel 2.1,
shown at level 0.000387, step 1, values float32
Opened Unknown-ring.mrc gaussian as #512, grid size 256,256,256, pixel 2.1,
shown at level 0.00109, step 1, values float32
Opened 0838-disk.mrc gaussian as #513, grid size 240,240,240, pixel 4.3, shown
at level 0.0153, step 1, values float32
Opened 0838-top.mrc gaussian as #514, grid size 240,240,240, pixel 4.3, shown
at level 0.00979, step 1, values float32
Opened FlgV_monomer.mrc gaussian as #259.1, grid size 160,160,160, pixel 4.2,
shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.2, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.3, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.4, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.5, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.6, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.7, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.8, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.9, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.10, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.11, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.12, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.13, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.14, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.15, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.16, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.17, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.18, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.19, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.20, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.21, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgY-with-joints.mrc as #93, grid size 220,220,220, pixel 4.3, shown at
level 2.81, step 1, values float32
Opened Cage_1unit.mrc copy as #85, grid size 240,240,240, pixel 2.1, shown at
level 0.0446, step 1, values float32
Opened FliL.mrc copy as #114, grid size 240,240,240, pixel 2.1, shown at level
0.0732, step 1, values float32
Opened PflA_new.mrc as #68, grid size 240,240,240, pixel 2.1, shown at level
0.162, step 1, values float32
Opened Unknown_near_PflA.mrc as #69, grid size 240,240,240, pixel 2.1, shown
at level 0.127, step 1, values float32
Opened PflB_new.mrc as #70, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32
Opened Top-cage.mrc as #71, grid size 240,240,240, pixel 2.1, shown at level
0.143, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.15, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #21, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #22, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #23, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #24, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #25, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #26, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #28, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #29, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #30, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #31, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #32, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #33, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #34, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #35, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #36, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #37, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Top-cage.mrc copy as #58, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #59, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #73, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #74, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #75, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #76, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #77, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #78, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #79, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #80, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #81, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #82, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #83, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #84, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #86, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #121, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #122, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #123, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened volume sum as #144, grid size 642,583,278, pixel 2.1, shown at level
0.162, step 1, values float32
Opened FlgY-with-joints.mrc copy as #143, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened FlgY-with-joints.mrc copy as #145, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened 1x_Cage-units.mrc as #89, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened PilNO_PL-ring.mrc as #95, grid size 120,120,120, pixel 8.59, shown at
level 6.53e-05, step 1, values float32
Opened New_PL-ring.mrc as #96, grid size 240,240,240, pixel 4.3, shown at
level 0.0141, step 1, values float32
Opened Outer-ring-near-PL.mrc as #97, grid size 240,240,240, pixel 4.3, shown
at level 0.0141, step 1, values float32
Opened Hpwt-L0.08-Global-PL.mrc as #115, grid size 240,240,240, pixel 4.3,
shown at level 0.0148, step 1, values float32
Opened Hpwt-L0.08-rev.mrc as #142, grid size 240,240,240, pixel 4.3, shown at
level 0.0425, step 1, values float32
Opened New_PL-ring.mrc gaussian as #165, grid size 240,240,240, pixel 4.3,
shown at level 0.0105, step 1, values float32
Opened FlgY-with-joints.mrc copy as #173, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #174, grid size 220,220,220, pixel 4.3, shown
at level 0.0868, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #1, grid size 220,220,220, pixel 4.3, shown at
level 0.000693, step 1, values float32
opened ChimeraX session
> close session
> open
> /Users/shoichitachiyama/Desktop/fold_2024_10_31_17_26flbb/fold_2024_10_31_17_26flbb_model_0.cif
Chain information for fold_2024_10_31_17_26flbb_model_0.cif #1
---
Chain | Description
A B | .
