![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 19 months ago
Closed 19 months ago
#15094 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.4.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 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 0x00007ff84c382100 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2000 in save_state
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 219 in take_snapshot
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1417 in take_snapshot
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 296 in process
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 273 in discovery
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 636 in save
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 912 in save
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95 in save
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, chimerax.segment._segment, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite (total: 62)
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{
"uptime" : 430000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 6202,
"osVersion" : {
"train" : "macOS 14.4.1",
"build" : "23E224",
"releaseType" : "User"
},
"captureTime" : "2024-05-02 19:42:56.1369 +0100",
"codeSigningMonitor" : 0,
"incident" : "58C8F883-0041-404C-A67C-06DD1B66BCF2",
"pid" : 88668,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-04-25 16:59:13.7822 +0100",
"procStartAbsTime" : 181062197525871,
"procExitAbsTime" : 430489690089495,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","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" : 29905,
"bridgeVersion" : {"build":"21P4222","train":"8.4"},
"sleepWakeUUID" : "C2C097EB-C33B-4572-8A72-187BD68C5E4C",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 4453363543\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10970f000-109713000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":88668},
"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" : "0xa9 is not in any region. Bytes before following region: 4453363543\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10970f000-109713000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
"name" : "math.cpython-311-darwin.so"
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"base" : 4474163200,
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"CFBundleIdentifier" : "org.python.python",
"size" : 4079616,
"uuid" : "24670b23-d78a-3eaa-bca8-22faf877f190",
"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
"name" : "Python",
"CFBundleVersion" : "3.11.2"
},
{
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"arch" : "x86_64",
"base" : 4453363712,
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"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
"uuid" : "194a3167-3db5-3029-8d22-1d742b826bb9",
"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.7.1.0"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703277580288,
"size" : 241656,
"uuid" : "50c9fa25-ed67-32a5-88f4-92de497b0ec1",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703277821952,
"size" : 49144,
"uuid" : "5a006814-83f4-3c80-ab1f-528cdd08c0ff",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703276429312,
"size" : 557048,
"uuid" : "6d02e870-f215-36ed-bf7d-435f66996bfe",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703278022656,
"size" : 45048,
"uuid" : "56a3704c-42f6-3fb2-b45c-5371848c9400",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
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{
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"base" : 140703571939328,
"size" : 24536,
"uuid" : "2c4eda02-ddfa-38cd-9149-bf38fb19668d",
"path" : "\/usr\/lib\/libffi.dylib",
"name" : "libffi.dylib"
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{
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"size" : 4829165,
"uuid" : "2780e326-c5fd-3a12-b906-b9449288005c",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "2420"
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{
"source" : "P",
"arch" : "x86_64",
"base" : 140703456882688,
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"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 2732028,
"uuid" : "5d06c99c-ac78-3bc4-8908-45a394e8180b",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
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{
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"name" : "AppKit",
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{
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"size" : 592736,
"uuid" : "899f1e34-b624-3162-8003-04daa6829461",
"path" : "\/usr\/lib\/dyld",
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}
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"sharedCache" : {
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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=10.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=10.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 492K 71 \nCG raster data 8K 1 \nColorSync 252K 30 \nCoreAnimation 2916K 209 \nCoreGraphics 24K 4 \nCoreUI image data 5184K 61 \nFoundation 32K 2 \nKernel Alloc Once 8K 1 \nMALLOC 9.0G 2251 \nMALLOC guard page 64K 16 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 104K 5 \nOpenGL GLSL 384K 4 \nSTACK GUARD 84K 21 \nStack 138.7M 22 \nStack Guard 56.0M 1 \nVM_ALLOCATE 1.0G 783 \nVM_ALLOCATE (reserved) 160.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 57.8M 848 \n__DATA_CONST 63.4M 467 \n__DATA_DIRTY 1853K 237 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 212.6M 157 \n__OBJC_RO 71.7M 1 \n__OBJC_RW 2196K 2 \n__TEXT 1.1G 854 \ndyld private memory 420K 6 \nmapped file 264.9M 80 \nshared memory 3516K 29 \n=========== ======= ======= \nTOTAL 12.1G 6173 \nTOTAL, minus reserved VM space 11.9G 6173 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "616b2338cfa78a248bf28f17d2615b5b6f44c640",
