![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 months ago
Closed 4 months ago
#18161 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1.1-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 0x00007ff858208b40 (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, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 53)
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{
"uptime" : 180000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 4531,
"osVersion" : {
"train" : "macOS 14.1.1",
"build" : "23B81",
"releaseType" : "User"
},
"captureTime" : "2025-07-09 16:21:08.0167 -0700",
"codeSigningMonitor" : 0,
"incident" : "566FAD78-7717-4A5D-AD6C-913E07120A45",
"pid" : 29953,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-07 10:48:11.0544 -0700",
"procStartAbsTime" : 108909520958126,
"procExitAbsTime" : 186627629173597,
"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":"DA100F13-B0F2-50F8-9C22-897DAE97C7E7","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "7925176F-E307-0012-8595-237223476599",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 24844,
"bridgeVersion" : {"build":"21P1069","train":"8.1"},
"sleepWakeUUID" : "BA667B33-EDD5-4836-B128-B9858DD20E8C",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4362981376\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1040dd000-1040e1000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":29953},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4362981376\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1040dd000-1040e1000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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"faultingThread" : 0,
"threads" : 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"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
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"arch" : "x86_64",
"base" : 140703475326976,
"size" : 557056,
"uuid" : "83c7b73c-86fe-32f9-85dd-f46fa2c1315b",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703476944896,
"size" : 40960,
"uuid" : "c94f952c-2787-30d2-ab77-ee474abd88d6",
"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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{
"source" : "P",
"arch" : "x86_64",
"base" : 140703567224832,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 4538357,
"uuid" : "14809357-5d5a-3255-9cd2-ec5bc50f24cb",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703475023872,
"size" : 290814,
"uuid" : "4472f1a5-1d47-3665-ac8d-7adb0e9d2d87",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703477161984,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4829165,
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{
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"arch" : "x86_64",
"base" : 140703654289408,
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"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 2736117,
"uuid" : "06bf0872-3b34-3c7b-ad5b-7a447d793405",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
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{
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"arch" : "x86_64",
"base" : 140703534096384,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 20996092,
"uuid" : "27fed5dd-d148-3238-bc95-1dac5dd57fa1",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2487.20.107"
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{
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"arch" : "x86_64",
"base" : 140703473041408,
"size" : 639968,
"uuid" : "d5406f23-6967-39c4-beb5-6ae3293c7753",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703475884032,
"size" : 520192,
"uuid" : "b0f79a73-e705-38c8-a162-2465ed2adfaa",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
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"sharedCache" : {
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"uuid" : "4f1c5bcd-3ba7-365c-9e1f-56c2b41cafa6"
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=10.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=10.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 2068K 45 \nCG raster data 8K 1 \nColorSync 264K 35 \nCoreAnimation 1276K 120 \nCoreGraphics 16K 3 \nCoreImage 24K 2 \nCoreUI image data 5144K 40 \nDispatch continuations 96.0M 1 \nFoundation 32K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 9.0G 648 \nMALLOC guard page 96K 24 \nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 160K 40 \nStack 163.3M 41 \nStack Guard 56.0M 1 \nVM_ALLOCATE 1.2G 423 \nVM_ALLOCATE (reserved) 96.0M 2 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 45.5M 789 \n__DATA_CONST 65.1M 460 \n__DATA_DIRTY 1849K 231 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 211.0M 149 \n__OBJC_RO 70.8M 1 \n__OBJC_RW 2157K 3 \n__TEXT 1.0G 795 \ndyld private memory 292K 4 \nmapped file 538.0M 94 \nshared memory 3512K 32 \n=========== ======= ======= \nTOTAL 12.5G 4003 \nTOTAL, minus reserved VM space 12.5G 4003 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "80dbd6617593c7ca9402bff45d4eacc1c423943e",
"trialInfo" : {
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{
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"factorPackIds" : {
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{
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}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/tessasmith/Downloads/cryosparc_P45_EscVc_monomer_16.mrc
Opened cryosparc_P45_EscVc_monomer_16.mrc as #1, grid size 288,288,288, pixel
1.11, shown at level 1.78e-05, step 2, values float32
> open "/Users/tessasmith/Downloads/cryosparc_P45_J213_011_volume_map (1).mrc"
Opened cryosparc_P45_J213_011_volume_map (1).mrc as #2, grid size 288,288,288,
pixel 1.11, shown at level 0.0821, step 2, values float32
> volume #1 step 1
> volume #2 step 1
> volume #1 level 0.05753
> volume #2 level 0.08591
> volume #2 level 0.06588
> open "/Users/tessasmith/Nextcloud/Tess/Phenix
> Data/EscV_325-675/EscVc_Final.pdb"
Chain information for EscVc_Final.pdb #3
---
Chain | Description
A B C D E F G H I | No description available
> hide #3 models
> show #3 models
> hide atoms
> show cartoons
> ui mousemode right "translate selected models"
> select add #3
23976 atoms, 24363 bonds, 2970 residues, 1 model selected
> view matrix models
> #3,-0.56576,0.81393,0.13205,107.76,0.82023,0.57192,-0.010999,-67.348,-0.084476,0.10209,-0.99118,380.09
> view matrix models
> #3,-0.56576,0.81393,0.13205,93.518,0.82023,0.57192,-0.010999,-88.972,-0.084476,0.10209,-0.99118,375.26
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> view matrix models
> #3,-0.56576,0.81393,0.13205,89.354,0.82023,0.57192,-0.010999,-83.258,-0.084476,0.10209,-0.99118,376.67
> view matrix models
> #3,-0.87829,0.443,0.17988,200.3,0.46729,0.87496,0.12681,-100.73,-0.10121,0.19543,-0.97548,360.23
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #!1 models
> fitmap #3 inMap #2
Fit molecule EscVc_Final.pdb (#3) to map cryosparc_P45_J213_011_volume_map
(1).mrc (#2) using 23976 atoms
average map value = 0.1286, steps = 120
shifted from previous position = 2.49
rotated from previous position = 13.4 degrees
atoms outside contour = 4277, contour level = 0.065877
Position of EscVc_Final.pdb (#3) relative to cryosparc_P45_J213_011_volume_map
(1).mrc (#2) coordinates:
Matrix rotation and translation
-0.91971052 0.39259694 0.00045105 252.51848360
0.39259709 0.91971052 0.00031027 -73.03445419
-0.00029302 0.00046244 -0.99999985 381.98409842
Axis 0.20036319 0.97972167 0.00019695
Axis point 133.76440556 0.00000000 190.97451615
Rotation angle (degrees) 179.97824291
Shift along axis -20.88279594
> select subtract #3
Nothing selected
> show #!1 models
> color #2 #ffffb288 models
> volume #2 level 0.09467
> volume #2 level 0.06963
> hide #3 models
> hide #!1 models
> volume gaussian #2 sDev 2
Opened cryosparc_P45_J213_011_volume_map (1).mrc gaussian as #4, grid size
288,288,288, pixel 1.11, shown at step 1, values float32
> volume #4 level 0.04306
> volume copy #4
Opened cryosparc_P45_J213_011_volume_map (1).mrc gaussian copy as #5, grid
size 288,288,288, pixel 1.11, shown at step 1, values float32
> volume #5 level 0.0463
> volume #5 level 0.03217
