![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17683 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Bus error
Current thread 0x0000000208ca4c80 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, 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.segment._segment, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree (total: 61)
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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Address size fault"},"pc":{"value":6876115916},"far":{"value":0}},"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":158},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":159},{"imageOffset":2118012,"imageIndex":45},{"imageOffset":2117824,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":45},{"imageOffset":4264588,"symbol":"QFileInfoGatherer::run()","symbolLocation":136,"imageIndex":50},{"imageOffset":2063036,"imageIndex":45},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":159},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":159}]},{"id":48149798,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":159}],"threadState":{"x":[{"value":13236727808},{"value":99755},{"value":13236191232},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13236727808},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6876351340},"far":{"value":0}}},{"id":48150079,"name":"QFileInfoGatherer","threadState":{"x":[{"value":260},{"value":0},{"value":1536},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13106752904},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8754645624},{"value":0},{"value":105553134500096},{"value":105553134500160},{"value":13106753760},{"value":0},{"value":0},{"value":1536},{"value":1537},{"value":1792},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6876373216},"cpsr":{"value":1610616832},"fp":{"value":13106753024},"sp":{"value":13106752880},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6876115916},"far":{"value":0}},"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":158},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":159},{"imageOffset":2118012,"imageIndex":45},{"imageOffset":2117824,"symbol":"QWaitCondition::wait(QMutex*, 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Address size fault"},"pc":{"value":6876351340},"far":{"value":0}}},{"id":48152777,"frames":[{"imageOffset":240888,"symbol":"_dispatch_kevent_mach_msg_recv.cold.3","symbolLocation":32,"imageIndex":164},{"imageOffset":158912,"symbol":"_dispatch_kevent_mach_msg_recv","symbolLocation":300,"imageIndex":164},{"imageOffset":148928,"symbol":"_dispatch_event_loop_merge","symbolLocation":148,"imageIndex":164},{"imageOffset":84684,"symbol":"_dispatch_workloop_worker_thread","symbolLocation":512,"imageIndex":164},{"imageOffset":11876,"symbol":"_pthread_wqthread","symbolLocation":292,"imageIndex":159},{"imageOffset":7028,"symbol":"start_wqthread","symbolLocation":8,"imageIndex":159}],"threadState":{"x":[{"value":389},{"value":105553159091840},{"value":13227960784},{"value":0},{"value":0},{"value":2303},{"value":0},{"value":0},{"value":528},{"value":2},{"value":2147483647},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0},{"value":11446537792},{"value":8754640928},{"value":0},{"value":2303},{"value":0},{"value":13227960784},{"value":0},{"value":389},{"value":356},{"value":105553159091840},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6874721472},"cpsr":{"value":1073745920},"fp":{"value":13227960384},"sp":{"value":13227960320},"esr":{"value":2449473543,"description":"(Data Abort) byte read Translation fault"},"pc":{"value":6874803448},"far":{"value":0}}},{"id":48152778,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":159}],"threadState":{"x":[{"value":13235990528},{"value":0},{"value":13235453952},{"value":0},{"value":278532},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13235990528},"esr":{"value":0,"description":" Address size fault"},"pc":{"value":6876351340},"far":{"value":0}}}],
"usedImages" : [
[deleted to fit within ticket limits]
],
"sharedCache" : {
"base" : 6871711744,
"size" : 5020123136,
"uuid" : "bb86a9b4-8362-37b8-b028-212703af6f30"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=4.3G written=151.7M(3%) resident=2923K(0%) swapped_out=148.9M(3%) unallocated=4.1G(97%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1152K 9 \nActivity Tracing 256K 1 \nCG image 6064K 69 \nColorSync 704K 38 \nCoreAnimation 6016K 260 \nCoreGraphics 112K 7 \nCoreImage 64K 2 \nCoreServices 624K 2 \nCoreUI image data 5472K 43 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 3.6G 146 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.7M 42 \nStack 194.4M 42 \nVM_ALLOCATE 364.8M 514 \nVM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)\n__AUTH 5486K 695 \n__AUTH_CONST 77.2M 942 \n__CTF 824 1 \n__DATA 34.3M 1089 \n__DATA_CONST 37.0M 1106 \n__DATA_DIRTY 2775K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 652.6M 159 \n__OBJC_RO 61.3M 1 \n__OBJC_RW 2391K 1 \n__TEXT 1.3G 1124 \n__TEXT (graphics) 208K 2 \n__TPRO_CONST 128K 2 \ndyld private memory 3616K 31 \nmapped file 656.5M 99 \npage table in kernel 2923K 1 \nshared memory 3424K 39 \n=========== ======= ======= \nTOTAL 7.1G 6841 \nTOTAL, minus reserved VM space 7.0G 6841 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "7b11e2041a356ced653b915858857415859140e7",
"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : {
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"deploymentId" : 240000004
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{
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"factorPackIds" : {
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},
"deploymentId" : 240000031
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],
"experiments" : [
{
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"experimentId" : "67f46877b1ea9f1f114b8d0b",
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}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/sahtelis/Downloads/cryosparc_P8_J146_006_volume_map.mrc
Opened cryosparc_P8_J146_006_volume_map.mrc as #1, grid size 384,384,384,
pixel 0.828, shown at level 0.0326, step 2, values float32
> volume gaussian #1 sDev 2
Opened cryosparc_P8_J146_006_volume_map.mrc gaussian as #2, grid size
384,384,384, pixel 0.828, shown at step 1, values float32
> volume #2 level 0.04504
> ui tool show "Segment Map"
> volume #2 level 0.07079
> surface dust #2 size 8.28
> volume #2 level 0.06934
> volume #2 level 0.05546
> volume #2 level 0.05141
> volume #2 level 0.05285
Segmenting cryosparc_P8_J146_006_volume_map.mrc gaussian, density threshold
0.052852
Only showing 60 of 60 regions.