"trialInfo" : {
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{
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"factorPackIds" : {
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{
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"factorPackIds" : {
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}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P388_J125_003_volume_map.mrc
Opened cryosparc_P388_J125_003_volume_map.mrc as #1, grid size 180,180,180,
pixel 2.85, shown at level 0.612, step 1, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P388_J181_002_volume_map.mrc
Opened cryosparc_P388_J181_002_volume_map.mrc as #2, grid size 180,180,180,
pixel 2.85, shown at level 0.614, step 1, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P388_J182_002_volume_map.mrc
Opened cryosparc_P388_J182_002_volume_map.mrc as #3, grid size 180,180,180,
pixel 2.85, shown at level 0.611, step 1, values float32
> hide #!2 models
> hide #!3 models
> volume #1 level 0.5077
> volume #1 level 0.4
> volume #1 level 0.45
> volume #2 level 0.45
> volume #1 level 0.4
> volume #1 level 0.45
> volume #2 level 0.4
> volume #3 level 0.4
> volume #3 level 0.45
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P310_J405_007_volume_map.mrc
Opened cryosparc_P310_J405_007_volume_map.mrc as #4, grid size 640,640,640,
pixel 0.95, shown at level 0.114, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P310_J408_007_volume_map.mrc
Opened cryosparc_P310_J408_007_volume_map.mrc as #5, grid size 640,640,640,
pixel 0.95, shown at level 0.111, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P310_J413_009_volume_map.mrc
Opened cryosparc_P310_J413_009_volume_map.mrc as #6, grid size 640,640,640,
pixel 0.95, shown at level 0.114, step 4, values float32
> hide #!3 models
> hide #!5 models
> hide #!6 models
> volume #4 step 1
> volume #4 level 0.1
> volume #4 level 0.12
> volume #5 step 1
> volume #5 level 0.12
> volume #4 level 0.1
> volume #4 level 0.12
> volume #5 level 0.1
> volume #6 step 1
> volume #6 level 0.12
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J408_008_volume_map.mrc
Opened cryosparc_P17_J408_008_volume_map.mrc as #7, grid size 294,294,294,
pixel 1.9, shown at level 0.354, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map.mrc
Opened cryosparc_P17_J368_007_volume_map.mrc as #8, grid size 294,294,294,
pixel 1.9, shown at level 0.37, step 2, values float32
> hide #!8 models
> hide #!7 models
> show #!8 models
> volume #8 step 1
> volume #8 level 0.4191
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J408_008_volume_map.mrc
Opened cryosparc_P17_J408_008_volume_map.mrc as #9, grid size 294,294,294,
pixel 1.9, shown at level 0.354, step 2, values float32
> close #9
> show #!7 models
> hide #!7 models
> volume #8 level 0.4
> volume #7 step 1
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J392_002_volume_map.mrc
Opened cryosparc_P17_J392_002_volume_map.mrc as #9, grid size 294,294,294,
pixel 1.9, shown at level 0.207, step 2, values float32
> hide #!7 models
> volume #9 step 1
> volume #9 level 0.3788
> volume #9 level 0.4816
> hide #!9 models
> show #!9 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J411_002_volume_map.mrc
Opened cryosparc_P17_J411_002_volume_map.mrc as #10, grid size 294,294,294,
pixel 1.9, shown at level 0.214, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J412_002_volume_map.mrc
Opened cryosparc_P17_J412_002_volume_map.mrc as #11, grid size 294,294,294,
pixel 1.9, shown at level 0.289, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J413_002_volume_map.mrc
Opened cryosparc_P17_J413_002_volume_map.mrc as #12, grid size 294,294,294,
pixel 1.9, shown at level 0.214, step 2, values float32
> volume #10 step 1
> volume #11 step 1
> volume #12 step 1
> volume #10 level 0.5137
> volume #10 level 0.4337
> volume #12 level 0.4965
> volume #12 level 0.4561
> hide #!9 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J401_007_volume_map.mrc
Opened cryosparc_P17_J401_007_volume_map.mrc as #13, grid size 294,294,294,
pixel 1.9, shown at level 0.357, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J403_008_volume_map.mrc
Opened cryosparc_P17_J403_008_volume_map.mrc as #14, grid size 294,294,294,
pixel 1.9, shown at level 0.357, step 2, values float32
> show #!8 models
> hide #!8 models
> volume #13 step 1
> volume #14 step 1
> volume #13 level 0.35
> volume #13 level 0.3
> volume #14 level 0.3
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J399_007_volume_map.mrc
Opened cryosparc_P17_J399_007_volume_map.mrc as #15, grid size 294,294,294,
pixel 1.9, shown at level 0.357, step 2, values float32
> hide #!14 models
> volume #15 step 1
> volume #15 level 0.2842
> volume #15 level 0.2923
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P388_J217_006_volume_map.mrc
Opened cryosparc_P388_J217_006_volume_map.mrc as #16, grid size 294,294,294,
pixel 1.9, shown at level 0.368, step 2, values float32
> hide #!15 models