> ui mousemode right "map eraser"
> volume erase #5 center 210.71,170.58,189.5 radius 50.828 outside true
> volume erase #5 center 189.03,140.56,198.97 radius 20.876
> volume erase #5 center 203.8,127.53,209.74 radius 20.876
> volume erase #5 center 225.79,125.06,191.8 radius 20.876
> volume erase #5 center 207.41,129,179.08 radius 20.876
> volume erase #5 center 187.92,120.07,181.26 radius 20.876
> show #3 models
> volume erase #5 center 193.43,128.62,156.76 radius 20.868
> volume erase #5 center 208.12,136.95,155.57 radius 20.868
> volume erase #5 center 217.06,142.08,175.67 radius 17.682
> volume erase #5 center 219.27,135.88,185.21 radius 17.682
> volume erase #5 center 193.97,142.96,184.37 radius 17.682
> volume erase #5 center 208.02,146.92,141.18 radius 17.682
> volume erase #5 center 201.1,161.63,139.34 radius 17.682
> volume erase #5 center 221.57,167.14,142.41 radius 17.682
> volume erase #5 center 229.74,167.98,144.6 radius 17.682
> volume erase #5 center 206.1,157.53,142.67 radius 17.682
> volume erase #5 center 204.09,178.34,140.04 radius 17.682
> volume erase #5 center 211.82,188.87,138.88 radius 17.682
> volume erase #5 center 192.14,172.26,143.68 radius 17.682
> color #5 #b2ffffbb models
> color #5 #b2ffffbd models
> volume erase #5 center 195.54,199.27,148.45 radius 17.682
> volume erase #5 center 206.93,213.16,149.09 radius 17.682
> volume erase #5 center 194.89,215.55,163.43 radius 17.682
> volume erase #5 center 186.05,205.04,167.57 radius 17.682
> volume erase #5 center 184.49,188.09,172.13 radius 7.3278
> volume erase #5 center 199.19,214.35,192.49 radius 14.974
> volume erase #5 center 211.59,212.4,201.4 radius 14.974
> volume erase #5 center 209.66,202.05,212.58 radius 14.974
> volume erase #5 center 192.64,200.25,215.72 radius 14.974
> volume erase #5 center 173.36,195.88,209.28 radius 14.974
> volume erase #5 center 166.31,189.98,199.1 radius 14.974
> volume erase #5 center 173.37,194.72,188.31 radius 14.974
> volume erase #5 center 187.24,204.55,195.07 radius 14.974
> volume erase #5 center 181.62,189.35,202.17 radius 8.7615
> volume erase #5 center 173.07,182.67,192.51 radius 8.7615
> volume erase #5 center 184.13,192.38,182.04 radius 8.7615
> volume erase #5 center 180.71,188.4,192.45 radius 8.7615
> volume erase #5 center 189.64,195.12,195.5 radius 8.7615
> volume erase #5 center 187.03,211.66,180.21 radius 8.7615
> volume erase #5 center 197.2,202.88,179.14 radius 8.7615
> volume erase #5 center 202.59,202.18,191.58 radius 8.7615
> volume erase #5 center 200.14,200.34,193.86 radius 8.7615
> volume erase #5 center 206.24,219.51,185.09 radius 8.7615
> volume erase #5 center 207.99,196.07,200.96 radius 8.7615
> volume erase #5 center 197.37,191.8,205.95 radius 8.7615
> volume erase #5 center 201.34,191.57,200.78 radius 8.7615
> volume erase #5 center 204.18,191.19,202.39 radius 8.7615
> hide #3 models
> hide #6 models
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> show #6 models
> ui mousemode right "map eraser"
> volume erase #5 center 172.3,205.49,187.88 radius 8.7615
> hide #6 models
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> save /Users/tessasmith/Desktop/EscVc-EspA_monomer.mrc models #5
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J216_class_00_00270_volume.mrc
Opened cryosparc_P45_J216_class_00_00270_volume.mrc as #7, grid size 72,72,72,
pixel 4.42, shown at level 0.586, step 1, values float32
> hide #!5 models
> volume #7 level 0.4026
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J216_class_01_00270_volume.mrc
Opened cryosparc_P45_J216_class_01_00270_volume.mrc as #6, grid size 72,72,72,
pixel 4.42, shown at level 0.586, step 1, values float32
> volume #7 level 0.3259
> open "/Users/tessasmith/Downloads/cryosparc_P45_J216_class_01_00270_volume
> (1).mrc"
Opened cryosparc_P45_J216_class_01_00270_volume (1).mrc as #8, grid size
72,72,72, pixel 4.42, shown at level 0.586, step 1, values float32
> hide #!7 models
> hide #!6 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!8 models
> volume #8 level 0.3492
> hide #!8 models
> show #!5 models
> open "/Users/tessasmith/Downloads/cryosparc_P45_J213_011_volume_map (2).mrc"
Opened cryosparc_P45_J213_011_volume_map (2).mrc as #9, grid size 288,288,288,
pixel 1.11, shown at level 0.0821, step 2, values float32
> hide #!5 models
> volume #9 step 1
> volume #9 level 0.05895
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J219_class_00_00270_volume.mrc
Opened cryosparc_P45_J219_class_00_00270_volume.mrc as #10, grid size
72,72,72, pixel 4.42, shown at level 0.586, step 1, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J219_class_01_00270_volume.mrc
Opened cryosparc_P45_J219_class_01_00270_volume.mrc as #11, grid size
72,72,72, pixel 4.42, shown at level 0.586, step 1, values float32
> hide #!9 models
> hide #!11 models
> show #!11 models
> volume #10 level 0.3894
> volume #11 level 0.3494
> volume #10 level 0.3594
> hide #!11 models
> hide #!10 models
> show #!4 models
> show #3 models
> hide #!4 models
> show #!5 models
> hide #3 models
> show #!1 models
> open /Users/tessasmith/Downloads/cryosparc_P45_J231_006_volume_map.mrc
Opened cryosparc_P45_J231_006_volume_map.mrc as #12, grid size 288,288,288,
pixel 1.11, shown at level 0.0814, step 2, values float32
> hide #!5 models
> hide #!1 models
> volume #12 step 1
> volume #12 level 0.05559
> volume #12 level 0.0543
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J229_class_00_00966_volume.mrc
Opened cryosparc_P45_J229_class_00_00966_volume.mrc as #13, grid size
84,84,84, pixel 3.79, shown at level 0.482, step 1, values float32
> hide #!12 models
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J229_class_01_00966_volume.mrc
Opened cryosparc_P45_J229_class_01_00966_volume.mrc as #14, grid size
84,84,84, pixel 3.79, shown at level 0.482, step 1, values float32
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> volume #13 level 0.4529
> volume #14 level 0.4851
> open /Users/tessasmith/Downloads/cryosparc_P45_J233_map_all_classes.cs
Unrecognized file suffix '.cs'
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J233_map_all_classes/J233_volume_class_01_map.mrc
Opened J233_volume_class_01_map.mrc as #15, grid size 288,288,288, pixel 1.11,
shown at level 0.0826, step 2, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J233_map_all_classes/J233_volume_class_00_map.mrc
Opened J233_volume_class_00_map.mrc as #16, grid size 288,288,288, pixel 1.11,
shown at level 0.0828, step 2, values float32
> hide #!13 models
> hide #!14 models
> volume #15 step 1
> volume #16 step 1
> hide #!15 models
> volume #16 level 0.06426
> hide #!16 models
> show #!15 models
> volume #15 level 0.06731
> volume #15 level 0.05476
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!15 models
> open /Users/tessasmith/Downloads/cryosparc_P45_J232_003_volume_map.mrc
Opened cryosparc_P45_J232_003_volume_map.mrc as #17, grid size 288,288,288,
pixel 1.11, shown at level 0.0819, step 2, values float32
> hide #!15 models
> volume #17 step 1
> show #!1 models
> hide #!1 models
> volume #17 level 0.05888
> close #2
> close #4
> close #6
> close #7
> close #8
> close #10
> close #11
> close #12
> close #13
> close #14
> close #15
> close #16
> volume #17 level 0.1292
> toolshed show
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_018.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_019.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_009.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_010.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_011.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_012.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_013.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_014.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_015.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_016.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_017.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_000.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_001.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_002.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_003.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_004.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_005.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_006.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_007.mrc