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> split #1
Split fold_2024_10_31_17_26flbb_model_0.cif (#1) into 2 models
Chain information for fold_2024_10_31_17_26flbb_model_0.cif A #1.1
---
Chain | Description
A | No description available
Chain information for fold_2024_10_31_17_26flbb_model_0.cif B #1.2
---
Chain | Description
B | No description available
> color #1.1 #a7db9dff
> color #1.2 #53db3fff
> color #1.2 #37912aff
> color #1.2 #41ab31ff
> save /Users/shoichitachiyama/Desktop/FlbB.png supersample 2
> transparentBackground true
> open
> /Users/shoichitachiyama/Downloads/cryosparc_P3_J334_011_volume_map_sharp.mrc
Opened cryosparc_P3_J334_011_volume_map_sharp.mrc as #2, grid size
100,100,100, pixel 4.27, shown at level 8.46, step 1, values float32
> volume #2 level 8.459
> volume #2 level 8.572
> volume #2 level 8.459
> volume #2 level 8.347
> volume #2 level 8.234
> volume #2 level 8.121
> volume #2 level 8.009
> volume #2 level 7.896
> volume #2 level 7.783
> volume #2 level 7.671
> volume #2 level 7.445
> volume #2 level 7.107
> volume #2 level 6.995
> volume #2 level 6.882
> volume #2 level 6.769
> volume #2 level 6.544
> volume #2 level 6.319
> volume #2 level 6.206
> volume #2 level 6.094
> volume #2 level 5.981
> volume #2 level 5.643
> volume #2 level 5.418
> volume #2 level 5.192
> volume #2 level 4.967
> volume #2 level 4.854
> volume #2 level 4.742
> volume #2 level 4.516
> volume #2 level 4.404
> volume #2 level 4.291
> view
> ui tool show "Side View"
> view orient
> volume #2 level 2.939
> surface dust #2 size 42.7
> open
> "/Users/shoichitachiyama/Downloads/cryosparc_P3_J334_011_volume_map_sharp
> (1).mrc"
Opened cryosparc_P3_J334_011_volume_map_sharp (1).mrc as #3, grid size
100,100,100, pixel 4.27, shown at level 8.46, step 1, values float32
> hide #!2 models
> volume #3 level 8.459
> volume #3 level 2.827
[deleted to fit within ticket limits]
> set bgColor #ffffff00
opened ChimeraX session
> color #313 #454545ff models
> color #316 #454545ff models
> color #484 #454545ff models
> save /Users/shoichitachiyama/Desktop/Model-half.png supersample 2
> transparentBackground true
> view name SideP1
> save "/Volumes/Backup-95/Chimera-2023/For_New England 2024/Model-half.cxs"
> includeMaps true
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!53 models
> hide #!52 models
> hide #!58-80 models
> hide #!122 models
> hide #!97 models
> hide #!513 models
> hide #!514 models
> hide #!316 models
> hide #!259 models
> show #!259 models
> hide #!312 models
> turn x -40
> turn x 40
> show #!185.1 models
> show #!185.13 models
> show #!185.14 models
> show #!185.44 models
> show #!185.47 models
> show #!185.48 models
> show #!185.51 models
> show #!185.52 models
> show #!184.8 models
> show #!184.9 models
> show #!184.10 models
> show #!184.11 models
> show #!184.12 models
> show #!184.13 models
> show #!184.26 models
> show #!184.27 models
> show #!184.28 models
> show #!184.29 models
> show #!184.30 models
Cell requested for row 91 is out of bounds for table with 161 rows! Resizing
table model.
> show #!183.8 models
> show #!183.9 models
> show #!183.10 models
> show #!183.11 models
> show #!183.12 models
> show #!183.13 models
Cell requested for row 77 is out of bounds for table with 244 rows! Resizing
table model.