> volume #16 step 1
> volume #16 level 0.3641
> show #!8 models
> volume #16 level 0.4
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> open /Users/cvetkom/Downloads/cs_P17_J486_009_volume_map.mrc
Opened cs_P17_J486_009_volume_map.mrc as #17, grid size 588,588,588, pixel
0.85, shown at level 0.169, step 4, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J486_005_volume_map.mrc
Opened cryosparc_P17_J486_005_volume_map.mrc as #18, grid size 588,588,588,
pixel 0.85, shown at level 0.169, step 4, values float32
> hide #!8 models
> hide #!16 models
> volume #18 step 1
> volume #17 step 1
> volume #17 level 0.1385
> volume #17 level 0.1646
> volume #17 level 0.1556
> ui tool show "Map Coordinates"
> save /Users/cvetkom/Downloads/cs_P17_J486_009_volume_map.mrc models #17
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> close #18
> open /Users/cvetkom/Downloads/cryosparc_P17_J491_011_volume_map.mrc
Opened cryosparc_P17_J491_011_volume_map.mrc as #18, grid size 588,588,588,
pixel 0.85, shown at level 0.166, step 4, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J492_012_volume_map.mrc
Opened cryosparc_P17_J492_012_volume_map.mrc as #19, grid size 588,588,588,
pixel 0.85, shown at level 0.166, step 4, values float32
> volume #18 step 1
> volume #18 level 0.139
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/initial_model_job502.mrc
Opened initial_model_job502.mrc as #20, grid size 588,588,588, pixel 0.95,
shown at level 0.00493, step 4, values float32
> hide #!18 models
> volume #20 step 1
> volume #20 level 0.005154
> volume #20 level 0.00473
> close #20
> show #!8 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J429_map_sharp.mrc
Opened cryosparc_P17_J429_map_sharp.mrc as #20, grid size 294,294,294, pixel
1.9, shown at level 0.000158, step 2, values float32
> hide #!8 models
> volume #20 step 1
> volume #20 level 0.123
> volume #20 level 0.1118
> hide #!20 models
> show #!18 models
> show #!19 models
> hide #!18 models
> volume #19 step 1
> volume #19 level 0.1482
> show #!18 models
> hide #!18 models
> volume #18 level 0.14
> volume #19 level 0.14
> volume #18 level 0.135
> volume #18 level 0.13
> volume #19 level 0.13
> open /Users/cvetkom/Downloads/cryosparc_P17_J489_013_volume_map.mrc
Opened cryosparc_P17_J489_013_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.85, shown at level 0.165, step 4, values float32
> hide #!21 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> hide #!19 models
> show #!21 models
> volume #21 step 1
> volume #21 level 0.14
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!20 models
> close #18-21
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J491_011_volume_map.mrc
Opened cryosparc_P17_J491_011_volume_map.mrc as #18, grid size 588,588,588,
pixel 0.85, shown at level 0.166, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J489_013_volume_map.mrc
Opened cryosparc_P17_J489_013_volume_map.mrc as #19, grid size 588,588,588,
pixel 0.85, shown at level 0.165, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J492_012_volume_map.mrc
Opened cryosparc_P17_J492_012_volume_map.mrc as #20, grid size 588,588,588,
pixel 0.85, shown at level 0.166, step 4, values float32
> volume #18 step 2
> volume #18 step 1
> volume #19 step 1
> volume #20 step 1
> volume #18 level 0.13
> volume #19 level 0.13
> volume #20 level 0.13
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!18 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/postprocess_masked_job511.mrc
Opened postprocess_masked_job511.mrc as #21, grid size 588,588,588, pixel
0.95, shown at level 0.00498, step 4, values float32
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #!21 models
> show #!18 models
> select add #21
2 models selected
> show #!21 models
> ui mousemode right "rotate selected models"
> view matrix models
> #21,-0.55287,0.83087,-0.063182,166.89,-0.5876,-0.33499,0.73655,276.93,0.59081,0.44434,0.67343,-162.06
> ui mousemode right "translate selected models"
> view matrix models
> #21,-0.55287,0.83087,-0.063182,188.59,-0.5876,-0.33499,0.73655,291.89,0.59081,0.44434,0.67343,-218.35
> view matrix models
> #21,-0.55287,0.83087,-0.063182,185.39,-0.5876,-0.33499,0.73655,288.19,0.59081,0.44434,0.67343,-212.32
> ui mousemode right zoom
> select subtract #21
Nothing selected
> ui tool show "Fit in Map"
> fitmap #21 inMap #18
Fit map postprocess_masked_job511.mrc in map
cryosparc_P17_J491_011_volume_map.mrc using 31756 points
correlation = 0.8968, correlation about mean = 0.2434, overlap = 42.45
steps = 180, shift = 7, angle = 10.3 degrees
Position of postprocess_masked_job511.mrc (#21) relative to
cryosparc_P17_J491_011_volume_map.mrc (#18) coordinates:
Matrix rotation and translation
-0.51920954 0.84749667 0.11032156 127.58974848
-0.54899809 -0.42966309 0.71693147 315.34926138
0.65499813 0.31167134 0.68835923 -196.84626713
Axis -0.26099112 -0.35077655 -0.89935502
Axis point 178.92637046 159.99291122 0.00000000
Rotation angle (degrees) 129.06906427
Shift along axis 33.11776092
> hide #!18 models
> volume #21 step 1
> volume #21 level 0.005527
> hide #!21 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job505_run_class001.mrc
Opened Ref3D_job505_run_class001.mrc as #22, grid size 588,588,588, pixel
0.95, shown at level 0.005, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job507_run_class001.mrc
Opened Ref3D_job507_run_class001.mrc as #23, grid size 588,588,588, pixel
