![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Closed 13 months ago
#16079 closed defect (duplicate)
Crash on Mac waking from sleep
| 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-14.6.1-x86_64-i386-64bit
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
Current thread 0x00007ff848dd8dc0 (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.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, 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, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, PIL._imagingmath (total: 120)
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{
"uptime" : 280000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 12972,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2024-10-07 11:00:18.4754 +0100",
"codeSigningMonitor" : 0,
"incident" : "C4E0BD6B-F7C7-42A1-8AA5-48A101C18E02",
"pid" : 82842,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-10-04 14:02:04.8053 +0100",
"procStartAbsTime" : 247428069331916,
"procExitAbsTime" : 288279864277661,
"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":"5FC18D3C-1898-50CA-92F1-24E40C066179","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "22AFD314-FBF5-45F4-A151-6BB76F846F16",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 106,
"bridgeVersion" : {"build":"21P6074","train":"8.6"},
"sleepWakeUUID" : "EA28EE74-4AB2-4A31-A088-6F9AB6CBCD0F",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4381319168\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10525a000-10525e000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/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":82842},
"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: 4381319168\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10525a000-10525e000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.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=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=29.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=29.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nActivity Tracing 256K 1 \nCG image 452K 35 \nCG raster data 8K 1 \nColorSync 252K 31 \nCoreAnimation 2336K 148 \nCoreGraphics 16K 3 \nCoreGraphics (reserved) 8K 1 reserved VM address space (unallocated)\nCoreServices 720K 3 \nCoreUI image data 256K 2 \nFoundation 32K 2 \nIOKit 23.3M 3 \nKernel Alloc Once 8K 1 \nMALLOC 27.9G 4033 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_REALLOC (reserved) 8K 1 reserved VM address space (unallocated)\nMach message 16K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 204K 51 \nStack 176.4M 52 \nStack Guard 56.0M 1 \nVM_ALLOCATE 913.6M 408 \nVM_ALLOCATE (reserved) 352.0M 3 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 47.9M 867 \n__DATA_CONST 65.6M 464 \n__DATA_DIRTY 1842K 231 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 220.2M 218 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2201K 2 \n__TEXT 1.1G 866 \ndyld private memory 40K 2 \nmapped file 261.5M 86 \nshared memory 2996K 29 \n=========== ======= ======= \nTOTAL 31.2G 7567 \nTOTAL, minus reserved VM space 30.9G 7567 \n",
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"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
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"logWritingSignature" : "fcc63f32cc2fe88f0f5d042cd2b2b7f5f6c50587",
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{
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"factorPackIds" : {
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},
"deploymentId" : 240000015
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],
"experiments" : [
{
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},
{
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"experimentId" : "6643969b3099cf28e049862f",
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32
Log from Fri Oct 4 13:17:26 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32
Log from Wed Sep 25 19:02:23 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32
Log from Tue Sep 24 13:00:23 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32
Log from Mon Sep 16 15:36:42 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Log from Wed Sep 11 12:56:29 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
[deleted to fit within ticket limits]
> color sel hot pink
> select #31/B #32/B #33/B
7806 atoms, 7926 bonds, 1002 residues, 3 models selected
> color sel yellow
> select #31/C #32/C #33/C
23784 atoms, 24171 bonds, 3051 residues, 3 models selected
> color sel orange
> select #31/D #32/D #33/D
15693 atoms, 15963 bonds, 1950 residues, 3 models selected
> color sel light gray
> select #31/E #32/E #33/E
29835 atoms, 30399 bonds, 3714 residues, 3 models selected
> ui tool show "Color Actions"
> color sel slate blue
> select #31/F #32/F #33/F
14724 atoms, 14886 bonds, 1821 residues, 3 models selected
> color sel red
> select add #31
47368 atoms, 48086 bonds, 5928 residues, 3 models selected
> select add #32
80012 atoms, 81286 bonds, 10035 residues, 3 models selected
> select subtract #31
42460 atoms, 43124 bonds, 5321 residues, 2 models selected
> select subtract #32
4908 atoms, 4962 bonds, 607 residues, 1 model selected
> select add #33
37552 atoms, 38162 bonds, 4714 residues, 1 model selected
> select subtract #33
Nothing selected
> select clear
> matchmaker #32/A to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_1.cif, chain A (#32),
sequence alignment score = 3505.1
RMSD between 253 pruned atom pairs is 0.693 angstroms; (across all 293 pairs:
1.550)
> matchmaker #33/A to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_2.cif, chain A (#33),
sequence alignment score = 3502.1
RMSD between 258 pruned atom pairs is 0.659 angstroms; (across all 293 pairs:
1.500)
> lighting simple
> hide #32 models
> hide #33 models
> show #33 models
> hide #33 models
> show #33 models
> hide #33 models
> show #33 models
> hide #33 models
> show #32 models
> hide #32 models
> show #32 models
> hide #31 models
> show #31 models
> hide #31 models
> show #31 models
> hide #31 models
> show #31 models
> hide #32 models
> show #32 models
> hide #32 models
> show #32 models
> hide #32 models
> show #32 models
> hide #32 models
> show #32 models
> hide #32 models
> show #32 models
> hide #32 models
> hide #!10 models
> show #!50 models
> hide #!50 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
\u2014\u2014\u2014 End of log from Tue Sep 24 13:00:23 2024 \u2014\u2014\u2014
opened ChimeraX session
> lighting simple
> open /Users/cvetkom/Documents/pdb/4c95_Ctf4_Sld5.pdb
4c95_Ctf4_Sld5.pdb title:
Crystal structure of the carboxy-terminal domain of yeast CTF4 bound to SLD5
[more info...]