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_008.mrc
Opened J235_component_000_frame_018.mrc as #2.1, grid size 288,288,288, pixel
1.11, shown at level 0.0755, step 2, values float32
Opened J235_component_000_frame_019.mrc as #2.2, grid size 288,288,288, pixel
1.11, shown at level 0.0757, step 2, values float32
Opened J235_component_000_frame_009.mrc as #2.3, grid size 288,288,288, pixel
1.11, shown at level 0.0743, step 2, values float32
Opened J235_component_000_frame_010.mrc as #2.4, grid size 288,288,288, pixel
1.11, shown at level 0.0743, step 2, values float32
Opened J235_component_000_frame_011.mrc as #2.5, grid size 288,288,288, pixel
1.11, shown at level 0.0744, step 2, values float32
Opened J235_component_000_frame_012.mrc as #2.6, grid size 288,288,288, pixel
1.11, shown at level 0.0745, step 2, values float32
Opened J235_component_000_frame_013.mrc as #2.7, grid size 288,288,288, pixel
1.11, shown at level 0.0747, step 2, values float32
Opened J235_component_000_frame_014.mrc as #2.8, grid size 288,288,288, pixel
1.11, shown at level 0.0749, step 2, values float32
Opened J235_component_000_frame_015.mrc as #2.9, grid size 288,288,288, pixel
1.11, shown at level 0.075, step 2, values float32
Opened J235_component_000_frame_016.mrc as #2.10, grid size 288,288,288, pixel
1.11, shown at level 0.0752, step 2, values float32
Opened J235_component_000_frame_017.mrc as #2.11, grid size 288,288,288, pixel
1.11, shown at level 0.0753, step 2, values float32
Opened J235_component_000_frame_000.mrc as #2.12, grid size 288,288,288, pixel
1.11, shown at level 0.0755, step 2, values float32
Opened J235_component_000_frame_001.mrc as #2.13, grid size 288,288,288, pixel
1.11, shown at level 0.0753, step 2, values float32
Opened J235_component_000_frame_002.mrc as #2.14, grid size 288,288,288, pixel
1.11, shown at level 0.0753, step 2, values float32
Opened J235_component_000_frame_003.mrc as #2.15, grid size 288,288,288, pixel
1.11, shown at level 0.0751, step 2, values float32
Opened J235_component_000_frame_004.mrc as #2.16, grid size 288,288,288, pixel
1.11, shown at level 0.0749, step 2, values float32
Opened J235_component_000_frame_005.mrc as #2.17, grid size 288,288,288, pixel
1.11, shown at level 0.0748, step 2, values float32
Opened J235_component_000_frame_006.mrc as #2.18, grid size 288,288,288, pixel
1.11, shown at level 0.0746, step 2, values float32
Opened J235_component_000_frame_007.mrc as #2.19, grid size 288,288,288, pixel
1.11, shown at level 0.0745, step 2, values float32
Opened J235_component_000_frame_008.mrc as #2.20, grid size 288,288,288, pixel
1.11, shown at level 0.0744, step 2, values float32
> hide #!17 models
> open /Downloads/cryosparc_P45_J235_component_000
Unknown command: vseries open /Downloads/cryosparc_P45_J235_component_000
> open
> /Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_*.mrc
Unknown command: vseries open
/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_*.mrc
> /Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_*.mrc
Unknown command: vseries
/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_*.mrc
> vseries play #2 loop true
No volume series specified
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_0*.mrc
Unknown command: vseries open
/Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_0*.mrc
> toolshed show
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_0*.mrc
> vseries true
Opened map series J235_component_000_frame_000.mrc as #4, 20 images, grid size
288,288,288, pixel 1.11, shown at level 0.0755, step 2, values float32
> hide #!2 models
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_002_frame_0*.mrc
> vseries true
No such file/path:
/Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_002_frame_0*.mrc
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_001/J235_component_001_frame_0*.mrc
> vseries true
Opened map series J235_component_001_frame_000.mrc as #6, 20 images, grid size
288,288,288, pixel 1.11, shown at level 0.075, step 2, values float32
> hide #!4 models
> hide #!2 models
> show #3 models
> hide #3 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> close #6
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_001/J235_component_001_frame_0*.mrc
> vseries true
Opened map series J235_component_001_frame_000.mrc as #6, 20 images, grid size
288,288,288, pixel 1.11, shown at level 0.075, step 2, values float32
> hide #!6 models
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J235_component_002/J235_component_002_frame_0*.mrc
> vseries true
Opened map series J235_component_002_frame_000.mrc as #7, 20 images, grid size
288,288,288, pixel 1.11, shown at level 0.0753, step 2, values float32
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!7 models
> volume #7.7 step 1
> volume #6.7 step 1
> volume #4.3 step 1
> volume #2.20 step 1
> volume #2.19 step 1
> volume #2.18 step 1
> volume #2.17 step 1
> volume #2.16 step 1
> volume #2.15 step 1
> volume #2.14 step 1
> volume #2.13 step 1
> volume #2.12 step 1
> volume #2.11 step 1
> volume #2.10 step 1
> volume #2.9 step 1
> volume #2.8 step 1
> volume #2.7 step 1
> volume #2.6 step 1
> volume #2.5 step 1
> volume #2.4 step 1
> volume #2.3 step 1
> volume #2.2 step 1
> volume #2.1 step 1
> open "/Users/tessasmith/Downloads/cryosparc_P45_J232_003_volume_map (1).mrc"
Opened cryosparc_P45_J232_003_volume_map (1).mrc as #8, grid size 288,288,288,
pixel 1.11, shown at level 0.0819, step 2, values float32
> hide #!7 models
> close #8
> show #!17 models
> volume #17 level 0.05618
> hide #!17 models
> show #!9 models
> volume #9 level 0.1066
> volume #9 level 0.06668
> volume #9 level 0.04477
> open "/Users/tessasmith/Downloads/cryosparc_P45_J207_006_volume_map (1).mrc"
Opened cryosparc_P45_J207_006_volume_map (1).mrc as #8, grid size 288,288,288,
pixel 1.11, shown at level 0.0847, step 2, values float32
> hide #!9 models
> volume #8 step 1
> volume #8 level 0.04188
> hide #!8 models
> show #!9 models
> open "/Users/tessasmith/Downloads/cryosparc_P45_J208_009_volume_map (1).mrc"
Opened cryosparc_P45_J208_009_volume_map (1).mrc as #10, grid size
288,288,288, pixel 1.11, shown at level 0.085, step 2, values float32
> hide #!9 models
> volume #10 step 1
> volume #10 level 0.07053
> volume #10 level 0.06658
> volume #10 level 0.05344
> hide #!10 models
> show #!17 models
> close #2
> show #!9 models
> hide #!17 models
> show #!17 models
> hide #!9 models
> show #!5 models
> hide #!5 models
> show #!9 models
> show #!5 models
> volume #5 level 0.01029
> volume #5 level 0.01496
> hide #!5 models
> hide #!17 models
> hide #!9 models
> show #!17 models
> hide #!17 models
> show #!9 models
> volume #9 level 0.07699
> volume #9 level 0.03575
> hide #!9 models
> show #!6 models
> show #3 models
> hide #3 models
> show #!1 models
> hide #!1 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!4 models
> hide #!4 models
> show #!8 models
> hide #!8 models
> show #!17 models
> open /Users/tessasmith/Downloads/cryosparc_P45_J237_005_volume_map.mrc
Opened cryosparc_P45_J237_005_volume_map.mrc as #2, grid size 288,288,288,
pixel 1.11, shown at level 0.0822, step 2, values float32
> hide #!17 models
> volume #2 step 1
> volume #2 level 0.06456
> volume #2 level 0.04569
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_00_map.mrc
Opened J239_volume_class_00_map.mrc as #11, grid size 288,288,288, pixel 1.11,
shown at level 0.083, step 2, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_01_map.mrc
Opened J239_volume_class_01_map.mrc as #12, grid size 288,288,288, pixel 1.11,
shown at level 0.0828, step 2, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_02_map.mrc
Opened J239_volume_class_02_map.mrc as #13, grid size 288,288,288, pixel 1.11,
shown at level 0.083, step 2, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_03_map.mrc
Opened J239_volume_class_03_map.mrc as #14, grid size 288,288,288, pixel 1.11,