0.95, shown at level 0.00501, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job505_run_class001.mrc
Opened Ref3D_job505_run_class001.mrc as #24, grid size 588,588,588, pixel
0.95, shown at level 0.005, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job507_run_class001.mrc
Opened Ref3D_job507_run_class001.mrc as #25, grid size 588,588,588, pixel
0.95, shown at level 0.00501, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job508_run_class001.mrc
Opened Ref3D_job508_run_class001.mrc as #26, grid size 588,588,588, pixel
0.95, shown at level 0.00502, step 4, values float32
> hide #!26 models
> hide #!25 models
> hide #!24 models
> hide #!23 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> close #22-26
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job505_run_class001.mrc
Opened Ref3D_job505_run_class001.mrc as #22, grid size 588,588,588, pixel
0.95, shown at level 0.005, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001.mrc
Opened Ref3D_job506_run_class001.mrc as #23, grid size 588,588,588, pixel
0.95, shown at level 0.00502, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job507_run_class001.mrc
Opened Ref3D_job507_run_class001.mrc as #24, grid size 588,588,588, pixel
0.95, shown at level 0.00501, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job508_run_class001.mrc
Opened Ref3D_job508_run_class001.mrc as #25, grid size 588,588,588, pixel
0.95, shown at level 0.00502, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job509_run_class001.mrc
Opened Ref3D_job509_run_class001.mrc as #26, grid size 588,588,588, pixel
0.95, shown at level 0.005, step 4, values float32
> hide #!23 models
> hide #!24 models
> hide #!25 models
> hide #!26 models
> volume #22 step 1
> volume #22 level 0.004523
> volume #22 level 0.004
> volume #23 step 1
> volume #23 level 0.004
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/postprocess_masked_job514.mrc
Opened postprocess_masked_job514.mrc as #27, grid size 588,588,588, pixel
0.95, shown at level 0.00499, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/postprocess_masked_job515.mrc
Opened postprocess_masked_job515.mrc as #28, grid size 588,588,588, pixel
0.95, shown at level 0.00499, step 4, values float32
> hide #!27 models
> hide #!28 models
> hide #!22 models
> hide #!23 models
> show #!24 models
> show #!22 models
> hide #!22 models
> volume #24 step 1
> volume #24 level 0.004649
> show #!25 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!26 models
> hide #!25 models
> hide #!26 models
> show #!22 models
> hide #!22 models
> show #!23 models
> hide #!23 models
> show #!24 models
> show #!25 models
> volume #25 step 1
> volume #24 level 0.0045
> volume #24 level 0.0046
> hide #!24 models
> volume #25 level 0.0046
> show #!24 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> hide #!24 models
> show #!27 models
> show #!21 models
> hide #!21 models
> volume #27 step 1
> volume #27 level 0.00489
> volume #28 step 1
> show #!27 models
> hide #!28 models
> show #!28 models
> hide #!27 models
> hide #!28 models
> show #!23 models
> volume #23 level 0.0035
> volume #23 level 0.0045
> ui tool show "Segment Map"
Segmenting Ref3D_job506_run_class001.mrc, density threshold 0.004500
Only showing 60 of 67 regions.
Showing 60 of 67 region surfaces
277 watershed regions, grouped to 67 regions
Showing Ref3D_job506_run_class001.seg - 67 regions, 60 surfaces
> select #29.26
1 model selected
> select add #29.13
2 models selected
> select add #29.6
3 models selected
> select add #29.1
4 models selected
> select add #29.38
5 models selected
Grouped 5 regions
> select add #29.11
2 models selected
> select add #29.31
3 models selected
Grouped 3 regions
> 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
Only showing 60 of 61 regions.
Showing 60 of 61 region surfaces
Only showing 60 of 61 regions.
Showing 60 of 61 region surfaces
Opened Ref3D_job506_run_class001_imasked as #30, grid size 588,588,588, pixel
0.95, shown at step 1, values float32
> hide #!23 models
> hide #!29 models
> show #!29 models
> hide #!30 models
> show #!30 models
> hide #!29 models
> show #!29 models
> hide #!30 models
Only showing 60 of 61 regions.
Showing 60 of 61 region surfaces
> show #!30 models
> hide #!29 models
> show #!29 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> hide #!29 models
> select add #29
61 models selected
> select subtract #29
Nothing selected
> show #!30 models
> ui tool show "Map Eraser"
> volume erase #30 center 322.28,330.54,256.92 radius 31.628
> hide #!30 models
> show #!30 models
> save
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001_NCP.mrc
> models #30
> volume #30 level 0.004
> volume #30 level 0.0045
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J288_006_volume_map.mrc
Opened cryosparc_P17_J288_006_volume_map.mrc as #31, grid size 294,294,294,
pixel 1.9, shown at level 0.258, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J288_006_volume_map_sharp.mrc
Opened cryosparc_P17_J288_006_volume_map_sharp.mrc as #32, grid size
294,294,294, pixel 1.9, shown at level 0.251, step 2, values float32
> volume #32 step 1
> volume #32 level 0.5717
> volume #31 step 1
> volume #31 level 0.6543
> open 4C93 fromDatabase pdb format mmcif
Summary of feedback from opening 4C93 fetched from pdb
---
note | Fetching compressed mmCIF 4c93 from
http://files.rcsb.org/download/4c93.cif
4c93 title:
Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Pol
alpha. [more info...]