Chain information for 4c95_Ctf4_Sld5.pdb #34
---
Chain | Description
A B C | No description available
D E | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #34
9660 atoms, 9722 bonds, 4 pseudobonds, 1360 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select subtract #34
Nothing selected
> select #34/A
3494 atoms, 3493 bonds, 2 pseudobonds, 510 residues, 2 models selected
> select #34/B
3531 atoms, 3550 bonds, 1 pseudobond, 498 residues, 2 models selected
> select #34/C
2427 atoms, 2473 bonds, 1 pseudobond, 326 residues, 2 models selected
> select #34/D
104 atoms, 103 bonds, 13 residues, 1 model selected
> select #34/E
104 atoms, 103 bonds, 13 residues, 1 model selected
> select #34/D,E
208 atoms, 206 bonds, 26 residues, 1 model selected
> color sel red
> hide #31 models
> open
> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_3c_ctf4_mrc1_1081_1096/fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif
Chain information for fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif #35
---
Chain | Description
A B C | .
D | .
> show #!10 models
> hide #!23 models
> select clear
> ui tool show Matchmaker
> matchmaker #34/B to #10/S pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain S (#10) with 4c95_Ctf4_Sld5.pdb, chain B
(#34), sequence alignment score = 2232.7
RMSD between 391 pruned atom pairs is 0.878 angstroms; (across all 424 pairs:
1.248)
> matchmaker #35/A to #10/S pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain S (#10) with
fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif, chain A (#35), sequence
alignment score = 2301.6
RMSD between 411 pruned atom pairs is 0.645 angstroms; (across all 425 pairs:
0.817)
> hide #!10 models
> show #!10 models
> show #!23 models
> hide #!23 models
> show #!42 models
> color #42 #b2b2ffeb models
> color #42 #b2b2ffff models
> color #42 #b2b2ffb7 models
> color #42 #b2b2ff95 models
> color #42 #b2b2ff84 models
> hide #!10 models
> lighting soft
> lighting full
> lighting simple
> ui tool show "Side View"
> hide #!42 models
> show #!42 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #35 models
> show #35 models
> hide #!42 models
> show #!42 models
> hide #35 models
> show #35 models
> select #35/D
128 atoms, 129 bonds, 16 residues, 1 model selected
> color sel orange
> color sel orange red
> color sel orange
> select clear
> hide #!34 models
> show #!34 models
> ui tool show "Fit in Map"
> hide #!42 models
> show #!42 models
> fitmap #34 inMap #42
Fit molecule 4c95_Ctf4_Sld5.pdb (#34) to map sharpened_replisome.mrc copy
(#42) using 9660 atoms
average map value = 0.381, steps = 128
shifted from previous position = 2.63
rotated from previous position = 6.17 degrees
atoms outside contour = 4354, contour level = 0.3
Position of 4c95_Ctf4_Sld5.pdb (#34) relative to sharpened_replisome.mrc copy
(#42) coordinates:
Matrix rotation and translation
0.28572805 -0.31647925 0.90454429 338.42345045
-0.43402411 -0.88427381 -0.17228725 294.11719747
0.85439016 -0.34336673 -0.39002146 373.35631167
Axis -0.80114939 0.23486712 -0.55045172
Axis point 0.00000000 201.64420355 57.39058667
Rotation angle (degrees) 173.87077288
Shift along axis -407.56390486
> fitmap #35 inMap #42
Fit molecule fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif (#35) to map
sharpened_replisome.mrc copy (#42) using 11336 atoms
average map value = 0.4111, steps = 68
shifted from previous position = 0.628
rotated from previous position = 1.83 degrees
atoms outside contour = 4371, contour level = 0.3
Position of fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif (#35) relative
to sharpened_replisome.mrc copy (#42) coordinates:
Matrix rotation and translation
-0.98706242 -0.07882972 0.13961966 285.86123137
0.08488406 0.48183004 0.87214363 299.11678968
-0.13602378 0.87271169 -0.46890494 372.10103280
Axis 0.00177188 0.85978425 0.51065438
Axis point 149.35362784 0.00000000 83.84935178
Rotation angle (degrees) 170.77580491
Shift along axis 447.69744149
> hide #35 models
> hide #!42 models
> show #!42 models
> hide #!34 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> hide #!42 models