shown at level 0.0834, step 2, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_04_map.mrc
Opened J239_volume_class_04_map.mrc as #15, grid size 288,288,288, pixel 1.11,
shown at level 0.0832, step 2, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_05_map.mrc
Opened J239_volume_class_05_map.mrc as #16, grid size 288,288,288, pixel 1.11,
shown at level 0.0832, step 2, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_06_map.mrc
Opened J239_volume_class_06_map.mrc as #18, grid size 288,288,288, pixel 1.11,
shown at level 0.0829, step 2, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_07_map.mrc
Opened J239_volume_class_07_map.mrc as #19, grid size 288,288,288, pixel 1.11,
shown at level 0.0827, step 2, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_08_map.mrc
Opened J239_volume_class_08_map.mrc as #20, grid size 288,288,288, pixel 1.11,
shown at level 0.0828, step 2, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_09_map.mrc
Opened J239_volume_class_09_map.mrc as #21, grid size 288,288,288, pixel 1.11,
shown at level 0.0833, step 2, values float32
> hide #!21 models
> hide #!20 models
> hide #!19 models
> hide #!18 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> hide #!12 models
> hide #!13 models
> hide #!2 models
> volume #11 step 1
> volume #12 step 1
> volume #13 step 1
> volume #14 step 1
> volume #15 step 1
> volume #16 step 1
> volume #18 step 1
> volume #19 step 1
> volume #20 step 1
> volume #21 step 1
> show #!1 models
> hide #!1 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> show #!16 models
> hide #!15 models
> hide #!16 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!14 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!18 models
> show #!19 models
> hide #!18 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> show #!20 models
> show #!11 models
> hide #!20 models
> show #!20 models
> show #!10 models
> hide #!10 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!20 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!20 models
> show #!21 models
> hide #!20 models
> open "/Users/tessasmith/Downloads/cryosparc_P45_J212_009_volume_map (1).mrc"
Opened cryosparc_P45_J212_009_volume_map (1).mrc as #22, grid size
288,288,288, pixel 1.11, shown at level 0.0397, step 2, values float32
> hide #!21 models
> volume #22 step 1
> volume #22 level 0.1172
> volume #22 level 0.1079
> show #3 models
> select add #3
23976 atoms, 24363 bonds, 2970 residues, 1 model selected
> view matrix models
> #3,0.99822,-0.020185,-0.05607,-2.2089,0.03097,0.97957,0.1987,-57.974,0.050914,-0.20009,0.97845,27.476
> view matrix models
> #3,0.99822,-0.020185,-0.05607,0.60597,0.03097,0.97957,0.1987,-64.584,0.050914,-0.20009,0.97845,-3.3197
> fitmap #3 inMap #22
Fit molecule EscVc_Final.pdb (#3) to map cryosparc_P45_J212_009_volume_map
(1).mrc (#22) using 23976 atoms
average map value = 0.1674, steps = 176
shifted from previous position = 10.1
rotated from previous position = 18.6 degrees
atoms outside contour = 7426, contour level = 0.10793
Position of EscVc_Final.pdb (#3) relative to cryosparc_P45_J212_009_volume_map
(1).mrc (#22) coordinates:
Matrix rotation and translation
0.97510444 0.22174603 -0.00016921 -52.49615510
-0.22174594 0.97510438 0.00042526 25.87509294
0.00025930 -0.00037716 0.99999989 -40.01666926
Axis -0.00180932 -0.00096623 -0.99999790
Axis point 89.19609953 246.42701815 0.00000000
Rotation angle (degrees) 12.81163118
Shift along axis 40.08656620
> view matrix models
> #3,0.9751,0.22175,-0.00016921,-52.503,-0.22175,0.9751,0.00042526,25.834,0.0002593,-0.00037716,1,-39.98
> select clear
> color #22 #b2b2ffac models
> color #22 #b2b2ffab models
> volume #22 level 0.09862
Drag select of 5 residues, 22 cryosparc_P45_J212_009_volume_map (1).mrc
> select clear
> hide #!22 models
> select /A:593
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:594
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select add /A:593
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /A:594
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add /A:595
25 atoms, 22 bonds, 3 residues, 1 model selected
> select add /A:596
34 atoms, 30 bonds, 4 residues, 1 model selected
> select add /A:597
41 atoms, 36 bonds, 5 residues, 1 model selected
> select add /A:598
47 atoms, 41 bonds, 6 residues, 1 model selected
> select add /A:600
51 atoms, 44 bonds, 7 residues, 1 model selected
> select add /A:599
57 atoms, 49 bonds, 8 residues, 1 model selected
> select add /A:601
63 atoms, 54 bonds, 9 residues, 1 model selected
> select add /A:602
75 atoms, 66 bonds, 10 residues, 1 model selected
> select add /A:603
83 atoms, 73 bonds, 11 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 83 atom styles
> select clear
> show #!22 models
> select /A:605
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!22 models
> select add /A:604
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> select clear
> show #!22 models
Drag select of 220 residues, 22 cryosparc_P45_J212_009_volume_map (1).mrc
> select clear
> volume #22 level 0.09
> volume #22 level 0.11
> volume #22 level 0.085
> volume #22 level 0.08
> volume #22 level 0.065
> volume #22 level 0.06
> volume #22 level 0.055
> volume #22 level 0.065
> open /Users/tessasmith/Downloads/cryosparc_P45_J241_005_volume_map.mrc
Opened cryosparc_P45_J241_005_volume_map.mrc as #23, grid size 288,288,288,
pixel 1.11, shown at level 0.0393, step 2, values float32
> hide #!22 models
> hide #3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> volume #23 step 1
> volume #23 level 0.09136
> volume #23 level 0.06926
> volume #23 level 0.04242
> hide #!23 models
> show #!22 models
> hide #!22 models
> show #!20 models
> volume #20 level 0.03738
> volume #20 level 0.1056
> hide #!20 models
> show #!23 models
> hide #!23 models
> show #!19 models
> hide #!19 models
> show #!20 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!9 models
> volume #9 level 0.09633
> show #3 models
> select add #3
23976 atoms, 24363 bonds, 2970 residues, 1 model selected
> view matrix models
> #3,-0.38353,-0.69956,-0.60292,464.52,-0.70502,0.64348,-0.29814,226.62,0.59654,0.31073,-0.74,135.14
> view matrix models
> #3,0.99193,0.12665,0.0055187,-39.882,0.12673,-0.99176,-0.018552,313.09,0.0031236,0.019102,-0.99981,340.87
> view matrix models
> #3,0.99193,0.12665,0.0055187,-41.187,0.12673,-0.99176,-0.018552,306.77,0.0031236,0.019102,-0.99981,375.45
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #!20 models
> fitmap #3 inMap #9
Fit molecule EscVc_Final.pdb (#3) to map cryosparc_P45_J213_011_volume_map
(2).mrc (#9) using 23976 atoms
average map value = 0.1286, steps = 100
shifted from previous position = 9.65
rotated from previous position = 10.5 degrees
atoms outside contour = 8929, contour level = 0.096327
Position of EscVc_Final.pdb (#3) relative to cryosparc_P45_J213_011_volume_map
(2).mrc (#9) coordinates:
Matrix rotation and translation
0.99851990 -0.05438755 -0.00011933 -7.77777912
-0.05438760 -0.99851983 -0.00037562 345.73121958
-0.00009872 0.00038156 -0.99999992 381.96453630
Axis 0.99962987 -0.02720504 -0.00005436
Axis point 0.00000000 172.72359468 191.01475903
Rotation angle (degrees) 179.97830045
Shift along axis -17.20129833
> show #!8 models
> hide #!8 models
> save /Users/tessasmith/EscV325-aligned.pdb relModel #9
> hide #3 models
> select subtract #3
Nothing selected
> open /Users/tessasmith/EscV325-aligned.pdb
Chain information for EscV325-aligned.pdb #24
---
Chain | Description
A B C D E F G H I | No description available
> hide #24 atoms
> show #24 cartoons
> open /Users/tessasmith/Downloads/1xou.pdb
1xou.pdb title:
Crystal structure of the cesa-ESPA complex [more info...]
Chain information for 1xou.pdb #25
---
Chain | Description | UniProt
A | ESPA | Q47184_ECOLI 1-192
B | Z5138 gene product | O52124_ECOLI 1-95
> select #25/A:31-190
565 atoms, 569 bonds, 1 pseudobond, 72 residues, 2 models selected
> ui tool show "Selection Inspector"
> color sel #a35c87 target r
> view matrix models #25,1,0,0,-0.020978,0,1,0,0.00017177,0,0,1,0.0169
> select clear
> open /Users/tessasmith/Downloads/7k7k.pdb
7k7k.pdb title:
Structure of the epec type III secretion injectisome ESPA filament [more
info...]