Chain information for 4c93 #33
---
Chain | Description | UniProt
A B C | DNA POLYMERASE ALPHA-BINDING PROTEIN | CTF4_YEAST 471-927
D E | DNA POLYMERASE ALPHA CATALYTIC SUBUNIT A | DPOA_YEAST 137-149
> select add #33
9593 atoms, 9682 bonds, 4 pseudobonds, 1331 residues, 2 models selected
> hide (#!33 & sel) target a
> cartoon (#!33 & sel)
> select subtract #33
Nothing selected
> select add #33
9593 atoms, 9682 bonds, 4 pseudobonds, 1331 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #33,1,0,0,277.71,0,1,0,277.7,0,0,1,412.4
> ui mousemode right "rotate selected models"
> view matrix models
> #33,0.85071,0.51833,-0.087371,264.2,-0.5256,0.83678,-0.15343,265.2,-0.0064157,0.17644,0.98429,409.11
> ui mousemode right "translate selected models"
> view matrix models
> #33,0.85071,0.51833,-0.087371,206.06,-0.5256,0.83678,-0.15343,295.57,-0.0064157,0.17644,0.98429,358
> ui mousemode right "rotate selected models"
> view matrix models
> #33,0.85087,0.50579,-0.1421,203.77,-0.52472,0.80474,-0.2776,290.42,-0.026051,0.31077,0.95013,354.26
> view matrix models
> #33,0.74237,0.64892,-0.16668,199.01,-0.66761,0.73743,-0.10249,297.15,0.056405,0.18736,0.98067,358.62
> view matrix models
> #33,0.61879,0.74677,-0.24378,192.29,-0.78542,0.59391,-0.17432,294.16,0.014612,0.29934,0.95404,355.21
> view matrix models
> #33,0.9983,-0.034334,-0.047129,217.9,0.018839,0.95483,-0.29655,295.6,0.055182,0.29515,0.95386,355.87
> view matrix models
> #33,0.9358,0.25827,-0.23996,204.12,-0.34616,0.80203,-0.48675,283.69,0.066739,0.53856,0.83994,347.46
> view matrix models
> #33,0.4441,-0.059162,-0.89402,171.67,-0.18738,0.96962,-0.15725,298.59,0.87616,0.23736,0.41953,344.85
> view matrix models
> #33,0.35501,0.67532,-0.64646,171.15,-0.35267,0.73716,0.57639,332.55,0.86579,0.023365,0.49987,351.35
> ui mousemode right "translate selected models"
> view matrix models
> #33,0.35501,0.67532,-0.64646,241,-0.35267,0.73716,0.57639,296.24,0.86579,0.023365,0.49987,410.46
> fitmap #33 inMap #31
Fit molecule 4c93 (#33) to map cryosparc_P17_J288_006_volume_map.mrc (#31)
using 9593 atoms
average map value = 0.5941, steps = 164
shifted from previous position = 8.43
rotated from previous position = 36.7 degrees
atoms outside contour = 5817, contour level = 0.65427
Position of 4c93 (#33) relative to cryosparc_P17_J288_006_volume_map.mrc (#31)
coordinates:
Matrix rotation and translation
-0.11641260 0.77432829 -0.62198377 234.06062084
-0.72447465 0.36217880 0.58648359 303.04623599
0.67940017 0.51888555 0.51881904 403.24027766
Axis -0.03403562 -0.65524703 -0.75464753
Axis point 89.28765412 -151.08833550 0.00000000
Rotation angle (degrees) 96.75980732
Shift along axis -510.84082774
> fitmap #33 inMap #31
Fit molecule 4c93 (#33) to map cryosparc_P17_J288_006_volume_map.mrc (#31)
using 9593 atoms
average map value = 0.5941, steps = 40
shifted from previous position = 0.00237
rotated from previous position = 0.00559 degrees
atoms outside contour = 5819, contour level = 0.65427
Position of 4c93 (#33) relative to cryosparc_P17_J288_006_volume_map.mrc (#31)
coordinates:
Matrix rotation and translation
-0.11649075 0.77431865 -0.62198114 234.06168000
-0.72442922 0.36216631 0.58654742 303.05097408
0.67943522 0.51890866 0.51875003 403.23724883
Axis -0.03405645 -0.65526960 -0.75462700
Axis point 89.27779010 -151.08286692 0.00000000
Rotation angle (degrees) 96.76441303
Shift along axis -510.84511620
> open 6SKL fromDatabase pdb format mmcif
6skl title:
Cryo-EM structure of the CMG Fork Protection Complex at a replication fork -
Conformation 1 [more info...]
Chain information for 6skl #34
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
A | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208
B | DNA replication complex GINS protein PSF2 | PSF2_YEAST 1-213
C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194
D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294
E | Cell division control protein 45 | CDC45_YEAST 1-650
F G H | DNA polymerase alpha-binding protein | CTF4_YEAST 1-927
I | DNA fork, leading-strand template |
J | DNA fork, lagging-strand template |
X | Topoisomerase 1-associated factor 1 | TOF1_YEAST 1-1238
Y | Chromosome segregation in meiosis protein 3 | CSM3_YEAST 1-317
Non-standard residues in 6skl #34
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
ZN — zinc ion
> select subtract #33
Nothing selected
> select add #34
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> hide (#!34 & sel) target a
> cartoon (#!34 & sel)
> view matrix models #34,1,0,0,-105.11,0,1,0,63.093,0,0,1,60.805
> ui mousemode right "rotate selected models"
> view matrix models
> #34,0.89661,0.16888,-0.40936,-42.927,-0.024986,0.94224,0.33399,18.768,0.44212,-0.28923,0.84904,55.571
> view matrix models
> #34,0.18469,0.42907,0.88419,-184.99,-0.91736,-0.24753,0.31174,429.58,0.35262,-0.86869,0.34789,275.52
> view matrix models
> #34,-0.74581,-0.65341,0.12973,345.25,-0.31799,0.17808,-0.93122,453.04,0.58536,-0.73576,-0.34059,328.08
> view matrix models
> #34,-0.74688,-0.65706,0.10221,351.14,-0.29136,0.1852,-0.93852,447.68,0.59773,-0.73074,-0.32976,322.69
