![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Last modified 13 months ago
#16079 closed defect
Crash on Mac waking from sleep — 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-14.6.1-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 (1)
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 |
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