Chain information for 7k7k.pdb #26
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b | translocon ESPA | B7UM94_ECO27 1-192
> select add #26
36204 atoms, 36484 bonds, 4788 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select #26/A:22-192
1293 atoms, 1303 bonds, 171 residues, 1 model selected
> show sel cartoons
> view matrix models #26,1,0,0,-155.43,0,1,0,-158.53,0,0,1,-72.769
> select clear
Drag select of 9 cryosparc_P45_J213_011_volume_map (2).mrc
> select clear
> volume #9 level 0.05251
> hide #!9 models
> hide #24 models
> hide #26 models
> show #26 models
> hide #!25 models
> hide #26 models
> show #!21 models
> show #!1 models
> hide #!1 models
> hide #!21 models
> show #!20 models
> show #!21 models
> hide #!20 models
> show #!20 models
> hide #!21 models
> show #!21 models
> show #!19 models
> hide #!19 models
> hide #!21 models
> hide #!20 models
> show #!19 models
> hide #!19 models
> show #!18 models
> volume #18 level 0.07869
> hide #!18 models
> show #!16 models
> hide #!16 models
> show #!22 models
> show #!21 models
> hide #!22 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!19 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!16 models
> hide #!16 models
> show #!15 models
> volume #15 level 0.07244
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> show #!9 models
> volume #9 level 0.08859
> show #!5 models
> show #24 models
> hide #!5 models
> hide #!9 models
> show #!9 models
> volume #9 level 0.05122
> hide #!9 models
> log metadata #24
The model has no metadata
> log chains #24
Chain information for EscV325-aligned.pdb #24
---
Chain | Description
A B C D E F G H I | No description available
> select #24/A:346-675
2664 atoms, 2707 bonds, 330 residues, 1 model selected
> select clear
> select #24/A:346-675
2664 atoms, 2707 bonds, 330 residues, 1 model selected
> select clear
> select #24/B:346-675
2664 atoms, 2707 bonds, 330 residues, 1 model selected
> select clear
> hide #24 cartoons
> select #24/A:346-675
2664 atoms, 2707 bonds, 330 residues, 1 model selected
> show sel cartoons
> select #24/B:346-675
2664 atoms, 2707 bonds, 330 residues, 1 model selected
> show sel cartoons
Drag select of 660 residues
> show #!9 models
> volume zone #24 nearAtoms #9 range 15 newMap true
no atoms specified for zone
> volume zone #9 nearAtoms #24 range 15 newMap true
Opened cryosparc_P45_J213_011_volume_map (2).mrc zone as #27, grid size
288,288,288, pixel 1.11, shown at step 1, values float32
> hide #24 models
> show #24 models
> volume zone #9 nearAtoms #24 A/B range 15 newMap true
Expected a keyword
> hide #!27 models
> save /Users/tessasmith/Desktop/EscV325-A/B.pdb models #24 selectedOnly true
Cannot save '/Users/tessasmith/Desktop/EscV325-A/B.pdb': Unable to open file
'/Users/tessasmith/Desktop/EscV325-A/B.pdb' for writing
> save /Users/tessasmith/Desktop/EscVc-dimer.pdb models #24 selectedOnly true
> open /Users/tessasmith/Desktop/EscVc-dimer.pdb
Summary of feedback from opening /Users/tessasmith/Desktop/EscVc-dimer.pdb
---
warnings | Start residue of secondary structure not found: HELIX 25 25 ASP C 365 SER C 381 1 17
Start residue of secondary structure not found: HELIX 26 26 THR C 465 SER C
479 1 15
Start residue of secondary structure not found: HELIX 27 27 ALA C 481 PHE C
484 1 4
Start residue of secondary structure not found: HELIX 28 28 VAL C 487 ARG C
499 1 13
Start residue of secondary structure not found: HELIX 29 29 ASN C 502 GLN C
511 1 10
168 messages similar to the above omitted
Chain information for EscVc-dimer.pdb #28
---
Chain | Description
A B | No description available
> hide #24 models
> hide #28 models
> show #28 models
> select add #24
23976 atoms, 24363 bonds, 2970 residues, 1 model selected
> select subtract #24
Nothing selected
> show #!9 models
> volume zone #9 nearAtoms #28 range 15 newMap true
Opened cryosparc_P45_J213_011_volume_map (2).mrc zone as #29, grid size
288,288,288, pixel 1.11, shown at step 1, values float32
> volume #29 level 0.0166
> hide #28 models
> open /Users/tessasmith/Downloads/cryosparc_P45_J236_010_volume_map.mrc
Opened cryosparc_P45_J236_010_volume_map.mrc as #30, grid size 288,288,288,
pixel 1.11, shown at level 0.0375, step 2, values float32
> hide #!29 models
> volume #30 step 1
> volume #30 level 0.05788
> open /Users/tessasmith/Downloads/cryosparc_P45_J245_018_volume_map.mrc
Opened cryosparc_P45_J245_018_volume_map.mrc as #31, grid size 288,288,288,
pixel 1.11, shown at level 0.0373, step 2, values float32
> hide #!30 models
> volume #31 step 1
> volume #31 level 0.09313
> hide #!31 models
> show #!30 models
> show #!31 models
> hide #!31 models
> hide #!30 models
> show #!30 models
> show #3 models
> hide #!30 models
> hide #3 models
> show #28 models
> show #!29 models
> hide #28 models
> save /Users/tessasmith/Desktop/EscVc-dimer.mrc models #29
> volume #29 level 0.05
> volume #29 level 0.01
> volume #29 level 0.005
> volume #29 level 0.01
> hide #!29 models
> show #!5 models
> volume #5 level 0.05
> hide #!5 models
> show #!29 models
> volume #29 level 0.05
> volume #29 level 0.01
> show #28 models
> volume #29 level 0.04974
> volume #29 level 0.05
> volume #29 level 0.04
> volume #29 level 0.03
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J247_component_000/J247_component_000_frame_0*.mrc
> vseries true
Opened map series J247_component_000_frame_000.mrc as #32, 20 images, grid
size 288,288,288, pixel 1.11, shown at level 0.0793, step 2, values float32
> hide #28 models
> hide #!29 models
> volume #32.1 step 1
> hide #!32 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #5 level 0.05408
> hide #!5 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> close #4
> show #!5 models
> hide #!5 models
> close #5
> close #1
> show #!2 models
> hide #!2 models
> show #!6 models
> hide #!6 models
> show #!6 models
> close #2
> undo
> close #6
> show #!7 models
> hide #!7 models
> close #7
> show #!8 models
> close #8
> close #10
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!13 models
> close #11
> close #12-16
> show #!17 models
> close #17
> close #18-21
> close #22
> show #!23 models
> close #23
> show #24 models
> hide #24 models
> show #!27 models
> close #27
> show #28 models
> show #!29 models
> hide #!29 models
> hide #28 models
> show #!30 models
> close #30
> show #!31 models
> close #31
> show #!32 models
> volume #32.20 level 0.06555
> volume #32.20 level 0.06568
> volume #32.1 level 0.05765
> volume #32.1 level 0.04696
> show #28 models
> color #32 #cccc99b9 models
> color #32 #cccc9990 models
> color #32 #cccc9991 models
> volume #32.5 level 0.04512
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_00_00193_volume.mrc
Opened J250_class_00_00193_volume.mrc as #1, grid size 112,112,112, pixel
2.84, shown at level 0.329, step 1, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_01_00193_volume.mrc
Opened J250_class_01_00193_volume.mrc as #2, grid size 112,112,112, pixel
2.84, shown at level 0.336, step 1, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_02_00193_volume.mrc
Opened J250_class_02_00193_volume.mrc as #4, grid size 112,112,112, pixel
2.84, shown at level 0.324, step 1, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_03_00193_volume.mrc
Opened J250_class_03_00193_volume.mrc as #5, grid size 112,112,112, pixel
2.84, shown at level 0.33, step 1, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_04_00193_volume.mrc