Showing 60 region surfaces
136 watershed regions, grouped to 60 regions
Showing cryosparc_P8_J146_006_volume_map gaussian.seg - 60 regions, 60
surfaces
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> hide #3.2 models
> hide #3.3 models
> show #3.3 models
> hide #3.3 models
> hide #3.4 models
> hide #3.5 models
> show #3.5 models
> hide #3.5 models
> hide #3.6 models
> hide #3.7 models
> show #3.7 models
> hide #3.8 models
> show #3.8 models
> hide #3.9 models
> show #3.9 models
> hide #3.10 models
> show #3.10 models
> hide #3.11 models
> show #3.11 models
> hide #3.12 models
> show #3.12 models
> hide #3.13 models
> show #3.13 models
> hide #3.13 models
> hide #3.14 models
> hide #3.15 models
> hide #3.16 models
> hide #3.17 models
> show #3.17 models
> hide #3.18 models
> show #3.18 models
> hide #3.19 models
> hide #3.20 models
> hide #3.21 models
> show #3.21 models
> hide #3.22 models
> show #3.22 models
> hide #3.23 models
> show #3.23 models
> hide #3.24 models
> show #3.24 models
> hide #3.25 models
> show #3.25 models
> hide #3.26 models
> show #3.26 models
> hide #3.27 models
> show #3.27 models
> hide #3.26 models
> show #3.26 models
> hide #3.27 models
> show #3.27 models
> hide #3.28 models
> show #3.28 models
> hide #3.29 models
> show #3.29 models
> hide #3.30 models
> show #3.30 models
> hide #3.31 models
> show #3.31 models
> hide #3.31 models
> show #3.31 models
> hide #3.32 models
> show #3.32 models
> hide #3.33 models
> show #3.33 models
> hide #3.34 models
> show #3.34 models
> hide #3.35 models
> show #3.35 models
> hide #3.36 models
> show #3.36 models
> hide #3.37 models
> show #3.37 models
> hide #3.38 models
> show #3.38 models
> hide #3.39 models
> show #3.39 models
> hide #3.40 models
> show #3.40 models
> hide #3.41 models
> show #3.41 models
> hide #3.42 models
> show #3.42 models
> hide #3.42 models
> show #3.42 models
> hide #3.43 models
> show #3.43 models
> hide #3.43 models
> hide #3.44 models
> show #3.44 models
> hide #3.44 models
> hide #3.45 models
> hide #3.46 models
> hide #3.47 models
> hide #3.48 models
> show #3.48 models
> hide #3.48 models
> hide #3.49 models
> show #3.49 models
> hide #3.49 models
> show #3.49 models
> hide #3.50 models
> show #3.50 models
> hide #3.51 models
> show #3.51 models
> hide #3.51 models
> show #3.51 models
> hide #3.52 models
> show #3.52 models
> hide #3.53 models
> show #3.53 models
> hide #3.54 models
> show #3.54 models
> hide #3.55 models
> show #3.55 models
> hide #3.56 models
> show #3.56 models
> hide #3.56 models
> hide #3.57 models
> hide #3.58 models
> show #3.58 models
> hide #3.58 models
> hide #3.59 models
> hide #3.60 models
> show #3.60 models
> hide #3.60 models
> hide #3.55 models
> volume #2 level 0.04834
> select #3.53
1 model selected
Ungrouped to 2 regions
> select #3.62
1 model selected
> hide #3.62 models
> hide #3.61 models
> show #3.61 models
> select subtract #3.62
Nothing selected
> select add #3.62
1 model selected
> select subtract #3.62
Nothing selected
> select #3.52
1 model selected
Ungrouped to 2 regions, but did not show all surfaces, see Options
> hide #3.61 models
> show #3.61 models
> select subtract #3.53
Nothing selected
> select #3.50
1 model selected
Ungrouped to 2 regions, but did not show all surfaces, see Options
> select subtract #3.52
Nothing selected
> select #3.54
1 model selected
Ungrouped to 2 regions, but did not show all surfaces, see Options
> select subtract #3.50
Nothing selected
> select #3.51
1 model selected
Ungrouped to 2 regions, but did not show all surfaces, see Options
> select subtract #3.54
Nothing selected
> select #3.49
1 model selected
Ungrouped to 2 regions, but did not show all surfaces, see Options
> select subtract #3.51
Nothing selected
> select add #3.7
1 model selected
> select add #3.8
2 models selected
> select add #3.9
3 models selected
> select add #3.10
4 models selected
> select add #3.11
5 models selected
> select add #3.12
6 models selected
> select add #3.17
7 models selected
> select add #3.18
8 models selected
> select subtract #3.18
7 models selected
> select add #3.18
8 models selected
> select add #3.21
9 models selected
> select add #3.22
10 models selected
> select add #3.23
11 models selected
> select add #3.24
12 models selected
> select add #3.25
13 models selected
> select add #3.26
14 models selected
> select add #3.27
15 models selected
> select add #3.28
16 models selected
> select add #3.29
17 models selected
> select add #3.30
18 models selected
> select add #3.31
19 models selected
> select add #3.32
20 models selected
> select add #3.33
21 models selected
> select add #3.34
22 models selected
> select add #3.35
23 models selected
> select add #3.36
24 models selected
> select add #3.37
25 models selected
> select add #3.38
26 models selected
> select add #3.39
27 models selected
> select add #3.40
28 models selected
> select add #3.41
29 models selected
> select add #3.42
30 models selected
> select add #3.50
31 models selected
> select add #3.51
32 models selected
> select add #3.52
33 models selected
> select add #3.53
34 models selected
> select add #3.54
35 models selected
> select add #3.61
36 models selected
Saving 36 regions to mrc file...
Opened cryosparc_P8_J146_006_volume_map_36_regions.mrc as #4, grid size
97,103,84, pixel 0.828, shown at step 1, values float32
Wrote cryosparc_P8_J146_006_volume_map_36_regions.mrc
> select add #4
38 models selected
> hide #!4 models
> select subtract #4
36 models selected
> select add #4
38 models selected
> select add #3
64 models selected
> select subtract #3
2 models selected
> hide #!3 models
> hide #!4 models
> select subtract #4
Nothing selected
> show #!4 models
> volume #4 level 0.05405
> select add #4
2 models selected
> select subtract #4
Nothing selected
> volume resample #4 onGrid #1
Opened cryosparc_P8_J146_006_volume_map_36_regions.mrc resampled as #5, grid
size 384,384,384, pixel 0.828, shown at step 1, values float32
> volume #5 level 0.0538
> select add #5
2 models selected
> save /Users/sahtelis/Desktop/J146_resampled_mask.mrc models #5
> select subtract #5
Nothing selected
> hide #!5 models
> show #!5 models
> volume #1 color #ffd479
> volume #1 level 0.09445
> surface dust #1 size 8.28
> volume #1 level 0.1004
> volume #1 level 0.05346
> volume #1 level 0.09547
> volume #1 level 0.1034
> show #!5 models
> volume #5 level 0.05356
> volume #1 level 0.09764
> volume #1 level 0.09909
> volume #5 level 0.05308
> open /Users/sahtelis/Downloads/cryosparc_P8_J167_mask.mrc
Opened cryosparc_P8_J167_mask.mrc as #6, grid size 384,384,384, pixel 0.828,
shown at level 0.378, step 2, values float32