> show #!167.6 models
> show #!167.7 models
> show #!167.8 models
> show #!167.9 models
> show #!167.10 models
> show #!167.11 models
> show #!167.12 models
> show #!168.6 models
> show #!168.7 models
> show #!168.8 models
> show #!168.9 models
> show #!168.10 models
> show #!168.11 models
> show #!168.12 models
> show #!169.6 models
> show #!169.7 models
> show #!169.8 models
> show #!169.9 models
> show #!169.10 models
> show #!169.11 models
> show #!169.12 models
> save /Users/shoichitachiyama/Desktop/Model-40tilt-half.png supersample 2
> transparentBackground true
> save "/Volumes/Backup-95/Chimera-2023/For_New England 2024/Model-40tilted-
> half.cxs" includeMaps true
> close session
> open "/Volumes/Backup-95/Chimera-2023/For_New England 2024/Model-half.cxs"
> format session
Opened 0838-bottom.mrc as #16, grid size 240,240,240, pixel 4.3, shown at
level 0.0144, step 1, values float32
Opened Hpwt-L0.08-Global-Rod-no-MS.mrc as #113, grid size 240,240,240, pixel
4.3, shown at level 0.0151, step 1, values float32
Opened Disk.mrc gaussian as #312, grid size 250,250,250, pixel 4.3, shown at
level 0.0186, step 1, values float32
Opened IM-old-maps.mrc gaussian as #313, grid size 120,120,120, pixel 8.8,
shown at level 0.0702, step 1, values float32
Opened OM.mrc copy gaussian as #316, grid size 240,240,240, pixel 4.3, shown
at level 0.0323, step 1, values float32
Opened New_FliF.mrc gaussian as #479, grid size 256,256,256, pixel 2.1, shown
at level 0.0115, step 1, values float32
Opened New_FlhA.mrc gaussian as #481, grid size 256,256,256, pixel 2.1, shown
at level 0.00316, step 1, values float32
Opened PflBC13.mrc as #482, grid size 256,256,256, pixel 2.1, shown at level
0.00615, step 1, values float32
Opened New_IM_Bottom2.mrc as #483, grid size 256,256,256, pixel 2.1, shown at
level 0.0072, step 1, values float32
Opened New_IM_Bottom2.mrc gaussian as #484, grid size 256,256,256, pixel 2.1,
shown at level 0.0072, step 1, values float32
Opened PflB_C13.mrc as #507, grid size 256,256,256, pixel 2.1, shown at level
0.0015, step 1, values float32
Opened PflB_monomer.mrc as #508, grid size 256,256,256, pixel 2.1, shown at
level 0.00116, step 1, values float32
Opened Unknown-ring.mrc as #509, grid size 256,256,256, pixel 2.1, shown at
level 0.000608, step 1, values float32
Opened PflB_C13.mrc gaussian as #510, grid size 256,256,256, pixel 2.1, shown
at level 0.00108, step 1, values float32
Opened PflB_monomer.mrc gaussian as #511, grid size 256,256,256, pixel 2.1,
shown at level 0.000387, step 1, values float32
Opened Unknown-ring.mrc gaussian as #512, grid size 256,256,256, pixel 2.1,
shown at level 0.00109, step 1, values float32
Opened 0838-disk.mrc gaussian as #513, grid size 240,240,240, pixel 4.3, shown
at level 0.0153, step 1, values float32
Opened 0838-top.mrc gaussian as #514, grid size 240,240,240, pixel 4.3, shown
at level 0.00979, step 1, values float32
Opened FlgV_monomer.mrc gaussian as #259.1, grid size 160,160,160, pixel 4.2,
shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.2, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.3, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.4, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.5, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.6, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.7, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.8, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.9, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.10, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.11, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.12, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.13, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.14, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.15, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.16, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.17, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.18, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.19, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.20, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.21, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgY-with-joints.mrc as #93, grid size 220,220,220, pixel 4.3, shown at
level 2.81, step 1, values float32
Opened Cage_1unit.mrc copy as #85, grid size 240,240,240, pixel 2.1, shown at
level 0.0446, step 1, values float32
Opened FliL.mrc copy as #114, grid size 240,240,240, pixel 2.1, shown at level
0.0732, step 1, values float32
Opened PflA_new.mrc as #68, grid size 240,240,240, pixel 2.1, shown at level
0.162, step 1, values float32
Opened Unknown_near_PflA.mrc as #69, grid size 240,240,240, pixel 2.1, shown
at level 0.127, step 1, values float32
Opened PflB_new.mrc as #70, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32
Opened Top-cage.mrc as #71, grid size 240,240,240, pixel 2.1, shown at level
0.143, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.15, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #21, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #22, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #23, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #24, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #25, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #26, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #28, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #29, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #30, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #31, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #32, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #33, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #34, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #35, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #36, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #37, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Top-cage.mrc copy as #58, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #59, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #73, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #74, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #75, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #76, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #77, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #78, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #79, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #80, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #81, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #82, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #83, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #84, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #86, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #121, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #122, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #123, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened volume sum as #144, grid size 642,583,278, pixel 2.1, shown at level
0.162, step 1, values float32
Opened FlgY-with-joints.mrc copy as #143, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened FlgY-with-joints.mrc copy as #145, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened 1x_Cage-units.mrc as #89, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened PilNO_PL-ring.mrc as #95, grid size 120,120,120, pixel 8.59, shown at
level 6.53e-05, step 1, values float32
Opened New_PL-ring.mrc as #96, grid size 240,240,240, pixel 4.3, shown at
level 0.0141, step 1, values float32
Opened Outer-ring-near-PL.mrc as #97, grid size 240,240,240, pixel 4.3, shown
at level 0.0141, step 1, values float32
Opened Hpwt-L0.08-Global-PL.mrc as #115, grid size 240,240,240, pixel 4.3,
shown at level 0.0148, step 1, values float32
Opened Hpwt-L0.08-rev.mrc as #142, grid size 240,240,240, pixel 4.3, shown at
level 0.0425, step 1, values float32
Opened New_PL-ring.mrc gaussian as #165, grid size 240,240,240, pixel 4.3,
shown at level 0.0105, step 1, values float32
Opened FlgY-with-joints.mrc copy as #173, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #174, grid size 220,220,220, pixel 4.3, shown
at level 0.0868, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #1, grid size 220,220,220, pixel 4.3, shown at
level 0.000693, step 1, values float32
opened ChimeraX session
> lighting simple
> hide #!52 models
> show #!52 models
> hide #!53 models
> show #!53 models
> hide #!65 models
> show #!65 models
> view name SideP1
> turn y 3 120 models #65 center #481
Invalid "center" argument: Center argument has no object bounds
> hide #!67 models
> show #!67 models
> turn y 3 120 models #65 center #67
> view name SideP1
> turn y 3 120 models #172#52#182#65 center #67
> view name SideP1
> turn y -12 120 models #167.13 center #167.13
> view name SideP1
> close session
> open "/Volumes/Backup-95/Chimera-2023/For_New England 2024/Model-half.cxs"
> format session
Opened 0838-bottom.mrc as #16, grid size 240,240,240, pixel 4.3, shown at
level 0.0144, step 1, values float32
Opened Hpwt-L0.08-Global-Rod-no-MS.mrc as #113, grid size 240,240,240, pixel
4.3, shown at level 0.0151, step 1, values float32
Opened Disk.mrc gaussian as #312, grid size 250,250,250, pixel 4.3, shown at
level 0.0186, step 1, values float32
Opened IM-old-maps.mrc gaussian as #313, grid size 120,120,120, pixel 8.8,
shown at level 0.0702, step 1, values float32
Opened OM.mrc copy gaussian as #316, grid size 240,240,240, pixel 4.3, shown
at level 0.0323, step 1, values float32
Opened New_FliF.mrc gaussian as #479, grid size 256,256,256, pixel 2.1, shown
at level 0.0115, step 1, values float32
Opened New_FlhA.mrc gaussian as #481, grid size 256,256,256, pixel 2.1, shown
at level 0.00316, step 1, values float32
Opened PflBC13.mrc as #482, grid size 256,256,256, pixel 2.1, shown at level
0.00615, step 1, values float32
Opened New_IM_Bottom2.mrc as #483, grid size 256,256,256, pixel 2.1, shown at
level 0.0072, step 1, values float32
Opened New_IM_Bottom2.mrc gaussian as #484, grid size 256,256,256, pixel 2.1,
shown at level 0.0072, step 1, values float32
Opened PflB_C13.mrc as #507, grid size 256,256,256, pixel 2.1, shown at level
0.0015, step 1, values float32
Opened PflB_monomer.mrc as #508, grid size 256,256,256, pixel 2.1, shown at
level 0.00116, step 1, values float32
Opened Unknown-ring.mrc as #509, grid size 256,256,256, pixel 2.1, shown at
level 0.000608, step 1, values float32
Opened PflB_C13.mrc gaussian as #510, grid size 256,256,256, pixel 2.1, shown
at level 0.00108, step 1, values float32
Opened PflB_monomer.mrc gaussian as #511, grid size 256,256,256, pixel 2.1,
shown at level 0.000387, step 1, values float32
Opened Unknown-ring.mrc gaussian as #512, grid size 256,256,256, pixel 2.1,
shown at level 0.00109, step 1, values float32
Opened 0838-disk.mrc gaussian as #513, grid size 240,240,240, pixel 4.3, shown
at level 0.0153, step 1, values float32
Opened 0838-top.mrc gaussian as #514, grid size 240,240,240, pixel 4.3, shown
at level 0.00979, step 1, values float32
Opened FlgV_monomer.mrc gaussian as #259.1, grid size 160,160,160, pixel 4.2,
shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.2, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.3, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.4, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.5, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.6, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.7, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.8, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.9, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.10, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.11, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.12, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.13, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.14, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.15, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.16, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.17, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.18, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.19, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.20, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.21, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgY-with-joints.mrc as #93, grid size 220,220,220, pixel 4.3, shown at