> view matrix models
> #34,-0.79277,-0.59486,-0.13289,390.85,-0.15343,0.40576,-0.90101,370.97,0.58989,-0.6939,-0.41295,332.21
> view matrix models
> #34,-0.80975,-0.58676,0.0025381,368.19,-0.2818,0.38509,-0.8788,396.52,0.51467,-0.71233,-0.47718,362.38
> volume #31 level 0.5196
> volume #31 flipNormals
Missing "flipNormals" keyword's argument
> volume flip #31
Opened cryosparc_P17_J288_006_volume_map.mrc z flip as #35, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
> select subtract #34
Nothing selected
> select add #35
2 models selected
> view matrix models
> #35,0.78895,-0.57985,-0.20332,272.36,0.063773,-0.25184,0.96567,82.546,-0.61114,-0.77483,-0.16171,684.21
> view matrix models
> #35,0.28797,-0.87982,-0.37814,542.26,-0.92038,-0.36335,0.14448,602.17,-0.26451,0.30642,-0.91441,478.11
> view matrix models
> #35,0.19939,-0.94065,-0.27463,557.88,-0.84145,-0.30798,0.44396,488.1,-0.50219,0.14257,-0.85292,575.32
> view matrix models
> #35,0.056907,-0.98144,-0.18311,586.32,-0.81292,-0.15202,0.56218,406.67,-0.57958,0.11686,-0.80649,592.58
> view matrix models
> #35,-0.4142,-0.82661,-0.38098,727.63,-0.85036,0.50069,-0.16185,421.02,0.32454,0.25694,-0.91031,323.5
> view matrix models
> #35,-0.05329,-0.9466,-0.31798,642.33,-0.99846,0.055466,0.0022138,544.59,0.015542,0.31761,-0.94809,404.07
> view matrix models
> #35,-0.12565,-0.99206,-0.005759,595.9,-0.98907,0.12572,-0.077001,542.65,0.077114,-0.003979,-0.99701,488.13
> view matrix models
> #35,-0.028832,-0.99711,0.070342,550.41,-0.98983,0.038289,0.13704,512.53,-0.13933,-0.065675,-0.98807,564.4
> ui mousemode right "translate selected models"
> view matrix models
> #35,-0.028832,-0.99711,0.070342,558.82,-0.98983,0.038289,0.13704,502.05,-0.13933,-0.065675,-0.98807,609.85
> select subtract #35
Nothing selected
> fitmap #33 inMap #35
Fit molecule 4c93 (#33) to map cryosparc_P17_J288_006_volume_map.mrc z flip
(#35) using 9593 atoms
average map value = 0.748, steps = 156
shifted from previous position = 23.9
rotated from previous position = 52.9 degrees
atoms outside contour = 2729, contour level = 0.51963
Position of 4c93 (#33) relative to cryosparc_P17_J288_006_volume_map.mrc z
flip (#35) coordinates:
Matrix rotation and translation
0.31609082 -0.94869655 0.00783922 290.47366164
-0.57784462 -0.18596222 0.79467833 322.70855084
-0.75245079 -0.25572037 -0.60698014 144.58037287
Axis -0.77884069 0.56373337 0.27497613
Axis point 0.00000000 302.79412564 42.56571290
Rotation angle (degrees) 137.59748776
Shift along axis -4.55497724
> volume #35 color #ffffb280
> volume #35 color #ffffb29a
> ui tool show Matchmaker
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x600001698de0, name="DELL U2415") screenTo: QScreen(0x0) wdgScreen:
QScreen(0x6000016ad580, name="Built-in Retina Display") orgWdgScreen
QScreen(0x6000016ad580, name="Built-in Retina Display")
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x600001698de0, name="DELL U2415") screenTo: QScreen(0x0) wdgScreen:
QScreen(0x600001698de0, name="DELL U2415") orgWdgScreen
QScreen(0x6000016ad580, name="Built-in Retina Display")
> matchmaker #33/A to #34/G 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 6skl, chain G (#34) with 4c93, chain A (#33), sequence alignment
score = 2250.7
RMSD between 395 pruned atom pairs is 0.975 angstroms; (across all 421 pairs:
1.137)
> select add #33
9593 atoms, 9682 bonds, 4 pseudobonds, 1331 residues, 2 models selected
> select add #34
127813 atoms, 129087 bonds, 134 pseudobonds, 8652 residues, 6 models selected
> view matrix models
> #33,0.20694,0.33166,-0.92042,219.01,-0.50314,0.84292,0.19061,241.4,0.83906,0.42366,0.3413,390.93,#34,-0.80975,-0.58676,0.0025381,554.75,-0.2818,0.38509,-0.8788,387.59,0.51467,-0.71233,-0.47718,400.46
> view matrix models
> #33,0.20694,0.33166,-0.92042,219.86,-0.50314,0.84292,0.19061,243.18,0.83906,0.42366,0.3413,387.91,#34,-0.80975,-0.58676,0.0025381,555.6,-0.2818,0.38509,-0.8788,389.37,0.51467,-0.71233,-0.47718,397.44
> select subtract #34
9593 atoms, 9682 bonds, 4 pseudobonds, 1331 residues, 2 models selected
> select subtract #33
Nothing selected
> fitmap #34 inMap #35
Fit molecule 6skl (#34) to map cryosparc_P17_J288_006_volume_map.mrc z flip
(#35) using 118220 atoms
average map value = 0.6269, steps = 156
shifted from previous position = 29.5
rotated from previous position = 20.7 degrees
atoms outside contour = 51602, contour level = 0.51963
Position of 6skl (#34) relative to cryosparc_P17_J288_006_volume_map.mrc z
flip (#35) coordinates:
Matrix rotation and translation
0.46209162 -0.10482145 0.88061558 50.05829992
0.51912918 0.83705154 -0.17277039 61.05331656
-0.71901059 0.53698899 0.44121038 233.04243695
Axis 0.38201772 0.86097564 0.33583240
Axis point 167.96409560 0.00000000 110.80343384
Rotation angle (degrees) 68.27348026
Shift along axis 149.95177710
> matchmaker #33/A to #34/G 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 6skl, chain G (#34) with 4c93, chain A (#33), sequence alignment
score = 2250.7
RMSD between 395 pruned atom pairs is 0.975 angstroms; (across all 421 pairs:
1.137)
> ui mousemode right zoom