> show #!42 models
> color #42 #b2b2ffff models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Side View"
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!47 models
> show #!46 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> hide #!42 models
> hide #!46 models
> show #!43 models
> hide #!43 models
> show #!34 models
> show #33 models
> hide #33 models
> show #35 models
> hide #!34 models
> show #!34 models
> hide #35 models
> show #35 models
> show #!2 models
> hide #!2 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
\u2014\u2014\u2014 End of log from Wed Sep 25 19:02:23 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!34 models
> hide #35 models
> show #35 models
> hide #35 models
> close #2-3
> close #7
> close #11
> close #9
> show #!50 models
> hide #!50 models
> show #!53 models
> close #53
> show #!52 models
> close #52
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!10 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
\u2014\u2014\u2014 End of log from Fri Oct 4 13:17:26 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!10 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J819_005_volume_map_EMready.mrc
Opened cryosparc_P17_J819_005_volume_map_EMready.mrc as #2, grid size
588,588,588, pixel 0.95, shown at level 0.0383, step 4, values float32
> volume #2 step 1
> volume #2 level 0.9283
> volume #2 level 1.647
> ui tool show "Side View"
> hide #!2 models
> show #!21 models
> show #!2 models
> select add #2
2 models selected
> lighting simple
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.21372,0.65189,-0.72758,228.01,-0.15215,0.75791,0.63437,-52.313,0.96497,-0.024879,0.26116,-76.828
> view matrix models
> #2,-0.22904,0.42092,-0.8777,455.06,-0.48229,0.73415,0.47793,87.401,0.84554,0.53277,0.034859,-139.12
> view matrix models
> #2,-0.30253,0.24312,-0.92161,536.06,-0.68897,0.61238,0.38771,202.38,0.65863,0.75225,-0.017761,-133.46
> view matrix models
> #2,-0.17917,0.019523,-0.98362,578.75,-0.64564,0.75206,0.13253,216.8,0.74233,0.65881,-0.12214,-104.65
> view matrix models
> #2,-0.39996,0.21624,-0.89066,563.08,-0.18128,0.93391,0.30815,-9.3049,0.89843,0.28471,-0.33432,8.6733
> view matrix models
> #2,-0.45252,0.485,-0.74833,467.43,0.38691,0.86285,0.32525,-154.48,0.80345,-0.14235,-0.57811,215.56
> view matrix models
> #2,-0.19899,0.25008,-0.94756,511.54,0.14679,0.96359,0.22349,-88.484,0.96895,-0.094621,-0.22845,66.354
> view matrix models
> #2,-0.40366,0.20697,-0.89119,566.81,-0.0090314,0.97313,0.23009,-48.812,0.91486,0.10093,-0.39095,69.189
> view matrix models
> #2,-0.42359,0.12332,-0.89742,597.11,0.0008642,0.99074,0.13574,-32.363,0.90585,0.056721,-0.41978,91.291
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.42359,0.12332,-0.89742,572.5,0.0008642,0.99074,0.13574,-244.94,0.90585,0.056721,-0.41978,20.155
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.42268,0.11844,-0.8985,573.87,0.0011522,0.99149,0.13015,-243.8,0.90628,0.053978,-0.41923,20.651
> view matrix models
> #2,-0.54332,-0.16268,-0.82361,666.33,-0.42868,0.89727,0.10557,-90.185,0.72182,0.41043,-0.55725,9.6598
> view matrix models
> #2,-0.59204,-0.092954,-0.80053,654.96,-0.41205,0.88859,0.20156,-117.01,0.6926,0.44919,-0.56439,9.0402
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.59204,-0.092954,-0.80053,657.43,-0.41205,0.88859,0.20156,-126.64,0.6926,0.44919,-0.56439,12.296
> view matrix models
> #2,-0.59204,-0.092954,-0.80053,663.52,-0.41205,0.88859,0.20156,-124.44,0.6926,0.44919,-0.56439,2.3033
> ui mousemode right zoom
> ui tool show "Fit in Map"
> fitmap #2 inMap #21
Fit map cryosparc_P17_J819_005_volume_map_EMready.mrc in map
cryosparc_P17_J819_005_volume_map.mrc using 740829 points
correlation = 0.938, correlation about mean = 0.7691, overlap = 1.576e+06
steps = 160, shift = 3.85, angle = 10.8 degrees
Position of cryosparc_P17_J819_005_volume_map_EMready.mrc (#2) relative to
cryosparc_P17_J819_005_volume_map.mrc (#21) coordinates:
Matrix rotation and translation
0.99999999 0.00005310 -0.00009395 0.01216343
-0.00005312 0.99999998 -0.00020453 0.08100750
0.00009394 0.00020453 0.99999998 -0.07859161