level 2.81, step 1, values float32
Opened Cage_1unit.mrc copy as #85, grid size 240,240,240, pixel 2.1, shown at
level 0.0446, step 1, values float32
Opened FliL.mrc copy as #114, grid size 240,240,240, pixel 2.1, shown at level
0.0732, step 1, values float32
Opened PflA_new.mrc as #68, grid size 240,240,240, pixel 2.1, shown at level
0.162, step 1, values float32
Opened Unknown_near_PflA.mrc as #69, grid size 240,240,240, pixel 2.1, shown
at level 0.127, step 1, values float32
Opened PflB_new.mrc as #70, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32
Opened Top-cage.mrc as #71, grid size 240,240,240, pixel 2.1, shown at level
0.143, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.15, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #21, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #22, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #23, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #24, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #25, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #26, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #28, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #29, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #30, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #31, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #32, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #33, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #34, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #35, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #36, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #37, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Top-cage.mrc copy as #58, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #59, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #73, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #74, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #75, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #76, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #77, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #78, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #79, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #80, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #81, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #82, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #83, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #84, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #86, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #121, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #122, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #123, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened volume sum as #144, grid size 642,583,278, pixel 2.1, shown at level
0.162, step 1, values float32
Opened FlgY-with-joints.mrc copy as #143, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened FlgY-with-joints.mrc copy as #145, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened 1x_Cage-units.mrc as #89, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened PilNO_PL-ring.mrc as #95, grid size 120,120,120, pixel 8.59, shown at
level 6.53e-05, step 1, values float32
Opened New_PL-ring.mrc as #96, grid size 240,240,240, pixel 4.3, shown at
level 0.0141, step 1, values float32
Opened Outer-ring-near-PL.mrc as #97, grid size 240,240,240, pixel 4.3, shown
at level 0.0141, step 1, values float32
Opened Hpwt-L0.08-Global-PL.mrc as #115, grid size 240,240,240, pixel 4.3,
shown at level 0.0148, step 1, values float32
Opened Hpwt-L0.08-rev.mrc as #142, grid size 240,240,240, pixel 4.3, shown at
level 0.0425, step 1, values float32
Opened New_PL-ring.mrc gaussian as #165, grid size 240,240,240, pixel 4.3,
shown at level 0.0105, step 1, values float32
Opened FlgY-with-joints.mrc copy as #173, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #174, grid size 220,220,220, pixel 4.3, shown
at level 0.0868, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #1, grid size 220,220,220, pixel 4.3, shown at
level 0.000693, step 1, values float32
opened ChimeraX session
> view name SideP1
> movie record
> turn y 3 120 models #172#52#182#65 center #67
> turn y -12 120 models #167.1 center #167.1
> turn y -12 120 models #167.2 center #167.2
> turn y -12 120 models #167.3 center #167.3
> turn y -12 120 models #167.4 center #167.4
> turn y -12 120 models #167.5 center #167.5
> turn y -12 120 models #167.13 center #167.13
> turn y -12 120 models #167.14 center #167.14
> turn y -12 120 models #167.15 center #167.15
> turn y -12 120 models #167.16 center #167.16
> turn y -12 120 models #167.17 center #167.17
> turn y -12 120 models #167.18 center #167.18
> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov
Movie encoding failed because no images were recorded.
> view SideP1
> movie record
> turn y 3 120 models #172#52#182#65 center #67
> turn y -12 120 models #167.1 center #167.1
> turn y -12 120 models #167.2 center #167.2
> turn y -12 120 models #167.3 center #167.3
> turn y -12 120 models #167.4 center #167.4
> turn y -12 120 models #167.5 center #167.5
> turn y -12 120 models #167.13 center #167.13
> turn y -12 120 models #167.14 center #167.14
> turn y -12 120 models #167.15 center #167.15
> turn y -12 120 models #167.16 center #167.16
> turn y -12 120 models #167.17 center #167.17
> turn y -12 120 models #167.18 center #167.18
> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov
Movie encoding failed because no images were recorded.