> transparency #6 80
> open /Users/sahtelis/Downloads/cryosparc_P8_J168_mask.mrc
Opened cryosparc_P8_J168_mask.mrc as #7, grid size 384,384,384, pixel 0.828,
shown at level 5e-05, step 2, values float32
> hide #!6 models
> hide #!5 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> select add #7
2 models selected
> select subtract #7
Nothing selected
> show #!7 models
> close #7
> show #!6 models
> show #!5 models
> hide #!5 models
> volume #6 color #00fdff
> transparency #6 80
> volume #5 level 0.05951
> volume #5 level 0.05478
> open /Users/sahtelis/Downloads/cryosparc_P8_J146_006_volume_mask_refine.mrc
Opened cryosparc_P8_J146_006_volume_mask_refine.mrc as #7, grid size
384,384,384, pixel 0.828, shown at level 1, step 2, values float32
> volume #7 level 0.9514
> volume #7 level 1
> transparency #7 80
> open /Users/sahtelis/Downloads/cryosparc_P8_J169_mask.mrc
Opened cryosparc_P8_J169_mask.mrc as #8, grid size 384,384,384, pixel 0.828,
shown at level 0.256, step 2, values float32
> transparency #8 90
> transparency #8 95
> transparency #8 75
> transparency #7 50
> open /Users/sahtelis/Downloads/cryosparc_P8_J172_mask.mrc
Opened cryosparc_P8_J172_mask.mrc as #9, grid size 384,384,384, pixel 0.828,
shown at level 0.756, step 2, values float32
> transparency #9 75
> volume #5 level 0.06374
> open /Users/sahtelis/Downloads/cryosparc_P8_J173_mask.mrc
Opened cryosparc_P8_J173_mask.mrc as #10, grid size 384,384,384, pixel 0.828,
shown at level 0.152, step 2, values float32
> transparency #10 75
> volume #4 level 0.07771
> volume #5 level 0.06922
> open /Users/sahtelis/Desktop/J146_resampled_mask.mrc
Opened J146_resampled_mask.mrc as #11, grid size 384,384,384, pixel 0.828,
shown at level 6.87e-06, step 2, values float32
> volume #11 level 0.05469
> volume #11 step 1
> volume #11 level 0.1382
> volume #11 level 0.1116
> volume #11 level 0.07321
> volume #11 level 0.05403
> volume #11 level 0.000996
> volume #11 level 0.1327
> volume #11 level 0.063
> volume #5 level 0.06399
> open /Users/sahtelis/Downloads/cryosparc_P8_J176_mask.mrc
Opened cryosparc_P8_J176_mask.mrc as #12, grid size 384,384,384, pixel 0.828,
shown at level 0.212, step 2, values float32
> transparency #12 75
> open /Users/sahtelis/Downloads/cryosparc_P8_J116_mask.mrc
Opened cryosparc_P8_J116_mask.mrc as #13, grid size 192,192,192, pixel 1.84,
shown at level 0.179, step 1, values float32
> select add #13
2 models selected
> ui mousemode right "move picked models"
> view matrix models #13,1,0,0,20.055,0,1,0,43.827,0,0,1,49.464
> view matrix models #13,1,0,0,24.889,0,1,0,44.173,0,0,1,57.051
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.969,0.22642,0.098841,-26.29,-0.18339,0.9273,-0.32633,142.36,-0.16554,0.29809,0.94007,42.414
> view matrix models
> #13,0.77265,0.63481,0.005494,-50.043,-0.34268,0.42434,-0.83816,343.7,-0.5344,0.64571,0.5454,108.74
> view matrix models
> #13,0.94942,-0.085736,0.30208,1.4694,0.30374,0.0067551,-0.95273,321.05,0.079643,0.99629,0.032455,16.116
> select subtract #13
Nothing selected
> open /Users/sahtelis/Downloads/cryosparc_P7_mask_resampled.mrc
Opened cryosparc_P7_mask_resampled.mrc as #14, grid size 192,192,192, pixel
1.84, shown at level 0.000176, step 1, values float32
> volume #14 level 0.2349
> select add #14
2 models selected
> ui mousemode right "move picked models"
> view matrix models #14,1,0,0,61.128,0,1,0,17.604,0,0,1,-28.738
> select subtract #14
Nothing selected
> volume #5 level 0.05503
> volume #14 level 0.5205
> volume #14 level 0.552
> volume #14 level 0.349
> open /Users/sahtelis/Downloads/cryosparc_P8_J178_mask.mrc
Opened cryosparc_P8_J178_mask.mrc as #15, grid size 384,384,384, pixel 0.92,
shown at level 0.0542, step 2, values float32
> volume #15 level 0.7947
> select add #15
2 models selected
> view matrix models #15,1,0,0,27.383,0,1,0,45.79,0,0,1,-19.521
> select subtract #15
Nothing selected
> select add #15
2 models selected
> view matrix models #15,1,0,0,61.368,0,1,0,30.138,0,0,1,-34.39
> select subtract #15
Nothing selected
> volume #15 level 0.7533
> select add #15
2 models selected
> view matrix models #15,1,0,0,4.9698,0,1,0,-10.529,0,0,1,-28.507
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.87644,-0.48144,0.0076299,111.96,-0.032724,-0.075366,-0.99662,348.23,0.48039,0.87323,-0.081809,-96.359
> ui mousemode right "move picked models"
> view matrix models
> #15,0.87644,-0.48144,0.0076299,88.355,-0.032724,-0.075366,-0.99662,328.39,0.48039,0.87323,-0.081809,-92.977
> ui tool show "Fit in Map"
> close #11
> fitmap #15 inMap #5
Fit map cryosparc_P8_J178_mask.mrc in map J146_resampled_mask.mrc using 40336
points
correlation = 0.5494, correlation about mean = 0.3775, overlap = 766
steps = 284, shift = 28, angle = 32.2 degrees
Position of cryosparc_P8_J178_mask.mrc (#15) relative to
J146_resampled_mask.mrc (#5) coordinates:
Matrix rotation and translation
0.83678446 -0.41196724 0.36065878 25.81452186
0.06044072 -0.58517270 -0.80865309 384.27295098
0.54418626 0.69846682 -0.46476383 14.64019992
Axis 0.94784378 -0.11542239 0.29710240
Axis point 0.00000000 188.68159462 103.11819006
Rotation angle (degrees) 127.34233772
Shift along axis -15.53592919
> select subtract #15
Nothing selected
> transparency #15 75
> volume #15 level 0.5029
> volume #15 level 0.9697
> volume #12 level 0.5271
> open /Users/sahtelis/Downloads/cryosparc_P8_J170_004_volume_map.mrc
Opened cryosparc_P8_J170_004_volume_map.mrc as #11, grid size 384,384,384,
pixel 0.828, shown at level 0.0323, step 2, values float32
> volume #11 level 0.092
> surface dust #1 size 8.28
> surface dust #11 size 8.28
> volume #11 level 0.09824
> tile
2 models tiled
> surface dust #1 size 8.28
> surface dust #11 size 8.28
> volume #11 level 0.09894
> volume #5 level 0.06195
> volume #5 level 0.06106
> volume #5 level 0.07289
> volume #5 level 0.05347
> volume #5 level 0.1091
> volume #5 level 0.07177
> volume #5 level 0.06843
> open /Users/sahtelis/Downloads/cryosparc_P8_J177_005_volume_map_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P8_J177_005_volume_map.mrc
Opened cryosparc_P8_J177_005_volume_map_sharp.mrc as #16.1, grid size
384,384,384, pixel 0.828, shown at level 0.0282, step 2, values float32
Opened cryosparc_P8_J177_005_volume_map.mrc as #16.2, grid size 384,384,384,
pixel 0.828, shown at level 0.0276, step 2, values float32
> volume #16.2 level 0.0537
> volume #16.2 level 0.07109
> surface dust #16.2 size 8.28
> volume #16.2 level 0.1015
> volume #16.1 level 0.1717
> view matrix models #16.1,1,0,0,8.3771,0,1,0,45.183,0,0,1,-9.4037
> surface dust #16.1 size 8.28
> view matrix models