> hide #!35 models
> open "/Users/cvetkom/Downloads/ranked_0 (1).pdb"
Chain information for ranked_0 (1).pdb #36
---
Chain | Description
A | No description available
B C D | No description available
> matchmaker #36/B to #34/H 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 6skl, chain H (#34) with ranked_0 (1).pdb, chain B (#36), sequence
alignment score = 2258.6
RMSD between 415 pruned atom pairs is 0.607 angstroms; (across all 425 pairs:
0.788)
> show #!35 models
> select #36/B
7269 atoms, 7356 bonds, 457 residues, 1 model selected
> select clear
> select #36/A
277 atoms, 276 bonds, 17 residues, 1 model selected
> color sel red
> select clear
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> open 8B9D fromDatabase pdb format mmcif
files.rcsb.org failed to respond
> open 8B9D fromDatabase pdb format mmcif
files.rcsb.org failed to respond
> open 8B9D fromDatabase pdb format mmcif
Summary of feedback from opening 8B9D fetched from pdb
---
warnings | Atom H1 is not in the residue template for MET /C:1
Atom H1 is not in the residue template for MET /D:1
Atom H1 is not in the residue template for MET /E:1
Atom H1 is not in the residue template for MET /P:1
note | Fetching compressed mmCIF 8b9d from
http://files.rcsb.org/download/8b9d.cif
8b9d title:
Human replisome bound by Pol α [more info...]
Chain information for 8b9d #37
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904
3 | DNA replication licensing factor MCM3 | MCM3_HUMAN 1-808
4 | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863
5 | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734
6 | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821
7 | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719
A | DNA polymerase alpha subunit B | DPOA2_HUMAN 1-598
B | DNA polymerase alpha catalytic subunit | DPOLA_HUMAN 1-1462
C | Cell division control protein 45 homolog | CDC45_HUMAN 1-134 135-566
D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN 1-196
E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN 1-185
F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN 1-216
G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN 1-223
H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN 1-1129
K | Protein timeless homolog | TIM_HUMAN 1-1208
L | TIMELESS-interacting protein | TIPIN_HUMAN 1-301
M | Leading strand DNA |
N | DNA Molecule |
O | DNA primase small subunit | PRI1_HUMAN 1-420
P | DNA primase large subunit | PRI2_HUMAN 1-509
Q | Claspin | CLSPN_HUMAN 1-1339
Non-standard residues in 8b9d #37
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
ZN — zinc ion
> hide #33-37 target a
> cartoon #33-37
> hide #!37 models
> hide #!35 models
> show #!35 models
> save
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J288_006_volume_map_zflip.mrc
> models #35
> hide #36 models
> hide #!35 models
> hide #!34 models
> hide #!33 models
> show #!31 models
> show #!32 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> volume #32 level 0.7272
> volume flip #32
Opened cryosparc_P17_J288_006_volume_map_sharp.mrc z flip as #38, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
> volume #32 level 0.7618
> volume #38 level 0.7618
> volume #38 level 0.7272
> save
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J288_006_volume_map_sharp_zflip.mrc
> models #38
> hide #!38 models
> show #!34 models
> select #34/E
9129 atoms, 9213 bonds, 4 pseudobonds, 564 residues, 2 models selected
> hide #!34 models
> select add #34
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> select subtract #34
Nothing selected
> show #!31 models
> hide #!31 models
> show #!19 models
> show #!27 models
> hide #!27 models
> hide #!19 models
> open
> /Users/cvetkom/Documents/AlphaFold/yMrc1_H3H4_tetr/yMrc1_H3H4_tetr_ranked_0.pdb
Chain information for yMrc1_H3H4_tetr_ranked_0.pdb #39
---
Chain | Description
A | No description available
B C | No description available
D E | No description available
> select add #39
25142 atoms, 25299 bonds, 1574 residues, 1 model selected
> view sel
> select subtract #39
Nothing selected
> hide #39 models
> show #39 models
> hide #39 target a
> cartoon #39
> ui tool show "Show Sequence Viewer"
> sequence chain #39/A
Alignment identifier is 39/A
> select #39/A:657
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #39/A:657-660
63 atoms, 62 bonds, 4 residues, 1 model selected
> color sel red
> select #39/A:678
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #39/A:678-712
621 atoms, 621 bonds, 35 residues, 1 model selected
> select #39/A:746
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #39/A:746-751
96 atoms, 95 bonds, 6 residues, 1 model selected
> select #39/A:612
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #39/A:612-616
83 atoms, 83 bonds, 5 residues, 1 model selected
> select #39/A:746-747
23 atoms, 22 bonds, 2 residues, 1 model selected
> select #39/A:746-751
96 atoms, 95 bonds, 6 residues, 1 model selected
> select #39/A:657
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #39/A:657-660
63 atoms, 62 bonds, 4 residues, 1 model selected