> view SideP1
> movie record
> turn y 3 120 models #172#52#182#65 center #67
> turn y -12 120 models #167.1 center #167.1
> turn y -12 120 models #167.2 center #167.2
> turn y -12 120 models #167.3 center #167.3
> turn y -12 120 models #167.4 center #167.4
> turn y -12 120 models #167.5 center #167.5
> turn y -12 120 models #167.13 center #167.13
> turn y -12 120 models #167.14 center #167.14
> turn y -12 120 models #167.15 center #167.15
> turn y -12 120 models #167.16 center #167.16
> turn y -12 120 models #167.17 center #167.17
> turn y -12 120 models #167.18 center #167.18
> movie stop
> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov
Movie encoding failed because no images were recorded.
> view SideP1
> movie record
> turn y 3 120 models #172#52#182#65 center #67
> turn y -12 120 models #167.1 center #167.1
> turn y -12 120 models #167.2 center #167.2
> turn y -12 120 models #167.3 center #167.3
> turn y -12 120 models #167.4 center #167.4
> turn y -12 120 models #167.5 center #167.5
> turn y -12 120 models #167.13 center #167.13
> turn y -12 120 models #167.14 center #167.14
> turn y -12 120 models #167.15 center #167.15
> turn y -12 120 models #167.16 center #167.16
> turn y -12 120 models #167.17 center #167.17
> turn y -12 120 models #167.18 center #167.18
> movie stop
> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov
Movie encoding failed because no images were recorded.
> view SideP1
> movie record
> view SideP1
> wait 10
> turn y 3 120 models #172#52#182#65 center #67
> turn y -12 120 models #167.1 center #167.1
> turn y -12 120 models #167.2 center #167.2
> turn y -12 120 models #167.3 center #167.3
> turn y -12 120 models #167.4 center #167.4
> turn y -12 120 models #167.5 center #167.5
> turn y -12 120 models #167.13 center #167.13
> turn y -12 120 models #167.14 center #167.14
> turn y -12 120 models #167.15 center #167.15
> turn y -12 120 models #167.16 center #167.16
> turn y -12 120 models #167.17 center #167.17
> turn y -12 120 models #167.18 center #167.18
> movie stop
> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov
Movie saved to /Users/shoichitachiyama/Desktop/Hp_rotate.mov
> view SideP1
> movie record
> turn y 3 120 models #172#52#182#65 center #67
> turn y -12 120 models #167.1 center #167.1
> turn y -12 120 models #167.2 center #167.2
> turn y -12 120 models #167.3 center #167.3
> turn y -12 120 models #167.4 center #167.4
> turn y -12 120 models #167.5 center #167.5
> turn y -12 120 models #167.13 center #167.13
> turn y -12 120 models #167.14 center #167.14
> turn y -12 120 models #167.15 center #167.15
> turn y -12 120 models #167.16 center #167.16
> turn y -12 120 models #167.17 center #167.17
> turn y -12 120 models #167.18 center #167.18
> wait 240
> movie stop
> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov
Movie saved to /Users/shoichitachiyama/Desktop/Hp_rotate.mov
> lighting soft
> lighting simple
> show #!72 models
> hide #!72 models
> hide #!172 models
> show #!170 models
> show #171 models
> hide #!170 models
> show #!172 models
> hide #171 models
> select add #172
280839 atoms, 284349 bonds, 35529 residues, 40 models selected
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> select subtract #172
234 models selected
> turn x 90
> select add #172.28
7201 atoms, 7291 bonds, 911 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #172.28,-0.51825,0.84298,-0.14421,1043.1,0.82082,0.53762,0.1929,190.19,0.24014,-0.018402,-0.97056,227.61
> turn x 90
> view matrix models
> #172.28,-0.51825,0.84298,-0.14421,1043.1,0.82082,0.53762,0.1929,192.35,0.24014,-0.018402,-0.97056,232.64
> show sel surfaces
> select add #172
280839 atoms, 284349 bonds, 35529 residues, 46 models selected
> select subtract #172.28
273638 atoms, 277058 bonds, 34618 residues, 273 models selected
> select add #172
280839 atoms, 284349 bonds, 35529 residues, 268 models selected
> select subtract #172
234 models selected
> select add #172.28
7201 atoms, 7291 bonds, 911 residues, 1 model selected
> hide sel surfaces
> save "/Volumes/Backup-95/Chimera-2023/For_New England 2024/Shifted-8uox-
> mono.pdb" selectedOnly true
> select add #172
280839 atoms, 284349 bonds, 35529 residues, 46 models selected
> select subtract #172
234 models selected
> hide #!172 models
> open "/Volumes/Backup-95/Chimera-2023/For_New England 2024/Shifted-8uox-
> mono.pdb"
Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/For_New
England 2024/Shifted-8uox-mono.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 78 1 77