Opened J250_class_04_00193_volume.mrc as #6, grid size 112,112,112, pixel
2.84, shown at level 0.33, step 1, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_05_00193_volume.mrc
Opened J250_class_05_00193_volume.mrc as #7, grid size 112,112,112, pixel
2.84, shown at level 0.333, step 1, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_06_00193_volume.mrc
Opened J250_class_06_00193_volume.mrc as #8, grid size 112,112,112, pixel
2.84, shown at level 0.336, step 1, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_07_00193_volume.mrc
Opened J250_class_07_00193_volume.mrc as #10, grid size 112,112,112, pixel
2.84, shown at level 0.336, step 1, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_08_00193_volume.mrc
Opened J250_class_08_00193_volume.mrc as #11, grid size 112,112,112, pixel
2.84, shown at level 0.333, step 1, values float32
> open
> /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_09_00193_volume.mrc
Opened J250_class_09_00193_volume.mrc as #12, grid size 112,112,112, pixel
2.84, shown at level 0.321, step 1, values float32
> show #!29 models
> hide #!29 models
> hide #!32 models
> hide #28 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #3 models
> hide #3 models
> close #1-2
> close #4-8
> close #10-12
> open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_00_map.mrc
Opened cryosparc_P45_J255_volume_class_00_map.mrc as #1, grid size
288,288,288, pixel 1.11, shown at level 0.0859, step 2, values float32
> volume #1 step 1
> volume #1 level 0.06882
> open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_01_map.mrc
Opened cryosparc_P45_J255_volume_class_01_map.mrc as #2, grid size
288,288,288, pixel 1.11, shown at level 0.0866, step 2, values float32
> volume #2 step 1
> hide #!1 models
> volume #2 level 0.06146
> volume #1 level 0.0615
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_02_map.mrc
Opened cryosparc_P45_J255_volume_class_02_map.mrc as #4, grid size
288,288,288, pixel 1.11, shown at level 0.084, step 2, values float32
> hide #!2 models
> volume #4 step 1
> volume #4 level 0.08398
> volume #4 level 0.07346
> volume #4 level 0.06689
> open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_03_map.mrc
Opened cryosparc_P45_J255_volume_class_03_map.mrc as #5, grid size
288,288,288, pixel 1.11, shown at level 0.0759, step 2, values float32
> hide #!4 models
> volume #5 step 1
> volume #5 level 0.05189
> show #!29 models
> hide #!29 models
> close #5
> open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_04_map.mrc
Opened cryosparc_P45_J255_volume_class_04_map.mrc as #5, grid size
288,288,288, pixel 1.11, shown at level 0.087, step 2, values float32
> volume #5 step 1
> volume #5 level 0.06451
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!5 models
> open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_05_map.mrc
Opened cryosparc_P45_J255_volume_class_05_map.mrc as #6, grid size
288,288,288, pixel 1.11, shown at level 0.0842, step 2, values float32
> hide #!5 models
> volume #6 step 1
> volume #6 level 0.05659
> open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_06_map.mrc
Opened cryosparc_P45_J255_volume_class_06_map.mrc as #7, grid size
288,288,288, pixel 1.11, shown at level 0.087, step 2, values float32
> hide #!6 models
> volume #7 step 1
> volume #7 level 0.07861
> volume #7 level 0.06887
> open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_08_map.mrc
Opened cryosparc_P45_J255_volume_class_08_map.mrc as #8, grid size
288,288,288, pixel 1.11, shown at level 0.0857, step 2, values float32
> hide #!7 models
> volume #8 step 1
> volume #8 level 0.06739
> open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_09_map.mrc
Opened cryosparc_P45_J255_volume_class_09_map.mrc as #10, grid size
288,288,288, pixel 1.11, shown at level 0.0868, step 2, values float32
> hide #!8 models
> volume #10 step 1
> volume #10 level 0.06496
> hide #!10 models
> show #!8 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!8 models
> show #!8 models
> show #!7 models
> hide #!8 models
> hide #!7 models
> show #!6 models
> show #!5 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!2 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> hide #!4 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!4 models
> hide #!2 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> show #!29 models
> hide #!29 models
> show #28 models
> color #4 #b2ffff93 models
> color #4 #b2ffff94 models
> hide #!4 models
> show #26 models
> log metadata #26
Metadata for 7k7k.pdb #26
---
Title | Structure of the epec type III secretion injectisome ESPA filament
Citation | Cryo-em structure of the ESPA filament from enteropathogenicescherichia coli: revealing the mechanism of effectortranslocation In the T3SS. PMID: 33453150
Source (natural) | Escherichia coli O127:H6 (strain E2348/69 / epec)
Experimental method | Electron microscopy
Resolution | 3.56Å
> log chains #26
Chain information for 7k7k.pdb #26
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b | translocon ESPA | B7UM94_ECO27 1-192
> select #26/B:22-192
1293 atoms, 1303 bonds, 171 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select add #26
36204 atoms, 36484 bonds, 4788 residues, 1 model selected
> select subtract #26
Nothing selected
> hide #26 models
> show #!4 models
> volume #4 level 0.06952
> open /Users/tessasmith/Downloads/cryosparc_P45_J258_004_volume_map.mrc
Opened cryosparc_P45_J258_004_volume_map.mrc as #11, grid size 288,288,288,
pixel 1.11, shown at level 0.0753, step 2, values float32
> volume #11 step 1
> hide #!4 models
> volume #11 level 0.06961
> volume #11 level 0.06392
> volume #11 level 0.0412
> volume #11 level 0.045
> volume #11 level 0.05
> volume #11 level 0.055
> volume #11 level 0.06
> open /Users/tessasmith/Downloads/cryosparc_P45_J256_004_volume_map.mrc
Opened cryosparc_P45_J256_004_volume_map.mrc as #12, grid size 288,288,288,
pixel 1.11, shown at level 0.082, step 2, values float32
> hide #!11 models
> hide #!12 models
> show #!12 models
> hide #28 models
> volume #12 step 1
> volume #12 level 0.06923
> volume #12 level 0.0514
> hide #!12 models
> show #!11 models
> open "/Users/tessasmith/Downloads/cryosparc_P45_J208_009_volume_map (2).mrc"
Opened cryosparc_P45_J208_009_volume_map (2).mrc as #13, grid size
288,288,288, pixel 1.11, shown at level 0.085, step 2, values float32
> hide #!11 models
> volume #13 step 1
> volume #13 level 0.07579
> volume #13 level 0.06658
> volume #13 level 0.1534
> volume #13 level 0.0771
> hide #!13 models
> show #!9 models
> volume #9 level 0.03446
> volume #9 level 0.05508
> volume #9 level 0.05122
> volume #9 level 0.1131
> hide #!9 models
> open /Users/tessasmith/Downloads/cryosparc_P45_J259_004_volume_map.mrc
Opened cryosparc_P45_J259_004_volume_map.mrc as #14, grid size 288,288,288,
pixel 1.11, shown at level 0.078, step 2, values float32
> show #!1 models
> hide #!1 models
> volume #14 step 1
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> volume #14 level 0.07369
> volume #14 level 0.06063
> hide #!14 models
> show #26 models
> log metadata #26
Metadata for 7k7k.pdb #26
---
Title | Structure of the epec type III secretion injectisome ESPA filament
Citation | Cryo-em structure of the ESPA filament from enteropathogenicescherichia coli: revealing the mechanism of effectortranslocation In the T3SS. PMID: 33453150
Source (natural) | Escherichia coli O127:H6 (strain E2348/69 / epec)