> #16.2,0.65387,0.7444,0.13533,-77.567,-0.7551,0.65333,0.054662,203.16,-0.047724,-0.13793,0.98929,27.934
> volume #16.2 level 0.07631
> volume #1 level 0.0864
> tile
2 models tiled
> volume #16.2 level 0.1154
> open /Users/sahtelis/Downloads/cryosparc_P8_J179_006_volume_map.mrc
Opened cryosparc_P8_J179_006_volume_map.mrc as #17, grid size 384,384,384,
pixel 0.828, shown at level 0.028, step 2, values float32
> volume #17 level 0.07377
> surface dust #1 size 8.28
> surface dust #16.2 size 8.28
> surface dust #17 size 8.28
> tile
3 models tiled
> view matrix models
> #17,0.47554,0.4184,-0.77382,157.77,-0.16641,0.90655,0.38791,60.323,0.86381,-0.055694,0.50073,44.248
> volume #17 level 0.08984
> volume #17 level 0.1096
> volume #17 level 0.0577
> volume #17 level 0.05523
> surface dust #1 size 8.28
> surface dust #16.2 size 8.28
> surface dust #17 size 8.28
> volume #17 level 0.07377
> volume #17 level 0.1034
> volume #17 level 0.1195
> volume #17 level 0.03669
> volume #17 level 0.08366
> open /Users/sahtelis/Downloads/cryosparc_P8_J185_class_00_00120_volume.mrc
Opened cryosparc_P8_J185_class_00_00120_volume.mrc as #18, grid size
384,384,384, pixel 0.828, shown at level 0.037, step 2, values float32
> volume #18 level 0.06319
> tile
4 models tiled
> volume #18 level 0.09629
> surface dust #1 size 8.28
> surface dust #16.2 size 8.28
> surface dust #17 size 8.28
> surface dust #18 size 8.28
> volume #18 level 0.07836
> volume #18 level 0.0656
> volume #18 level 0.09353
> close #18
> volume #16.2 level 0.1189
> volume #1 level 0.0717
> view matrix models
> #1,0.47454,0.77795,-0.41184,38.299,-0.79748,0.57802,0.17296,216.9,0.3726,0.24636,0.89469,-52.118
> surface dust #1 size 8.28
> volume #1 level 0.04431
> volume #1 level 0.1024
> view matrix models
> #1,0.89837,-0.38805,0.20577,63.905,0.39915,0.91678,-0.013729,13.146,-0.18332,0.094467,0.9785,69.612
> surface dust #1 size 8.28
> surface dust #1 size 15
> surface dust #1 size 50
> surface dust #1 size 20
> volume #1 level 0.09308
> volume #1 level 0.08172
> volume #1 level 0.08373
> volume #!1 step 2
> volume #!1 step 1
> volume #!1 step 2
> volume #!1 step 1
> volume #!1 step 2
> volume #!1 step 1
> volume #!1 step 2
> volume #!1 step 1
> volume #!1 step 2
> volume #1 level 0.07838
> volume #1 level 0.07704
> volume #1 level 0.07905
> volume #1 level 0.08439
> volume #1 level 0.08907
> open /Users/sahtelis/Desktop/connexin-str_analysis/cx45hexamer.pdb
Summary of feedback from opening /Users/sahtelis/Desktop/connexin-
str_analysis/cx45hexamer.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
6855 messages similar to the above omitted
Chain information for cx45hexamer.pdb #18
---
Chain | Description
A B C D E F | No description available
> select add #18
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> view sel
> hide sel atoms
> show sel cartoons
Computing secondary structure
> close #3
> close #2
> show #!4 models
> hide #!4 models
> select add #1
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 5 models selected
> view sel
> select subtract #1
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> view matrix models
> #18,0.67271,-0.10281,-0.73273,53.915,0.49824,0.79507,0.34587,201.84,0.54702,-0.59774,0.58607,127.5
> view matrix models
> #18,0.65263,-0.18568,0.73457,80.66,0.16639,0.98096,0.10013,206.43,-0.73918,0.056873,0.6711,156.55
> view matrix models
> #18,-0.48157,0.44067,0.75756,132.25,0.3554,0.88832,-0.29081,218.52,-0.80111,0.12919,-0.58441,229.86
> view sel
> select subtract #18
Nothing selected
> view
> select add #18
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> hide #!16 models
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.8207,-0.30231,-0.48484,65.717,0.41115,-0.27676,0.86854,235.87,-0.39675,-0.91215,-0.10284,223.64
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.04203, steps = 440
shifted from previous position = 72
rotated from previous position = 19 degrees
atoms outside contour = 7335, contour level = 0.08907
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.62827515 0.56637961 -0.53337069 180.96682766
-0.27468713 -0.80291085 -0.52903777 145.82572500
-0.72788539 -0.18587124 0.66002620 193.22784077
Axis 0.36940384 0.20938662 -0.90537177
Axis point 151.95084883 66.74020583 0.00000000
Rotation angle (degrees) 152.32297507
Shift along axis -77.55923579
> ui mousemode right "move picked models"
> view matrix models
> #18,0.408,0.64653,-0.64462,147.58,0.87411,-0.072791,0.48025,201.28,0.26357,-0.75941,-0.59484,187.09
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.04411, steps = 188
shifted from previous position = 6
rotated from previous position = 15.1 degrees
atoms outside contour = 7153, contour level = 0.08907
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.42157068 0.70860795 -0.56582043 161.67004188
-0.41484147 -0.70556264 -0.57453262 159.41959278
-0.80634021 -0.00748033 0.59140454 196.59579498
Axis 0.44258615 0.18772647 -0.87685590
Axis point 166.14099186 60.86457326 0.00000000
Rotation angle (degrees) 140.16250230
Shift along axis -70.90598535
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.94804,-0.0057125,-0.31811,140.29,0.30787,0.26865,0.91271,229.59,0.080248,-0.96322,0.25645,210.82
> view matrix models
> #18,0.92714,0.050192,-0.37134,140.07,0.36236,0.13223,0.92261,227.71,0.095409,-0.98995,0.10441,207.38
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.07109, steps = 144
shifted from previous position = 2.25
rotated from previous position = 20.5 degrees
atoms outside contour = 5950, contour level = 0.08907
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.07623670 0.95061425 -0.30086597 159.80223870
-0.59044282 -0.28619075 -0.75463366 160.68651464
-0.80347064 0.12011338 0.58310165 196.83088560
Axis 0.47491174 0.27287072 -0.83666027
Axis point 204.26142170 40.69782489 0.00000000
Rotation angle (degrees) 112.93352754
Shift along axis -44.94197741
> transparency (#!18 & sel) 40
> transparency (#!18 & sel) 90
> select subtract #18
Nothing selected
> transparency #1,18 50
> volume #1 level 0.07437
> volume #1 level 0.07838
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.07109, steps = 72
shifted from previous position = 2.55
rotated from previous position = 0.0135 degrees
atoms outside contour = 5304, contour level = 0.078381
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.07646471 0.95058674 -0.30089504 159.79817882
-0.59039354 -0.28635254 -0.75461084 160.68736830
-0.80348519 0.11994539 0.58311619 196.83082526
Axis 0.47484909 0.27288637 -0.83669072
Axis point 204.23457920 40.71727241 0.00000000
Rotation angle (degrees) 112.94520133
Shift along axis -44.95711231
> select add #18