Axis 0.88443714 -0.40622568 -0.22967726
Axis point 0.00000000 388.90207101 387.88928499
Rotation angle (degrees) 0.01324986
Shift along axis -0.00409883
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!20 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!20 models
> show #!42 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map_sharp.mrc
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #3, grid size
588,588,588, pixel 0.95, shown at level 0.15, step 4, values float32
> volume #3 step 1
> volume #3 level 0.2175
> volume #3 level 0.4032
> select add #3
3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.96087,0.15628,0.2287,-100.29,-0.086083,0.95323,-0.28971,123.99,-0.26328,0.25869,0.92939,24.765
> view matrix models
> #3,0.94784,0.022072,0.31799,-87.222,0.026112,0.98887,-0.14647,39.853,-0.31769,0.14713,0.93671,67.954
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.94784,0.022072,0.31799,-188.13,0.026112,0.98887,-0.14647,-129.94,-0.31769,0.14713,0.93671,62.858
> view matrix models
> #3,0.94784,0.022072,0.31799,-118.63,0.026112,0.98887,-0.14647,-168.34,-0.31769,0.14713,0.93671,-44.135
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.79338,0.092061,0.60172,-179.94,0.1255,0.94252,-0.30967,-134.37,-0.59565,0.32121,0.73623,46.771
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.79338,0.092061,0.60172,-166.19,0.1255,0.94252,-0.30967,-142.23,-0.59565,0.32121,0.73623,35.37
> view matrix models
> #3,0.79338,0.092061,0.60172,-165.26,0.1255,0.94252,-0.30967,-141.13,-0.59565,0.32121,0.73623,35.671
> select subtract #3
Nothing selected
> fitmap #3 inMap #42
Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
sharpened_replisome.mrc copy using 329084 points
correlation = 1, correlation about mean = 0.9999, overlap = 1.568e+05
steps = 236, shift = 0.4, angle = 16.9 degrees
Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) relative to
sharpened_replisome.mrc copy (#42) coordinates:
Matrix rotation and translation
1.00000000 -0.00001351 0.00004557 -0.02152036
0.00001352 1.00000000 -0.00003397 0.01017840
-0.00004557 0.00003397 1.00000000 0.00711885
Axis 0.58150158 0.77996616 0.23131947
Axis point 171.08172050 0.00000000 434.91154679
Rotation angle (degrees) 0.00334730
Shift along axis -0.00292859
> hide #!42 models
> show #!42 models
> volume #3 level 0.3
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> ui mousemode right zoom
> ui tool show "Hide Dust"
> surface undust #42
> fitmap #3 inMap #42
Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
sharpened_replisome.mrc copy using 586182 points
correlation = 1, correlation about mean = 0.9999, overlap = 1.874e+05
steps = 28, shift = 0.0238, angle = 0.00733 degrees
Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) relative to
sharpened_replisome.mrc copy (#42) coordinates:
Matrix rotation and translation
1.00000000 0.00000906 -0.00005933 0.02130757
-0.00000906 1.00000000 0.00003559 -0.01782195
0.00005933 -0.00003559 1.00000000 0.00029158
Axis -0.51008916 -0.85026779 -0.12982191
Axis point -14.19118466 0.00000000 395.65343560
Rotation angle (degrees) 0.00399795
Shift along axis 0.00424682
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> open
> /Users/cvetkom/Documents/cryoSPARC/Jacob_cryosparc_P5_J117_006_volume_map.mrc
Opened Jacob_cryosparc_P5_J117_006_volume_map.mrc as #7, grid size
480,480,480, pixel 0.95, shown at level 0.152, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc
Opened Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc as #9, grid size
480,480,480, pixel 0.95, shown at level 0.28, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc
Opened Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc as #11, grid size
480,480,480, pixel 0.95, shown at level 0.569, step 2, values float32
> volume #11 level 2.423
> volume #9 level 0.9574
> volume #11 step 1
> volume #9 step 1
> volume #7 step 1
> volume #7 level 0.2399
> select add #7
2 models selected
> select add #9
4 models selected
> select add #11