Start residue of secondary structure not found: HELIX 2 2 LEU A 79 ILE A 81 1
3
Start residue of secondary structure not found: HELIX 3 3 LYS A 107 LEU A 118
1 12
Start residue of secondary structure not found: HELIX 4 4 ASN A 119 MET A 121
1 3
Start residue of secondary structure not found: HELIX 5 5 GLU A 154 ILE A 156
1 3
14 messages similar to the above omitted
Chain information for Shifted-8uox-mono.pdb #2
---
Chain | Description
A1 | No description available
B1 | No description available
C1 | No description available
D1 E1 | No description available
F1 | No description available
> select add #2
7201 atoms, 7291 bonds, 911 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> turn x -90
> show #!113 models
> sym #2 C39 copies true center #113
Made 39 copies for Shifted-8uox-mono.pdb symmetry C39
> select subtract #2
Nothing selected
> color #3 #727272ff models
> select add #3
280839 atoms, 284349 bonds, 35529 residues, 40 models selected
> hide sel cartoons
> show sel surfaces
> view SideP1
> select subtract #3
234 models selected
> hide #!113 models
> lighting soft
> movie record
> turn y 3 120 models #172#52#182#65 center #67
> turn y -12 120 models #167.1 center #167.1
> turn y -12 120 models #167.2 center #167.2
> turn y -12 120 models #167.3 center #167.3
> turn y -12 120 models #167.4 center #167.4
> turn y -12 120 models #167.5 center #167.5
> turn y -12 120 models #167.13 center #167.13
> turn y -12 120 models #167.14 center #167.14
> turn y -12 120 models #167.15 center #167.15
> turn y -12 120 models #167.16 center #167.16
> turn y -12 120 models #167.17 center #167.17
> turn y -12 120 models #167.18 center #167.18
> wait 120
> movie stop
> view SideP1
> movie record
> turn y 3 120 models #3#52#182#65 center #67
> turn y -12 120 models #167.1 center #167.1
> turn y -12 120 models #167.2 center #167.2
> turn y -12 120 models #167.3 center #167.3
> turn y -12 120 models #167.4 center #167.4
> turn y -12 120 models #167.5 center #167.5
> turn y -12 120 models #167.13 center #167.13
> turn y -12 120 models #167.14 center #167.14
> turn y -12 120 models #167.15 center #167.15
> turn y -12 120 models #167.16 center #167.16
> turn y -12 120 models #167.17 center #167.17
> turn y -12 120 models #167.18 center #167.18
> wait 120
> movie stop
> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov
Movie saved to /Users/shoichitachiyama/Desktop/Hp_rotate.mov
> view SideP1
> set bgColor black
> set bgColor transparent
> movie record
> turn y 3 120 models #3#52#182#65 center #67
> turn y -12 120 models #167.1 center #167.1
> turn y -12 120 models #167.2 center #167.2
> turn y -12 120 models #167.3 center #167.3
> turn y -12 120 models #167.4 center #167.4
> turn y -12 120 models #167.5 center #167.5
> turn y -12 120 models #167.13 center #167.13
> turn y -12 120 models #167.14 center #167.14
> turn y -12 120 models #167.15 center #167.15
> turn y -12 120 models #167.16 center #167.16
> turn y -12 120 models #167.17 center #167.17
> turn y -12 120 models #167.18 center #167.18
> wait 120
> movie stop
> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov
Movie saved to /Users/shoichitachiyama/Desktop/Hp_rotate.mov
> view SideP1
> save /Users/shoichitachiyama/Desktop/New-side1.png supersample 2
> transparentBackground true
> save "/Volumes/Backup-95/Chimera-2023/For_New England 2024/Model-half-
> ShiftCring.cxs" includeMaps true
> close session
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/For-FlgY_Local-Segment/Send-to-
> Jun_Sep20-2024/FlgY_Local-model09202024.cxs
> set bgColor #ffffff00
opened ChimeraX session
> close session
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/For-FlgY_Local-
> Segment/Fig3_FlgY_Loca-Sep17-2024l.cxs
Opened 13X_FlgY-ring.mrc as #1, grid size 220,220,220, pixel 2.15, shown at
level 0.539, step 1, values float32
Opened FliF_local.mrc as #2, grid size 220,220,220, pixel 2.15, shown at level
0.378, step 1, values float32
Opened Internal-ring_local.mrc as #3, grid size 220,220,220, pixel 2.15, shown
at level 0.299, step 1, values float32
Opened Unknown_near_PflA.mrc as #4, grid size 240,240,240, pixel 2.1, shown at
level 0.147, step 1, values float32
Opened Rod_local.mrc as #5, grid size 220,220,220, pixel 2.15, shown at level