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/mask_job518.mrc
Opened mask_job518.mrc as #40, grid size 588,588,588, pixel 0.95, shown at
level 5e-05, step 4, values float32
> select add #39
25142 atoms, 25299 bonds, 1574 residues, 1 model selected
> select subtract #39
Nothing selected
> hide #39 models
> hide #!40 models
> show #!30 models
> show #!40 models
> hide #!40 models
> show #!40 models
> volume #40 step 1
> volume #40 level 1
> volume #40 color #ffb2b280
> volume #40 level 1
> show #!29 models
> hide #!29 models
> show #!23 models
> hide #!30 models
> hide #!23 models
> hide #!40 models
> show #!30 models
> volume #30 level 0.005
> volume #30 level 0.004
> volume #30 level 0.0045
> volume #30 level 0.005
> show #!40 models
> hide #!40 models
> show #!40 models
> volume #30 level 0.0045
> close #40
> show #39 models
> hide #39 models
> show #!37 models
> hide #!37 models
> close #37
> show #36 models
> hide #36 models
> hide #!30 models
> show #!18 models
> show #!20 models
> hide #!18 models
> show #!19 models
> hide #!20 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J492_012_volume_map_sharp.mrc
Opened cryosparc_P17_J492_012_volume_map_sharp.mrc as #37, grid size
588,588,588, pixel 0.85, shown at level 0.161, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J491_011_volume_map_sharp.mrc
Opened cryosparc_P17_J491_011_volume_map_sharp.mrc as #40, grid size
588,588,588, pixel 0.85, shown at level 0.17, step 4, values float32
> hide #!19 models
> hide #!37 models
> volume #40 level 0.2312
> volume #40 step 1
> volume #40 level 0.3499
> volume #37 level 0.1763
> volume #37 step 1
> volume #37 level 0.2223
> volume #37 level 0.2
> volume #37 level 0.1885
> volume #37 level 0.1742
> hide #!37 models
> show #!8 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map_sharp.mrc
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #41, grid size
294,294,294, pixel 1.9, shown at level 0.362, step 2, values float32
> hide #!8 models
> volume #41 step 1
> volume #41 level 0.4564
> hide #!41 models
> show #!35 models
> hide #!35 models
> show #!41 models
> hide #!41 models
> show #!33 models
> hide #!33 models
> show #36 models
> combine #36
> hide #36 models
> show #!41 models
> select add #42
22084 atoms, 22344 bonds, 1388 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #42,-0.66651,-0.41454,0.61961,272.25,-0.074937,-0.78968,-0.60893,371.9,0.74172,-0.45229,0.49526,320.86
> ui mousemode right "rotate selected models"
> view matrix models
> #42,0.88686,0.43938,0.14293,270.28,0.32258,-0.81026,0.4893,369.08,0.3308,-0.38784,-0.86032,324.19
> view matrix models
> #42,0.37114,0.92855,0.0068206,265.93,0.88732,-0.3568,0.29216,367.34,0.27372,-0.10238,-0.95634,322.18
> view matrix models
> #42,-0.31468,0.84864,0.42519,263.78,0.88685,0.10319,0.4504,363.22,0.33835,0.51881,-0.78509,316.9
> view matrix models
> #42,-0.23757,0.91024,0.33914,263.75,0.89188,0.06608,0.44741,363.53,0.38484,0.40877,-0.82753,317.99
> ui mousemode right "translate selected models"
> view matrix models
> #42,-0.23757,0.91024,0.33914,263.29,0.89188,0.06608,0.44741,364.95,0.38484,0.40877,-0.82753,225.17
> ui tool show "Fit in Map"
> fitmap #42 inMap #41
Fit molecule copy of ranked_0 (1).pdb (#42) to map
cryosparc_P17_J368_007_volume_map_sharp.mrc (#41) using 22084 atoms
average map value = 0.6576, steps = 148
shifted from previous position = 10.7
rotated from previous position = 27.8 degrees
atoms outside contour = 5619, contour level = 0.45638
Position of copy of ranked_0 (1).pdb (#42) relative to
cryosparc_P17_J368_007_volume_map_sharp.mrc (#41) coordinates:
Matrix rotation and translation
0.11572590 0.95057234 0.28813146 269.08018829
0.98967501 -0.13504383 0.04802635 358.27183284
0.08456290 0.27959862 -0.95638576 219.12378513
Axis 0.74509125 0.65498843 0.12581411
Axis point 0.00000000 52.42448167 89.73927147
Rotation angle (degrees) 171.06008584
Shift along axis 462.72206245
> select subtract #42
Nothing selected
> color #41 #99bfe584 models
> color #41 #99bfe582 models
> color #41 #99bfe580 models
> volume #41 level 0.5
> volume #41 level 0.55
> save
> /Users/cvetkom/Documents/chimera_sessions/20240502_CMGC4MCT_Fpl20MN_krios_merged_misc.cxs
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
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: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0)
OS Loader Version: 580~1678
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 11 days, 2 hours, 56 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: 24-Bit Color (ARGB8888)
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: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
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: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
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: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
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: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 19 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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