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> ui mousemode right "move picked models"
> view matrix models
> #18,-0.19505,-0.90637,0.37476,189.19,0.63208,0.17601,0.75465,214.27,-0.74995,0.38407,0.53857,242.75
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.33084,-0.88654,0.3234,192.53,0.62271,0.052404,0.78069,214.74,-0.70907,0.45967,0.53472,241.59
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.07109, steps = 96
shifted from previous position = 6.13
rotated from previous position = 8.59 degrees
atoms outside contour = 5308, contour level = 0.078381
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.07645871 0.95058024 -0.30091708 159.80286222
-0.59038603 -0.28636771 -0.75461095 160.68805984
-0.80349127 0.11996067 0.58310466 196.82911043
Axis 0.47485971 0.27287900 -0.83668710
Axis point 204.23698048 40.71608572 0.00000000
Rotation angle (degrees) 112.94584495
Shift along axis -44.95203936
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.18656,-0.91326,0.36215,186.7,0.62897,0.17215,0.75813,216,-0.75472,0.36922,0.5423,245.97
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.07109, steps = 60
shifted from previous position = 2.39
rotated from previous position = 0.0215 degrees
atoms outside contour = 5312, contour level = 0.078381
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.07631387 0.95055319 -0.30103928 159.79528380
-0.59064448 -0.28634261 -0.75441821 160.69975972
-0.80331508 0.12023462 0.58329096 196.83192728
Axis 0.47486493 0.27269467 -0.83674424
Axis point 204.24647067 40.68321509 0.00000000
Rotation angle (degrees) 112.93476308
Shift along axis -44.99483778
> select subtract #18
Nothing selected
> select add #18
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> ui mousemode right "move picked models"
> view matrix models
> #18,0.901,0.077379,-0.42686,139.77,0.40895,-0.47989,0.77619,220.96,-0.14479,-0.87391,-0.46402,202.8
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.07109, steps = 80
shifted from previous position = 4.96
rotated from previous position = 0.0322 degrees
atoms outside contour = 5307, contour level = 0.078381
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.07659949 0.95059415 -0.30083734 159.80728269
-0.59029227 -0.28639949 -0.75467224 160.68402416
-0.80354675 0.11977445 0.58306649 196.82870346
Axis 0.47481488 0.27296565 -0.83668428
Axis point 204.22472212 40.73364563 0.00000000
Rotation angle (degrees) 112.95240095
Shift along axis -44.94338686
> select subtract #18
Nothing selected
> transparency #1,18 0
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.07109, steps = 52
shifted from previous position = 0.738
rotated from previous position = 0.0163 degrees
atoms outside contour = 5305, contour level = 0.078381
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.07634683 0.95063372 -0.30077651 159.80071813
-0.59039635 -0.28619011 -0.75467025 160.69358050
-0.80349433 0.11996068 0.58310044 196.82964236
Axis 0.47486078 0.27293910 -0.83666689
Axis point 204.25246653 40.71641440 0.00000000
Rotation angle (degrees) 112.93697099
Shift along axis -44.93819016
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.07109, steps = 28
shifted from previous position = 0.00182
rotated from previous position = 0.0185 degrees
atoms outside contour = 5308, contour level = 0.078381
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.07641813 0.95055412 -0.30100988 159.79673951
-0.59053507 -0.28639572 -0.75448369 160.70003920
-0.80338560 0.12010067 0.58322143 196.82806468
Axis 0.47485251 0.27276313 -0.83672897
Axis point 204.23734910 40.70230813 0.00000000
Rotation angle (degrees) 112.94182141
Shift along axis -44.97881417
> transparency #1 40
> transparency #1 25
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting full
> lighting shadows false
> set bgColor gray
> set bgColor #80808000
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.07109, steps = 48
shifted from previous position = 1.46
rotated from previous position = 0.0121 degrees
atoms outside contour = 5310, contour level = 0.078381
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.07644755 0.95058754 -0.30089687 159.80724359
-0.59040260 -0.28634275 -0.75460746 160.69291023
-0.80348016 0.11996241 0.58311961 196.82770103
Axis 0.47485319 0.27288074 -0.83669024
Axis point 204.24120543 40.71545817 0.00000000
Rotation angle (degrees) 112.94425625
Shift along axis -44.94883593
> transparency #1 50
> volume #1 level 0.055
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.07109, steps = 84
shifted from previous position = 4.37
rotated from previous position = 0.00775 degrees
atoms outside contour = 3662, contour level = 0.054998
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.07636301 0.95062334 -0.30080523 159.80281748
-0.59038189 -0.28622439 -0.75466856 160.69123105
-0.80350342 0.11996120 0.58308782 196.83166777
Axis 0.47486703 0.27293239 -0.83666553
Axis point 204.25155538 40.71622640 0.00000000
Rotation angle (degrees) 112.93893353
Shift along axis -44.93933970
> volume #1 level 0.07905
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.07109, steps = 68
shifted from previous position = 4.15
rotated from previous position = 0.0178 degrees
atoms outside contour = 5349, contour level = 0.079049
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.07634430 0.95059997 -0.30088382 159.80185884
-0.59061851 -0.28624065 -0.75447723 160.69449089
-0.80333128 0.12010753 0.58329484 196.82812531
Axis 0.47481974 0.27278314 -0.83674104
Axis point 204.24502505 40.68757590 0.00000000
Rotation angle (degrees) 112.93241736
Shift along axis -44.98234656
> select add #18
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> view matrix models
> #18,0.89747,-0.27868,-0.34189,145.15,0.28876,-0.21471,0.93302,229.68,-0.33342,-0.93608,-0.11223,220.36
> select subtract #18
Nothing selected
> vop flip #1 axis z
Opened cryosparc_P8_J146_006_volume_map.mrc z flip as #2, grid size
384,384,384, pixel 0.828, shown at step 1, values float32
> volume #1 level 0.08306
> volume #2 level 0.1093
> vop flip #1 axis y
Opened cryosparc_P8_J146_006_volume_map.mrc y flip as #3, grid size
384,384,384, pixel 0.828, shown at step 1, values float32
> hide #!2 models
> volume #3 level 0.09892
> show #!1 models
> hide #!3 models
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.04268, steps = 188
shifted from previous position = 6.9
rotated from previous position = 8.96 degrees
atoms outside contour = 7042, contour level = 0.083057
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.93140714 -0.32135671 0.17091056 192.52505820
0.14796778 -0.76331386 -0.62885397 136.61718648
0.33254488 -0.56042988 0.75850650 155.86798788
Axis 0.13655545 -0.32257714 0.93664112