0.482, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.1, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.2, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.3, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.4, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.5, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.6, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.7, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.8, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.9, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.10, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.11, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.12, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.13, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.14, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.15, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.16, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.17, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27.18, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32
Opened 1X_FlgY_region.mrc as #10, grid size 220,220,220, pixel 2.15, shown at
level 0.539, step 1, values float32
Opened 3X_FlgY_region.mrc as #11, grid size 220,220,220, pixel 2.15, shown at
level 0.539, step 1, values float32
opened ChimeraX session
> hide #!13 models
> hide #!27 models
> show #!10 models
> hide #!8 models
> hide #!1 models
> show #!13 models
> show #!11 models
> hide #!10 models
> hide #!13.6 models
> show #!13.6 models
> hide #!13.7 models
> show #!13.7 models
> hide #!13.8 models
> show #!13.8 models
> hide #!13.9 models
> hide #!13.10 models
> hide #!13.11 models
> hide #!13.12 models
> hide #!13.13 models
> hide #!13.1 models
> view orient
> turn x -12 120 models #13 center #13
> select add #13.6
2624 atoms, 2640 bonds, 326 residues, 3 models selected
> select add #13.7
5248 atoms, 5280 bonds, 652 residues, 8 models selected
> select add #13.8
7872 atoms, 7920 bonds, 978 residues, 13 models selected
> select add #13
34112 atoms, 34320 bonds, 4238 residues, 46 models selected
> select subtract #13
26 models selected
> select add #13
34112 atoms, 34320 bonds, 4238 residues, 40 models selected
> select subtract #13
26 models selected
> turn x -3 120 models #13#11 center #13
> movie record
> turn x -3 120 models #13#11 center #13
> movie stop
> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/FlgY_rotate.mov
Movie encoding failed because no images were recorded.
> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/FlgY_rotate.mov
Movie encoding failed because no images were recorded.
> movie record
> turn x -3 120 models #13#11 center #13
> movie stop
> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/FlgY_rotate.mov
Movie encoding failed because no images were recorded.
> movie record
> turn x -3 120 models #13#11 center #13
> wait 120
> movie stop
> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/FlgY_rotate.mov
Movie saved to /Users/shoichitachiyama/Desktop/FlgY_rotate.mov
> set bgColor black
> set bgColor transparent
> color #11 #72727200 models
> color #11 #72727266 models
> movie record
> turn x -3 120 models #13#11 center #13
> wait 120
> movie stop
> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/FlgY_rotate.mov
Movie saved to /Users/shoichitachiyama/Desktop/FlgY_rotate.mov
> hide #!13.8 models
> hide #!13 models
> show #!13 models
> hide #!11 models
> show #!8 models
> show #!13.1 models
> show #!13.2 models
> show #!13.3 models
> show #!13.4 models
> show #!13.5 models
> show #!13.8 models
> show #!13.10 models
> hide #!13.10 models
> show #!13.11 models
> show #!13.13 models
> show #!13.10 models
> show #!13.9 models
> show #!13.12 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!6 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!27 models
> hide #!27 models
> show #!12 models
> hide #!12 models
> show #!13 models
> show #!6 models
> hide #!13 models
> select add #6
41236 atoms, 41678 bonds, 5174 residues, 53 models selected
> show sel surfaces
> show #!13 models
> hide #!13 models
> select subtract #6
52 models selected
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac13,1
Model Number: Z14J000E1LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 6 days, 21 hours, 56 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Q24i-10:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
ASUS PA279:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.2.2
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-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (1)
comment:1 by , 12 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between displays |
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