6 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.31536,0.44395,0.83873,0.5068,-0.77807,0.38503,-0.49635,422.96,-0.54329,-0.80911,0.224,478.2,#9,-0.31536,0.44395,0.83873,0.5068,-0.77807,0.38503,-0.49635,422.96,-0.54329,-0.80911,0.224,478.2,#11,-0.31536,0.44395,0.83873,0.5068,-0.77807,0.38503,-0.49635,422.96,-0.54329,-0.80911,0.224,478.2
> view matrix models
> #7,-0.73321,-0.54683,0.4042,411.11,0.31221,-0.79877,-0.51428,443.38,0.60409,-0.25088,0.7564,-22.885,#9,-0.73321,-0.54683,0.4042,411.11,0.31221,-0.79877,-0.51428,443.38,0.60409,-0.25088,0.7564,-22.885,#11,-0.73321,-0.54683,0.4042,411.11,0.31221,-0.79877,-0.51428,443.38,0.60409,-0.25088,0.7564,-22.885
> view matrix models
> #7,-0.27775,-0.26716,0.92276,128.06,0.32065,-0.93125,-0.1731,391.13,0.90556,0.2478,0.34432,-103.14,#9,-0.27775,-0.26716,0.92276,128.06,0.32065,-0.93125,-0.1731,391.13,0.90556,0.2478,0.34432,-103.14,#11,-0.27775,-0.26716,0.92276,128.06,0.32065,-0.93125,-0.1731,391.13,0.90556,0.2478,0.34432,-103.14
> view matrix models
> #7,0.8345,-0.016866,0.55076,-87.575,-0.27678,-0.87711,0.39251,380.66,0.47645,-0.47999,-0.73662,402.79,#9,0.8345,-0.016866,0.55076,-87.575,-0.27678,-0.87711,0.39251,380.66,0.47645,-0.47999,-0.73662,402.79,#11,0.8345,-0.016866,0.55076,-87.575,-0.27678,-0.87711,0.39251,380.66,0.47645,-0.47999,-0.73662,402.79
> view matrix models
> #7,0.93667,-0.11461,-0.33094,116.1,-0.073314,-0.98817,0.13471,419.63,-0.34246,-0.10191,-0.93399,548.21,#9,0.93667,-0.11461,-0.33094,116.1,-0.073314,-0.98817,0.13471,419.63,-0.34246,-0.10191,-0.93399,548.21,#11,0.93667,-0.11461,-0.33094,116.1,-0.073314,-0.98817,0.13471,419.63,-0.34246,-0.10191,-0.93399,548.21
> view matrix models
> #7,0.73012,-0.060917,-0.6806,231.63,-0.11744,-0.99238,-0.03716,470.33,-0.67315,0.10706,-0.73172,529.05,#9,0.73012,-0.060917,-0.6806,231.63,-0.11744,-0.99238,-0.03716,470.33,-0.67315,0.10706,-0.73172,529.05,#11,0.73012,-0.060917,-0.6806,231.63,-0.11744,-0.99238,-0.03716,470.33,-0.67315,0.10706,-0.73172,529.05
> view matrix models
> #7,-0.001777,-0.5744,-0.81857,538.78,-0.99932,-0.029179,0.022644,442.03,-0.036892,0.81806,-0.57396,195.39,#9,-0.001777,-0.5744,-0.81857,538.78,-0.99932,-0.029179,0.022644,442.03,-0.036892,0.81806,-0.57396,195.39,#11,-0.001777,-0.5744,-0.81857,538.78,-0.99932,-0.029179,0.022644,442.03,-0.036892,0.81806,-0.57396,195.39
> view matrix models
> #7,-0.19049,-0.64648,-0.73876,577.96,-0.97965,0.17364,0.10066,375.18,0.063205,0.74291,-0.66641,211.06,#9,-0.19049,-0.64648,-0.73876,577.96,-0.97965,0.17364,0.10066,375.18,0.063205,0.74291,-0.66641,211.06,#11,-0.19049,-0.64648,-0.73876,577.96,-0.97965,0.17364,0.10066,375.18,0.063205,0.74291,-0.66641,211.06
> view matrix models
> #7,0.12078,-0.88633,-0.44703,493.31,-0.85691,-0.32042,0.40377,385.39,-0.50111,0.33429,-0.79821,456.57,#9,0.12078,-0.88633,-0.44703,493.31,-0.85691,-0.32042,0.40377,385.39,-0.50111,0.33429,-0.79821,456.57,#11,0.12078,-0.88633,-0.44703,493.31,-0.85691,-0.32042,0.40377,385.39,-0.50111,0.33429,-0.79821,456.57
> view matrix models
> #7,0.37394,-0.74381,-0.554,430.71,-0.52804,-0.66181,0.53214,357.01,-0.76246,0.093543,-0.64024,530.6,#9,0.37394,-0.74381,-0.554,430.71,-0.52804,-0.66181,0.53214,357.01,-0.76246,0.093543,-0.64024,530.6,#11,0.37394,-0.74381,-0.554,430.71,-0.52804,-0.66181,0.53214,357.01,-0.76246,0.093543,-0.64024,530.6
> view matrix models
> #7,0.094335,-0.81529,-0.57132,512.56,-0.75251,-0.43412,0.49525,365.75,-0.65179,0.38321,-0.65446,445.97,#9,0.094335,-0.81529,-0.57132,512.56,-0.75251,-0.43412,0.49525,365.75,-0.65179,0.38321,-0.65446,445.97,#11,0.094335,-0.81529,-0.57132,512.56,-0.75251,-0.43412,0.49525,365.75,-0.65179,0.38321,-0.65446,445.97
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.094335,-0.81529,-0.57132,537.82,-0.75251,-0.43412,0.49525,374.18,-0.65179,0.38321,-0.65446,478.27,#9,0.094335,-0.81529,-0.57132,537.82,-0.75251,-0.43412,0.49525,374.18,-0.65179,0.38321,-0.65446,478.27,#11,0.094335,-0.81529,-0.57132,537.82,-0.75251,-0.43412,0.49525,374.18,-0.65179,0.38321,-0.65446,478.27
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.11661,-0.85928,-0.49804,525.44,-0.7549,-0.40255,0.51777,362.57,-0.64539,0.31559,-0.69561,501.2,#9,0.11661,-0.85928,-0.49804,525.44,-0.7549,-0.40255,0.51777,362.57,-0.64539,0.31559,-0.69561,501.2,#11,0.11661,-0.85928,-0.49804,525.44,-0.7549,-0.40255,0.51777,362.57,-0.64539,0.31559,-0.69561,501.2