Experimental method | Electron microscopy
Resolution | 3.56Å
> log chains #26
Chain information for 7k7k.pdb #26
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b | translocon ESPA | B7UM94_ECO27 1-192
> select #26/B:22-192
1293 atoms, 1303 bonds, 171 residues, 1 model selected
> show sel cartoons
> select add #26
36204 atoms, 36484 bonds, 4788 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select subtract #26
Nothing selected
> select #26/A:22-192
1293 atoms, 1303 bonds, 171 residues, 1 model selected
> show sel cartoons
> select #26/F:22-192
1293 atoms, 1303 bonds, 171 residues, 1 model selected
> show sel cartoons
> select add #26
36204 atoms, 36484 bonds, 4788 residues, 1 model selected
> select subtract #26
Nothing selected
> show #28 models
> select add #26
36204 atoms, 36484 bonds, 4788 residues, 1 model selected
> view matrix models #26,1,0,0,-39.582,0,1,0,-71.057,0,0,1,9.0374
> view matrix models #26,1,0,0,-35.4,0,1,0,-77.43,0,0,1,-46.352
> view matrix models #26,1,0,0,-42.602,0,1,0,-64.863,0,0,1,-42.101
> view matrix models #26,1,0,0,-39.026,0,1,0,-71.05,0,0,1,-48.144
> select subtract #26
Nothing selected
> show #!9 models
> select add #28
5328 atoms, 5414 bonds, 660 residues, 1 model selected
> select add #26
41532 atoms, 41898 bonds, 5448 residues, 2 models selected
> select subtract #28
36204 atoms, 36484 bonds, 4788 residues, 1 model selected
> view matrix models #26,1,0,0,36.224,0,1,0,-85.69,0,0,1,-60.629
> view matrix models #26,1,0,0,47.345,0,1,0,-116.38,0,0,1,-75.699
Drag select of 10 residues
> select clear
> select add #28
5328 atoms, 5414 bonds, 660 residues, 1 model selected
> select subtract #28
Nothing selected
> select add #26
36204 atoms, 36484 bonds, 4788 residues, 1 model selected
> view matrix models #26,1,0,0,40.568,0,1,0,-64.131,0,0,1,-77.533
> view matrix models
> #26,-0.55081,0.47711,-0.68482,374.17,-0.20722,0.71664,0.66595,-87.68,0.8085,0.50872,-0.29586,-117.51
> view matrix models
> #26,-0.55081,0.47711,-0.68482,345.65,-0.20722,0.71664,0.66595,-107.28,0.8085,0.50872,-0.29586,-90.467
> view matrix models
> #26,-0.55081,0.47711,-0.68482,344.05,-0.20722,0.71664,0.66595,-99.642,0.8085,0.50872,-0.29586,-48.418
> view matrix models
> #26,-0.55081,0.47711,-0.68482,372.73,-0.20722,0.71664,0.66595,-78.07,0.8085,0.50872,-0.29586,-61.479
> view matrix models
> #26,-0.43358,-0.49501,-0.75298,595.27,-0.1922,0.86718,-0.45941,96.875,0.88038,-0.054474,-0.47113,92.477
> view matrix models
> #26,-0.43358,-0.49501,-0.75298,587.3,-0.1922,0.86718,-0.45941,110.46,0.88038,-0.054474,-0.47113,81.479
> view matrix models
> #26,-0.43358,-0.49501,-0.75298,600.43,-0.1922,0.86718,-0.45941,119.95,0.88038,-0.054474,-0.47113,71.226
> view matrix models
> #26,-0.43358,-0.49501,-0.75298,591.87,-0.1922,0.86718,-0.45941,131.09,0.88038,-0.054474,-0.47113,85.839
> view matrix models
> #26,-0.43358,-0.49501,-0.75298,592.39,-0.1922,0.86718,-0.45941,127.85,0.88038,-0.054474,-0.47113,92.777
> view matrix models
> #26,-0.42929,-0.11615,-0.89567,528,-0.8231,0.45853,0.33505,198.83,0.37177,0.88106,-0.29245,-64.963
> view matrix models
> #26,-0.42929,-0.11615,-0.89567,544.9,-0.8231,0.45853,0.33505,201.55,0.37177,0.88106,-0.29245,-57.926
> view matrix models
> #26,-0.94922,-0.12542,-0.28852,534.06,-0.28599,-0.038157,0.95747,96.359,-0.1311,0.99137,0.00035018,-40.991
> view matrix models
> #26,-0.94922,-0.12542,-0.28852,533.37,-0.28599,-0.038157,0.95747,92.988,-0.1311,0.99137,0.00035018,-22.286
> view matrix models
> #26,0.6269,0.41396,-0.66002,164.61,-0.50697,-0.42652,-0.74904,553.85,-0.59159,0.80418,-0.057525,124.17
> view matrix models
> #26,-0.18673,-0.33544,-0.92337,554.2,-0.98122,0.017376,0.19211,362.06,-0.048398,0.9419,-0.33238,36.525
> view matrix models
> #26,-0.18673,-0.33544,-0.92337,552.78,-0.98122,0.017376,0.19211,360.83,-0.048398,0.9419,-0.33238,44.341
> volume #9 level 0.05895
> view matrix models
> #26,-0.18673,-0.33544,-0.92337,542.85,-0.98122,0.017376,0.19211,356.6,-0.048398,0.9419,-0.33238,35.638
> view matrix models
> #26,-0.18673,-0.33544,-0.92337,541.13,-0.98122,0.017376,0.19211,358.96,-0.048398,0.9419,-0.33238,35.472
> view matrix models
> #26,0.053822,-0.26224,-0.9635,483.88,-0.99273,0.089947,-0.079936,395.57,0.10763,0.9608,-0.25549,-14.385
> view matrix models
> #26,0.053822,-0.26224,-0.9635,473.81,-0.99273,0.089947,-0.079936,395.88,0.10763,0.9608,-0.25549,-24.71
> view matrix models
> #26,0.053822,-0.26224,-0.9635,473.59,-0.99273,0.089947,-0.079936,395.55,0.10763,0.9608,-0.25549,-24.896
> view matrix models
> #26,0.053822,-0.26224,-0.9635,475.62,-0.99273,0.089947,-0.079936,405.55,0.10763,0.9608,-0.25549,-36.738
> view matrix models
> #26,0.053822,-0.26224,-0.9635,474.61,-0.99273,0.089947,-0.079936,408.44,0.10763,0.9608,-0.25549,-23.704
> view matrix models
> #26,0.053822,-0.26224,-0.9635,477.91,-0.99273,0.089947,-0.079936,406.11,0.10763,0.9608,-0.25549,-19.121
> view matrix models
> #26,0.053822,-0.26224,-0.9635,477.67,-0.99273,0.089947,-0.079936,405.81,0.10763,0.9608,-0.25549,-19.869
> color #9 #e5bf99b1 models
> color #9 #e5bf9982 models
> view matrix models
> #26,0.15889,-0.099731,-0.98225,421.66,-0.95867,0.22226,-0.17764,386.02,0.23603,0.96987,-0.060295,-84.425
> view matrix models
> #26,0.15889,-0.099731,-0.98225,418.81,-0.95867,0.22226,-0.17764,389.02,0.23603,0.96987,-0.060295,-91.713
> view matrix models
> #26,0.12545,-0.18708,-0.9743,444.79,-0.92568,0.33121,-0.18278,357.42,0.35689,0.92483,-0.13163,-91.166
> view matrix models
> #26,0.16632,-0.028972,-0.98565,401.06,-0.87657,0.45347,-0.16124,314.4,0.45163,0.8908,0.050025,-136.21
> view matrix models
> #26,0.16632,-0.028972,-0.98565,403.45,-0.87657,0.45347,-0.16124,314.81,0.45163,0.8908,0.050025,-143.06
> view matrix models
> #26,0.16632,-0.028972,-0.98565,402.77,-0.87657,0.45347,-0.16124,317.38,0.45163,0.8908,0.050025,-146.71
> view matrix models
> #26,0.16632,-0.028972,-0.98565,405.66,-0.87657,0.45347,-0.16124,316.8,0.45163,0.8908,0.050025,-147.52
> open /Users/tessasmith/Downloads/cryosparc_P45_J260_004_volume_map.mrc
Opened cryosparc_P45_J260_004_volume_map.mrc as #15, grid size 288,288,288,
pixel 1.11, shown at level 0.0792, step 2, values float32
> hide #!9 models
> hide #28 models
> select subtract #26
Nothing selected
> hide #26 models
> volume #15 step 1
> show #28 models
> hide #28 models
> volume #15 level 0.0703
> show #28 models
> show #26 models
> hide #!15 models
> select #28/A:657
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:606
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #28/A:605
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #28/A:604
22 atoms, 19 bonds, 3 residues, 1 model selected
> select add #28/A:603
30 atoms, 26 bonds, 4 residues, 1 model selected
> select add #28/A:602
42 atoms, 38 bonds, 5 residues, 1 model selected
> select add #28/A:601
48 atoms, 43 bonds, 6 residues, 1 model selected
> select add #28/A:600
52 atoms, 46 bonds, 7 residues, 1 model selected
> select add #28/A:599
58 atoms, 51 bonds, 8 residues, 1 model selected
> select add #28/A:598
64 atoms, 56 bonds, 9 residues, 1 model selected
> select add #28/A:597
71 atoms, 62 bonds, 10 residues, 1 model selected
> select add #28/A:596
80 atoms, 70 bonds, 11 residues, 1 model selected
> select add #28/A:595
91 atoms, 80 bonds, 12 residues, 1 model selected
> select add #28/A:594
99 atoms, 87 bonds, 13 residues, 1 model selected