Axis point 72.80606893 107.04206720 0.00000000
Rotation angle (degrees) 165.49077176
Shift along axis 128.21313107
> select add #18
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.72003,-0.33393,0.60832,175.01,0.63643,-0.031678,-0.77068,188.97,0.27662,0.94207,0.18971,209.75
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.0431, steps = 112
shifted from previous position = 4.86
rotated from previous position = 15.6 degrees
atoms outside contour = 6954, contour level = 0.083057
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.43520424 -0.45711484 -0.77565658 155.73526707
-0.01300825 -0.85824065 0.51308246 170.46981478
-0.90023769 0.23338562 0.36756374 192.99112649
Axis -0.51850735 0.23095084 0.82329328
Axis point 126.67965892 76.24589665 0.00000000
Rotation angle (degrees) 164.35278148
Shift along axis 117.50856501
> ui mousemode right "move picked models"
> view matrix models
> #18,0.85659,-0.34031,0.38786,163.87,0.40613,-0.019016,-0.91362,184.23,0.31829,0.94012,0.12192,212.32
> view matrix models
> #18,0.6955,-0.15062,-0.70256,149.32,-0.58134,0.45668,-0.67341,225.78,0.42227,0.87679,0.23006,208.04
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.04548, steps = 124
shifted from previous position = 7.58
rotated from previous position = 13 degrees
atoms outside contour = 6836, contour level = 0.083057
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.44719659 -0.61352490 -0.65084733 151.89572058
0.16780641 -0.77229109 0.61270492 165.67034441
-0.87855339 0.16478321 0.44831939 195.41323316
Axis -0.48217662 0.24511993 0.84108378
Axis point 112.42916162 85.90442710 0.00000000
Rotation angle (degrees) 152.32349733
Shift along axis 131.72743986
> view matrix models
> #18,-0.88476,-0.24805,0.39456,216.03,0.45856,-0.31214,0.83204,219.93,-0.083225,0.91708,0.38991,226.83
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.66468,-0.35183,0.6591,213.9,0.72457,-0.088409,0.68351,209.33,-0.18221,0.93188,0.31369,228.52
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.07109, steps = 84
shifted from previous position = 2.58
rotated from previous position = 8.86 degrees
atoms outside contour = 5622, contour level = 0.083057
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.47304500 -0.72329530 -0.50306280 160.04533695
0.36145273 -0.68004787 0.63787668 157.40902582
-0.80348006 0.11991096 0.58313035 196.82986870
Axis -0.41803832 0.24245992 0.87547539
Axis point 102.71456963 95.07055672 0.00000000
Rotation angle (degrees) 141.71894841
Shift along axis 143.58000196
> ui mousemode right "move picked models"
> view matrix models
> #18,0.72705,-0.16671,-0.66604,144.84,-0.68382,-0.08889,-0.72422,225.41,0.061528,0.98199,-0.17863,212.99
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.07109, steps = 52
shifted from previous position = 1.25
rotated from previous position = 0.0237 degrees
atoms outside contour = 5618, contour level = 0.083057
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.47332367 -0.72332458 -0.50275848 160.06744280
0.36152580 -0.67996883 0.63791953 157.39935366
-0.80328304 0.12018227 0.58334589 196.83005136
Axis -0.41784714 0.24254257 0.87554376
Axis point 102.70836556 95.05875121 0.00000000
Rotation angle (degrees) 141.71821323
Shift along axis 143.62564280
> select subtract #18
Nothing selected
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.1223
> volume #3 color #d783ff
> hide #!1 models
> volume #3 level 0.09968
> surface dust #3 size 8.28
> volume #3 level 0.09968
> close #2
> close #3
> show #!1 models
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J146_006_volume_map.mrc
(#1) using 8232 atoms
average map value = 0.04165, steps = 72
shifted from previous position = 2.53
rotated from previous position = 3.87 degrees
atoms outside contour = 7019, contour level = 0.083057
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J146_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.73138822 -0.37582273 -0.56905921 171.23333760
-0.14221003 -0.73204960 0.66624284 172.34664503
-0.66696882 0.56820815 0.48196673 189.75424915
Axis -0.36093920 0.36047870 0.86010348
Axis point 120.93448551 55.54066605 0.00000000
Rotation angle (degrees) 172.19482838
Shift along axis 163.53076028
> open /Users/sahtelis/Downloads/cryosparc_P8_J187_class_00_00120_volume.mrc
Opened cryosparc_P8_J187_class_00_00120_volume.mrc as #2, grid size
384,384,384, pixel 0.828, shown at level 0.0382, step 2, values float32
> volume #2 level 0.03505
> hide #!2 models
> hide #!1 models
> hide #!18 models
> show #!2 models
> volume #4 level 0.08217
> volume #2 level 0.02392
> surface dust #2 size 8.28
> volume #2 level 0.03648
> open /Users/sahtelis/Downloads/cryosparc_P8_J185_class_00_00120_volume.mrc
Opened cryosparc_P8_J185_class_00_00120_volume.mrc as #3, grid size
384,384,384, pixel 0.828, shown at level 0.037, step 2, values float32
> volume #3 level 0.05905
> surface dust #2 size 8.28
> surface dust #3 size 8.28
> surface dust #2 size 8.28
> surface dust #3 size 8.28
> volume #3 level 0.0625
> volume #3 level 0.04836
> volume #3 level 0.01871
> view matrix models
> #3,-0.15654,0.61328,0.7742,-66.162,0.50431,0.72361,-0.47124,40.31,-0.84922,0.31666,-0.42256,281.65
> view matrix models
> #3,-0.53577,0.76927,-0.34809,154.39,0.8156,0.36483,-0.4491,60.368,-0.21849,-0.52452,-0.82289,418.93
> view matrix models
> #3,-0.53577,0.76927,-0.34809,155.56,0.8156,0.36483,-0.4491,61.551,-0.21849,-0.52452,-0.82289,429.1
> surface dust #3 size 8.28
> volume #3 level 0.04388
> volume #3 level 0.06216
> volume #3 level 0.1028
> volume #3 level 0.08733
> view matrix models
> #1,-0.042936,-0.19542,-0.97978,368.15,0.98371,-0.17964,-0.007279,73.801,-0.17459,-0.96413,0.19995,332.97
> view matrix models
> #1,-0.72928,-0.097432,-0.67724,414.33,0.40175,0.74024,-0.53912,107.53,0.55385,-0.66525,-0.50069,282.74
> volume #1 level 0.04631
> volume #1 level 0.07838
> open /Users/sahtelis/Desktop/connexin-str_analysis/7z1t.pdb
7z1t.pdb title:
CONNEXIN43 gap junction channel structure In digitonin [more info...]
Chain information for 7z1t.pdb #19
---
Chain | Description | UniProt
A B C D E F G H I J K L | gap junction α-1 protein | CXA1_HUMAN 1-382
> view matrix models #19,1,0,0,3.8272,0,1,0,14.743,0,0,1,8.9671
> hide #!19 atoms
> show #!19 cartoons
> view
> ui tool show Orthoplanes
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> stereo cross
Unknown command: stereo cross
> stereo cross #19
Unknown command: stereo cross #19
> view #19
> stereo none
Unknown command: stereo none
> stereo cross
Unknown command: stereo cross
> camera stereo
Could not switch graphics mode. Graphics driver did not create OpenGL context.