> view matrix models
> #7,0.042668,-0.87433,-0.48344,541.79,-0.70941,-0.36724,0.60156,325.24,-0.70351,0.31729,-0.63593,499.88,#9,0.042668,-0.87433,-0.48344,541.79,-0.70941,-0.36724,0.60156,325.24,-0.70351,0.31729,-0.63593,499.88,#11,0.042668,-0.87433,-0.48344,541.79,-0.70941,-0.36724,0.60156,325.24,-0.70351,0.31729,-0.63593,499.88
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.042668,-0.87433,-0.48344,547.1,-0.70941,-0.36724,0.60156,161.23,-0.70351,0.31729,-0.63593,420.52,#9,0.042668,-0.87433,-0.48344,547.1,-0.70941,-0.36724,0.60156,161.23,-0.70351,0.31729,-0.63593,420.52,#11,0.042668,-0.87433,-0.48344,547.1,-0.70941,-0.36724,0.60156,161.23,-0.70351,0.31729,-0.63593,420.52
> view matrix models
> #7,0.042668,-0.87433,-0.48344,536.67,-0.70941,-0.36724,0.60156,152.08,-0.70351,0.31729,-0.63593,408.34,#9,0.042668,-0.87433,-0.48344,536.67,-0.70941,-0.36724,0.60156,152.08,-0.70351,0.31729,-0.63593,408.34,#11,0.042668,-0.87433,-0.48344,536.67,-0.70941,-0.36724,0.60156,152.08,-0.70351,0.31729,-0.63593,408.34
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.3552,-0.77911,-0.51654,454.02,-0.53271,-0.62278,0.57303,175.27,-0.76815,0.071622,-0.63625,476.51,#9,0.3552,-0.77911,-0.51654,454.02,-0.53271,-0.62278,0.57303,175.27,-0.76815,0.071622,-0.63625,476.51,#11,0.3552,-0.77911,-0.51654,454.02,-0.53271,-0.62278,0.57303,175.27,-0.76815,0.071622,-0.63625,476.51
> view matrix models
> #7,0.055668,-0.8551,-0.51546,537.02,-0.55774,-0.45484,0.6943,115.93,-0.82815,0.24884,-0.50224,419.95,#9,0.055668,-0.8551,-0.51546,537.02,-0.55774,-0.45484,0.6943,115.93,-0.82815,0.24884,-0.50224,419.95,#11,0.055668,-0.8551,-0.51546,537.02,-0.55774,-0.45484,0.6943,115.93,-0.82815,0.24884,-0.50224,419.95
> view matrix models
> #7,0.050991,-0.93462,-0.35197,517.42,-0.719,-0.27895,0.63657,126.78,-0.69313,0.2206,-0.68622,438.87,#9,0.050991,-0.93462,-0.35197,517.42,-0.719,-0.27895,0.63657,126.78,-0.69313,0.2206,-0.68622,438.87,#11,0.050991,-0.93462,-0.35197,517.42,-0.719,-0.27895,0.63657,126.78,-0.69313,0.2206,-0.68622,438.87
> view matrix models
> #7,-0.032857,-0.97559,-0.21713,513.67,-0.62463,-0.14955,0.76647,47.285,-0.78023,0.16081,-0.60447,452.3,#9,-0.032857,-0.97559,-0.21713,513.67,-0.62463,-0.14955,0.76647,47.285,-0.78023,0.16081,-0.60447,452.3,#11,-0.032857,-0.97559,-0.21713,513.67,-0.62463,-0.14955,0.76647,47.285,-0.78023,0.16081,-0.60447,452.3
> view matrix models
> #7,0.47176,-0.82185,-0.3194,391.59,-0.27024,-0.47958,0.83485,24.697,-0.8393,-0.30753,-0.44834,531.52,#9,0.47176,-0.82185,-0.3194,391.59,-0.27024,-0.47958,0.83485,24.697,-0.8393,-0.30753,-0.44834,531.52,#11,0.47176,-0.82185,-0.3194,391.59,-0.27024,-0.47958,0.83485,24.697,-0.8393,-0.30753,-0.44834,531.52
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!23 models
> hide #!23 models
> show #!23 models
> fitmap #7 inMap #23
Fit map Jacob_cryosparc_P5_J117_006_volume_map.mrc in map
cryosparc_P17_J842_005_volume_map.mrc using 611645 points
correlation = 0.8586, correlation about mean = 0.4556, overlap = 8.71e+04
steps = 244, shift = 17, angle = 22.5 degrees
Position of Jacob_cryosparc_P5_J117_006_volume_map.mrc (#7) relative to
cryosparc_P17_J842_005_volume_map.mrc (#23) coordinates:
Matrix rotation and translation
0.55644781 -0.77930109 0.28819374 245.87868586
-0.75685869 -0.33229301 0.56280215 362.24414012
-0.34282757 -0.53129197 -0.77472452 653.58997201
Axis -0.86611289 0.49953261 0.01776598
Axis point 0.00000000 386.34237031 252.82329186
Rotation angle (degrees) 140.83086649
Shift along axis -20.39427278
> hide #!7 models
> show #!7 models
> fitmap #9 inMap #23
Fit map Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc in map
cryosparc_P17_J842_005_volume_map.mrc using 166113 points
correlation = 0.8354, correlation about mean = 0.2023, overlap = 1.093e+05
steps = 240, shift = 17.3, angle = 22.5 degrees
Position of Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc (#9) relative to
cryosparc_P17_J842_005_volume_map.mrc (#23) coordinates:
Matrix rotation and translation