> select add #28/A:593
105 atoms, 92 bonds, 14 residues, 1 model selected
> style sel stick
Changed 105 atom styles
> show sel atoms
> select clear
> select #26/F:192
10 atoms, 9 bonds, 1 residue, 1 model selected
> select add #26/F:190
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #26/F:191
22 atoms, 19 bonds, 3 residues, 1 model selected
> select clear
> show #!15 models
> color #15 #b2b2ff76 models
> color #15 #b2b2ff75 models
Drag select of 1 residues, 15 cryosparc_P45_J260_004_volume_map.mrc
> select #26/A:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> hide #!15 models
> select #28/A:641
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #28/A:642
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #28/A:644
26 atoms, 23 bonds, 3 residues, 1 model selected
> select add #28/A:643
34 atoms, 30 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 34 atom styles
> select clear
> show #!15 models
> select #26/F:192
10 atoms, 9 bonds, 1 residue, 1 model selected
> select add #26/F:191
14 atoms, 12 bonds, 2 residues, 1 model selected
> hide #!15 models
> select add #26/F:190
22 atoms, 19 bonds, 3 residues, 1 model selected
> select add #26/F:189
28 atoms, 24 bonds, 4 residues, 1 model selected
> select clear
> select add #26
36204 atoms, 36484 bonds, 4788 residues, 1 model selected
> select clear
> select add #26
36204 atoms, 36484 bonds, 4788 residues, 1 model selected
> view matrix models
> #26,0.16632,-0.028972,-0.98565,405.28,-0.87657,0.45347,-0.16124,317.63,0.45163,0.8908,0.050025,-144.72
> show #!15 models
> select subtract #26
Nothing selected
> hide #!15 models
> select #28/A:638
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!15 models
> show #!25 models
> open /Users/tessasmith/Downloads/cryosparc_P45_J263_005_volume_map.mrc
Opened cryosparc_P45_J263_005_volume_map.mrc as #16, grid size 288,288,288,
pixel 1.11, shown at level 0.0816, step 2, values float32
> hide #!15 models
> hide #!25 models
> hide #26 models
> hide #28 models
> volume #16 step 1
> volume #16 level 0.05421
> volume #16 level 0.03779
> volume #16 level 0.05011
> open /Users/tessasmith/Downloads/cryosparc_P45_J254_005_volume_map.mrc
Opened cryosparc_P45_J254_005_volume_map.mrc as #17, grid size 288,288,288,
pixel 1.11, shown at level 0.0714, step 2, values float32
> hide #!16 models
> volume #17 step 1
> show #28 models
> hide #28 models
> show #!29 models
> hide #!29 models
> volume #17 level 0.05787
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!17 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> hide #!17 models
> show #!16 models
> volume #16 level 0.05011
> hide #!16 models
> show #!17 models
> color #17 #ffb2b297 models
> color #17 #ffb2b296 models
> show #28 models
> show #26 models
> hide #28 models
> hide #26 models
> show #28 models
> hide #!17 models
> show #!15 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!11 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> volume #11 level 0.07563
> volume #4 level 0.07346
> volume #11 level 0.0735
> hide #!4 models
> lighting soft
> set bgColor white
> show #!16 models
> hide #!11 models
> volume #16 level 0.01316
> volume #16 level 0.03506
> color #16 #941100ff models
> color #16 #0433ffff models
> color #16 #005493ff models
> volume #16 level 0.0419
> save /Users/tessasmith/Desktop/image2.png supersample 3
> volume #16 level 0.06516
> volume #16 level 0.05148
> save /Users/tessasmith/Desktop/image3.png supersample 3
> volume #16 level 0.07337
> hide #28 models
> show #28 models
> show #26 models
> show #!17 models
> hide #!16 models
> color #17 #ffb2b2b2 models
> color #17 #ffb2b2df models
> color #17 #ffb2b2c8 models
> color #17 #ffb2b2c7 models
> open /Users/tessasmith/Downloads/cryosparc_P45_J253_006_volume_map.mrc
Opened cryosparc_P45_J253_006_volume_map.mrc as #18, grid size 288,288,288,
pixel 1.11, shown at level 0.064, step 2, values float32
> hide #!17 models
> hide #26 models
> hide #28 models
> volume #18 step 1
> show #!29 models
> hide #!29 models
> volume #18 level 0.04923
> volume #18 level 0.03818
> volume #18 level 0.05291
> volume #18 level 0.07502
> volume #18 level 0.05476
> show #!9 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> color #9 #e5bf99ff models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> volume #18 level 0.06
> volume #18 level 0.07105
> hide #!9 models
> hide #!18 models
> show #!16 models
> ui tool show "Surface Color"
> open /Users/tessasmith/Downloads/cryosparc_P45_J266_map_locres.mrc
Opened cryosparc_P45_J266_map_locres.mrc as #19, grid size 288,288,288, pixel
1.11, shown at level 5.51, step 2, values float32
> hide #!19 models
> color sample #16.1 map #19 palette #ff0000:#ffffff:#0000ff
Map values for surface "surface": minimum 2.478, mean 2.685, maximum 4.185
> volume #16 level 0.05781
> volume #16 level 0.07207
> volume #16 level 0.03966
> volume #16 level 0.02022
> volume #16 level 0.025
> volume #16 level 0.0613
> hide #!17 models
> volume #16 level 0.09242
> volume #16 level 0.05223
> open /Users/tessasmith/Downloads/cryosparc_P45_J265_004_volume_map.mrc
Opened cryosparc_P45_J265_004_volume_map.mrc as #20, grid size 288,288,288,
pixel 1.11, shown at level 0.0388, step 2, values float32
> hide #!16 models
> volume #20 step 1
> volume #20 level 0.0544
> volume #20 level 0.07155
> volume #20 level 0.05128
> hide #!20 models
> show #!20 models
> volume #20 level 0.05284
> volume #20 level 0.05
> volume #20 level 0.04
> volume #20 level 0.03
> volume #20 level 0.02
> volume #20 level 0.05
> volume #20 level 0.06559
> volume #20 level 0.07651
> hide #!20 models
> show #!17 models
> show #!18 models
> hide #!17 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!16 models
> volume #18 level 0.04836
> hide #!18 models
> volume #16 level 0.04574
> volume #16 level 0.03019
> volume #16 level 0.05093
> open /Users/tessasmith/Downloads/cryosparc_P45_J267_005_volume_map.mrc
Opened cryosparc_P45_J267_005_volume_map.mrc as #21, grid size 288,288,288,
pixel 1.11, shown at level 0.0458, step 2, values float32
> hide #!16 models
> volume #21 step 1
> volume #21 level 0.02739
> volume #21 level 0.03581
> hide #!21 models
> show #!11 models
> show #!14 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!14 models
> hide #!11 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/tessasmith/Downloads/cryosparc_P45_J268_010_volume_map.mrc
Opened cryosparc_P45_J268_010_volume_map.mrc as #1, grid size 288,288,288,
pixel 1.11, shown at level 0.0421, step 2, values float32
> open /Users/tessasmith/Downloads/cryosparc_P45_J268_010_volume_map.mrc
Opened cryosparc_P45_J268_010_volume_map.mrc as #2, grid size 288,288,288,
pixel 1.11, shown at level 0.0421, step 2, values float32
OpenGL version: 4.1 ATI-5.1.35
OpenGL renderer: AMD Radeon Pro 5300M 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: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0)
OS Loader Version: 580~743
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 8 days, 18 hours, 40 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-019
Option ROM Version: 113-D32207P1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
SAMSUNG:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Adapter Firmware Version: 15.75
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 4 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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