> camera ortho
> stereo mode
Unknown command: stereo mode
> stereo
Unknown command: stereo
> \--stereo
Unknown command: --stereo
> unview
Unknown command: unview
> ui tool show "Side View"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 742, in
_onSliderMoved
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 742, in
_onSliderMoved
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> view
> view orient
> ui tool show "Side View"
> open /Users/sahtelis/Downloads/cryosparc_P8_J195_class_00_final_volume.mrc
Opened cryosparc_P8_J195_class_00_final_volume.mrc as #20, grid size
192,192,192, pixel 1.66, shown at level 0.096, step 1, values float32
> ui tool show "Side View"
> view
> volume #20 level 0.2037
> hide #!19 models
> view matrix models
> #20,0.53622,-0.43907,-0.72089,240.23,0.28649,0.89803,-0.33386,40.639,0.79397,-0.027502,0.60733,-64.017
> volume #20 level 0.253
> volume #20 level 0.1285
> volume #20 level 0.1882
> close #20
> open /Users/sahtelis/Downloads/cryosparc_P8_J197_class_00_final_volume.mrc
Opened cryosparc_P8_J197_class_00_final_volume.mrc as #20, grid size
192,192,192, pixel 1.66, shown at level 0.0902, step 1, values float32
> volume #20 level 0.143
> volume #20 level 0.247
> volume #20 level 0.2485
> surface dust #20 size 16.6
> volume #20 level 0.1119
> volume #20 level 0.1694
> volume #20 level 0.2051
> open /Users/sahtelis/Downloads/cryosparc_P8_J201_005_volume_map.mrc
> /Users/sahtelis/Downloads/cryosparc_P8_J200_005_volume_map.mrc
> /Users/sahtelis/Downloads/cryosparc_P8_J198_006_volume_map_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P8_J198_006_volume_map.mrc
> /Users/sahtelis/Downloads/cryosparc_P8_J197_class_00_final_volume.mrc
Opened cryosparc_P8_J201_005_volume_map.mrc as #21.1, grid size 384,384,384,
pixel 0.828, shown at level 0.0332, step 2, values float32
Opened cryosparc_P8_J200_005_volume_map.mrc as #21.2, grid size 384,384,384,
pixel 0.828, shown at level 0.037, step 2, values float32
Opened cryosparc_P8_J198_006_volume_map_sharp.mrc as #21.3, grid size
384,384,384, pixel 0.828, shown at level 0.0396, step 2, values float32
Opened cryosparc_P8_J198_006_volume_map.mrc as #21.4, grid size 384,384,384,
pixel 0.828, shown at level 0.0378, step 2, values float32
Opened cryosparc_P8_J197_class_00_final_volume.mrc as #21.5, grid size
192,192,192, pixel 1.66, shown at level 0.0902, step 1, values float32
> close #20
> volume #21.5 level 0.1321
> volume #21.4 level 0.09271
> surface dust #21.4 size 8.28
> volume #21.3 level 0.1525
> surface dust #21.3 size 8.28
> volume #21.3 level 0.135
> volume #21.4 level 0.09507
> volume #21.2 level 0.1023
> surface dust #21.2 size 8.28
> volume #21.2 level 0.1132
> volume #21.2 level 0.1233
> volume #21.2 level 0.1216
> volume #21.2 level 0.1191
> volume #21.2 level 0.05625
> volume #21.2 level 0.1048
> volume #21.1 level 0.07454
> surface dust #21.1 size 8.28
> volume #21.1 level 0.1044
> volume #21.1 level 0.07684
> volume #21.1 level 0.05845
> volume #21.1 level 0.06535
> volume #21.1 level 0.07914
> tile
2 models tiled
> volume #21.2 level 0.0839
> view matrix models
> #21.2,0.99985,-0.0018764,0.016978,105.83,-0.016073,0.23305,0.97233,-35.022,-0.0057812,-0.97246,0.23298,274.88
> volume #21.1 level 0.06305
> volume #21.1 level 0.08489
> show #!18 models
> select add #18
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.17246,-0.96591,-0.19306,179.24,-0.18437,0.22419,-0.95695,205.99,0.96761,-0.12944,-0.21675,178.73
> view matrix models
> #18,-0.2714,-0.93939,-0.20949,182.1,0.52904,0.036228,-0.84782,185.18,0.80403,-0.34093,0.48714,196.74
> view matrix models
> #18,-0.45377,-0.8642,-0.21737,187.87,0.71134,-0.20436,-0.67248,182.17,0.53674,-0.45978,0.70747,209.03
> view matrix models
> #18,-0.36778,-0.61996,-0.6931,176.73,0.91721,-0.1191,-0.38018,181.5,0.15315,-0.77554,0.61243,218.44
> ui mousemode right "move picked models"
> view matrix models
> #18,-0.36778,-0.61996,-0.6931,152.5,0.91721,-0.1191,-0.38018,125.85,0.15315,-0.77554,0.61243,218.44
> view matrix models
> #18,-0.53271,-0.84583,-0.028062,185.27,-0.37567,0.20663,0.90342,234.9,-0.75835,0.49181,-0.42783,230.51
> view matrix models
> #18,-0.55278,-0.71358,-0.43039,179.31,-0.7614,0.6424,-0.087169,240.99,0.33868,0.27951,-0.89843,186.53
> view matrix models
> #18,-0.44808,-0.72272,-0.52621,160.22,-0.21005,0.65724,-0.72382,158,0.86897,-0.2138,-0.4463,177.22
> view matrix models
> #18,-0.45325,-0.68558,-0.56969,158.05,0.8872,-0.28516,-0.3627,114.58,0.086202,-0.66983,0.7375,223.21
> view matrix models
> #18,-0.50224,-0.60762,-0.61526,158.82,-0.18895,0.77143,-0.60761,160.42,0.84383,-0.18891,-0.50226,177.01
> ui tool show "Fit in Map"
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = -0.0003347, steps = 1088
shifted from previous position = 37.3
rotated from previous position = 22.3 degrees
atoms outside contour = 8232, contour level = 0.083896
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
-0.59947670 -0.76339561 -0.24053047 11.08406634
-0.69594673 0.34872458 0.62773352 197.45546384
-0.39533012 0.54370799 -0.74033491 167.19638642
Axis -0.44550607 0.82075273 0.35761613
Axis point 61.71178558 0.00000000 37.47963761
Rotation angle (degrees) 174.58876881
Shift along axis 216.91621738
> view matrix models
> #18,-0.3358,-0.78675,-0.51794,153.75,-0.091601,0.57454,-0.81334,153.28,0.93747,-0.22568,-0.265,182.73
> view matrix models
> #18,-0.32698,-0.79656,-0.5085,156.77,0.87633,-0.054157,-0.47866,111.48,0.35374,-0.60213,0.71576,218.79
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = -0.001464, steps = 88
shifted from previous position = 6.18
rotated from previous position = 2.6 degrees
atoms outside contour = 8232, contour level = 0.083896
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
-0.43862575 -0.46519489 -0.76889612 27.99966253
0.01449408 0.85182026 -0.52363368 133.33302696