0.55535502 -0.78023657 0.28777020 246.41094031
-0.75768547 -0.33209636 0.56180488 362.67622759
-0.34277328 -0.53004046 -0.77560530 653.54700022
Axis -0.86582981 0.50001893 0.01788295
Axis point 0.00000000 386.54023823 252.88749245
Rotation angle (degrees) 140.91153143
Shift along axis -20.31760982
> fitmap #11 inMap #23
Fit map Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc in map
cryosparc_P17_J842_005_volume_map.mrc using 547647 points
correlation = 0.755, correlation about mean = 0.2272, overlap = 1.157e+06
steps = 244, shift = 16, angle = 22.6 degrees
Position of Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc (#11) relative
to cryosparc_P17_J842_005_volume_map.mrc (#23) coordinates:
Matrix rotation and translation
0.55439930 -0.78039733 0.28917368 246.34842101
-0.75807382 -0.33013049 0.56243927 362.20292573
-0.34346106 -0.53103093 -0.77462290 653.67877730
Axis -0.86543769 0.50070495 0.01766816
Axis point 0.00000000 386.83809960 252.79416826
Rotation angle (degrees) 140.82108735
Shift along axis -20.29310612
> ui mousemode right zoom
> select subtract #7
4 models selected
> select subtract #9
2 models selected
> select subtract #11
Nothing selected
> hide #!7 models
> show #!7 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> hide #!11 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> volume #9 level 0.7158
> volume #9 level 0.7
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.4
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!20 models
> hide #!9 models
> show #!9 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #26 models
> hide #26 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #26 models
> hide #!20 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!50 models
> hide #!9 models
> hide #!50 models
> show #!50 models
> color #50 #b2b2b29c models
> volume #50 level 3
> volume #50 level 3.5
> volume #50 level 3.6
> volume #50 level 3.8
> volume #50 level 4.5
> show #!42 models
> hide #!50 models
> hide #!42 models
> show #!3 models
> select add #3
2 models selected
> color #3.1 gray
> ui tool show "Color Actions"
> color sel light blue
> color sel light sky blue
[Repeated 4 time(s)]
> color sel aquamarine
> color sel light sky blue
> select subtract #3
Nothing selected
> color #3 #87cefaa8 models
> color #3 #87cefa98 models
> color #3 #87cefaa7 models
> color #3 #87cefa99 models
> color #3 #87cefaa4 models
> color #3 #87cefaa3 models
> volume #3 level 0.35
> fitmap #26 inMap #3
Fit molecule fold_mrc1_323_337_tof1_model_0.cif (#26) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) using 10075 atoms
average map value = 0.2438, steps = 52
shifted from previous position = 0.293
rotated from previous position = 0.36 degrees
atoms outside contour = 7077, contour level = 0.35
Position of fold_mrc1_323_337_tof1_model_0.cif (#26) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.84462737 0.15456521 -0.51255653 282.60576624
0.06681694 0.91949322 0.38738573 335.32756599
0.53116861 -0.36144406 0.76630157 241.89923621
Axis -0.58158875 -0.81062320 -0.06815088
Axis point -335.92841792 0.00000000 139.55904352
Rotation angle (degrees) 40.07422511
Shift along axis -452.67028623
> volume #3 level 0.34
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting simple
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_J842_sharp_Mrc1_323-337_overview.png
> supersample 6 width 1800 transparentBackground true
> ui tool show "Side View"
> rock y 20 136
[Repeated 1 time(s)]
> volume #3 level 0.32
> volume #3 level 0.33
> rock y 20 136
> movie record supersample 3 size 1800, 2000
> rock y 20 136
> wait
> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MTC_J842_sharp_Mrc1_323-337_zoomed.mp4
Movie saved to
/Users/cvetkom/.../Replication_meeting_Cambridge_2024/CMGC4MTC_J842_sharp_Mrc1_323-337_zoomed.mp4
> hide #!3 models
> show #!50 models
> volume #50 level 5
> volume #50 level 4.6
> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MTC_J842_EMReady_Mrc1_323-337_zoomed.mp4
No frames have been recorded
> movie record supersample 3 size 1800, 2000
> rock y 20 136
> wait
> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MTC_J842_EMReady_Mrc1_323-337_zoomed.mp4
Movie saved to
/Users/cvetkom/.../Replication_meeting_Cambridge_2024/CMGC4MTC_J842_EMReady_Mrc1_323-337_zoomed.mp4
> fitmap #26 inMap #50
Fit molecule fold_mrc1_323_337_tof1_model_0.cif (#26) to map
J842_005_volume_map_EMReady.mrc (#50) using 10075 atoms
average map value = 2.525, steps = 52
shifted from previous position = 0.107
rotated from previous position = 0.359 degrees
atoms outside contour = 7517, contour level = 4.6
Position of fold_mrc1_323_337_tof1_model_0.cif (#26) relative to
J842_005_volume_map_EMReady.mrc (#50) coordinates:
Matrix rotation and translation
0.84685173 0.15716115 -0.50807727 282.58642125
0.06188411 0.91973007 0.38764280 335.21799844
0.52821633 -0.35971789 0.76914923 241.85487927
Axis -0.58331859 -0.80883211 -0.07436418
Axis point -334.58664400 0.00000000 135.85619956
Rotation angle (degrees) 39.83740038
Shift along axis -453.95833613
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_J842_EMReady_Mrc1_323-337_overview.png
> supersample 6 width 1800 transparentBackground true
> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
> select add #26
10075 atoms, 10266 bonds, 1253 residues, 1 model selected
> cartoon hide sel
> show sel target ab
> style sel ball
Changed 10075 atom styles
> color sel byhetero
> select clear
> cartoon #26,50
> hide #26,50 target a
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #26 models
> show #26 models
> hide #!50 models
> show #!11 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!9 models
> show #!7 models
> hide #!11 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!7 models
> hide #!7 models
> show #!7 models
> select add #7
2 models selected
> ui tool show "Color Actions"
> color sel turquoise
> color sel light sea green
[Repeated 1 time(s)]
> color #7 #b2ffff9d models
> color #7 #b2ffffd9 models
> color #7 #b2ffffb7 models
> color #7 #b2ffffa7 models
> color #7 #b2ffffa6 models
> select clear
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/Jacob_J117_Mrc1_323-337_overview.png
> supersample 6 width 1800 transparentBackground true
> volume #7 level 0.22
> volume #7 level 0.2
> volume #7 level 0.18
> volume #7 level 0.16
> volume #7 level 0.18
> volume #7 level 0.2
> volume #7 level 0.18
> rock y 20 136
> movie record supersample 3 size 1800, 2000
> rock y 20 136
> wait
> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/Jacob_J117_Mrc1_323-337_zoomed.mp4
Movie saved to
/Users/cvetkom/.../Replication_meeting_Cambridge_2024/Jacob_J117_Mrc1_323-337_zoomed.mp4
> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
\u2014\u2014\u2014 End of log from Mon Oct 7 10:20:32 2024 \u2014\u2014\u2014
opened ChimeraX session
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
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: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
OS Loader Version: 580.140.1~8
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 11 days, 12 hours, 23 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: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
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: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2415:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 7MT016923MAL
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
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 (2)
comment:1 by , 13 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 on Mac waking from sleep |
comment:2 by , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
This crash is caused by a bug in the Mac Qt window toolkit used by ChimeraX and sometimes happens when disconnecting or connecting an external display or waking from sleep. We don't have a fix for this. We are using a newer version of Qt (6.7 instead of 6.6) in the ChimeraX daily build which may crash less often. You could try that. Best to save your work before switching displays or sleeping the computer.
We are looking for a way to work around this crash but have not yet come up with anything.
Mac Qt 6.6 crash in displayConfigFinalizedProc.