0.89855297 -0.24082365 -0.36688771 121.52555446
Axis 0.16087278 -0.94850659 0.27286479
Axis point -20.42350945 0.00000000 93.20818040
Rotation angle (degrees) 118.47964938
Shift along axis -88.80282651
> view matrix models
> #18,-0.44027,-0.68467,-0.58085,159.03,0.28733,0.50546,-0.8136,144.07,0.85065,-0.5251,-0.025812,194.23
> volume #21.1 level 0.05615
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = -3.311e-05, steps = 2000
shifted from previous position = 69.8
rotated from previous position = 30.9 degrees
atoms outside contour = 8232, contour level = 0.083896
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
-0.91923624 0.05980308 -0.38913801 -7.84647421
-0.09286363 0.92757373 0.36191628 180.26122229
0.38259788 0.36882331 -0.84710583 128.25456158
Axis 0.00877951 -0.98095151 -0.19405426
Axis point -12.42371596 0.00000000 45.66283333
Rotation angle (degrees) 156.83621537
Shift along axis -201.78475015
> volume #21.1 level 0.0642
> view matrix models
> #18,-0.61924,-0.40734,-0.67128,89.765,0.70613,0.085003,-0.70297,136.24,0.3434,-0.90931,0.23499,213.42
> select subtract #18
Nothing selected
> tile
2 models tiled
> view matrix models
> #18,-0.61924,-0.40734,-0.67128,120.55,0.70613,0.085003,-0.70297,147.33,0.3434,-0.90931,0.23499,213.42
> view matrix models
> #21.1,0.93469,0.33891,0.10723,-72.859,-0.08334,-0.084321,0.99295,35.693,0.34557,-0.93703,-0.050569,259.81
> view matrix models
> #21.2,0.91889,-0.38603,0.081343,40.572,-0.0063404,0.19171,0.98143,-102.27,-0.39445,-0.90235,0.17372,336.25
> open /Users/sahtelis/Downloads/cryosparc_P8_J201_005_volume_map_sharp.mrc
Opened cryosparc_P8_J201_005_volume_map_sharp.mrc as #20, grid size
384,384,384, pixel 0.828, shown at level 0.0369, step 2, values float32
> volume #20 level 0.1227
> surface dust #21.1 size 8.28
> surface dust #21.2 size 8.28
> surface dust #20 size 8.28
> hide #!18 models
> view matrix models #20,1,0,0,30.522,0,1,0,-16.384,0,0,1,0
> view matrix models
> #20,0.99892,0.00025921,-0.046485,51.952,-0.0035018,0.99756,-0.069687,-12.374,0.046354,0.069774,0.99649,-17.91
> volume #20 level 0.07859
> tile
2 models tiled
> volume #21.1 level 0.05385
> open /Users/sahtelis/Downloads/cryosparc_P8_J201_005_volume_mask_refine.mrc
Opened cryosparc_P8_J201_005_volume_mask_refine.mrc as #22, grid size
384,384,384, pixel 0.828, shown at level 0.447, step 2, values float32
> show #!12 models
> hide #!21.2 models
> hide #!21.1 models
> hide #!21 models
> hide #!20 models
> tile
2 models tiled
> open /Users/sahtelis/Downloads/cryosparc_P8_J198_006_volume_mask_refine.mrc
Opened cryosparc_P8_J198_006_volume_mask_refine.mrc as #23, grid size
384,384,384, pixel 0.828, shown at level 1, step 2, values float32
> volume #23 level 0.9144
> tile
3 models tiled
> volume #23 level 0.8885
> show #!15 models
> tile
4 models tiled
> close #13
> close #9
> close #8
> close #7
> volume #15 level 0.05331
> hide #!12 models
> show #!12 models
> view
> select add #21.4
2 models selected
> view
> select subtract #21.4
Nothing selected
> hide #!15 models
> hide #!12 models
> view
> select add #21.4
2 models selected
> view
> view sel
> hide #!21.4 models
> select subtract #21.4
Nothing selected
> show #!21.5 models
> hide #!21.5 models
> show #!21.4 models
> view matrix models
> #20,-0.052336,-0.99859,0.0093783,458.7,-0.20576,0.0015931,-0.9786,344.67,0.9772,-0.053146,-0.20555,85.131
> volume #20 level 0.1522
> volume #21.1 level 0.06995
> view
> tile
2 models tiled
> select add #21.2
2 models selected
> view matrix models
> #21.2,-0.58638,0.5781,0.56741,109.13,0.32024,-0.47797,0.81792,34.654,0.74405,0.66132,0.095137,-112.43
> view matrix models
> #21.2,-0.12867,0.75545,0.64245,-19.365,0.34376,-0.57369,0.74344,63.352,0.9302,0.31651,-0.18588,-55.358
> fitmap #21.2 inMap #21.1
Fit map cryosparc_P8_J200_005_volume_map.mrc in map
cryosparc_P8_J201_005_volume_map.mrc using 12950 points
correlation = 0.5746, correlation about mean = 0.1423, overlap = 52.52
steps = 404, shift = 31, angle = 15.3 degrees
Position of cryosparc_P8_J200_005_volume_map.mrc (#21.2) relative to
cryosparc_P8_J201_005_volume_map.mrc (#21.1) coordinates:
Matrix rotation and translation
0.52049717 -0.85384597 0.00545439 178.32015593
0.83401506 0.50701836 -0.21760340 -28.72923958
0.18303431 0.11781100 0.97602203 -50.38466517
Axis 0.19388076 -0.10264714 0.97564021
Axis point 120.79075206 143.65183909 0.00000000
Rotation angle (degrees) 59.88290925
Shift along axis -11.63548336
> view matrix models
> #21.2,-0.34885,-0.30707,0.88544,126.58,0.93714,-0.10614,0.33241,-32.977,-0.008094,0.94575,0.3248,-66.399
> view matrix models
> #21.2,0.77924,0.38448,0.49493,-97.146,0.55691,-0.78701,-0.26544,238.66,0.28746,0.48248,-0.82739,146.24
> ui mousemode right "rotate selected models"
> view matrix models
> #21.2,0.70684,0.28189,0.64878,-94.13,0.58353,-0.75079,-0.30954,235.78,0.39984,0.59737,-0.69518,88.792
> view matrix models
> #21.2,-0.48408,-0.51308,-0.70881,440.45,0.47202,-0.8352,0.2822,171.53,-0.73679,-0.19796,0.64649,179.63
> fitmap #21.2 inMap #21.1
Fit map cryosparc_P8_J200_005_volume_map.mrc in map
cryosparc_P8_J201_005_volume_map.mrc using 12950 points
correlation = 0.9116, correlation about mean = 0.5487, overlap = 186
steps = 220, shift = 34.8, angle = 2.06 degrees
Position of cryosparc_P8_J200_005_volume_map.mrc (#21.2) relative to
cryosparc_P8_J201_005_volume_map.mrc (#21.1) coordinates:
Matrix rotation and translation
0.50021156 -0.86590322 0.00001251 217.10735622
0.86590322 0.50021156 -0.00001393 -58.19886002
0.00000581 0.00001780 0.99999999 -1.08267179
Axis 0.00001832 0.00000387 1.00000000
Axis point 158.96959681 158.97412619 0.00000000
Rotation angle (degrees) 59.98600249
Shift along axis -1.07891914
> volume #21.2 level 0.09957
> select subtract #21.2
Nothing selected
> volume #21.1 level 0.08461
> surface dust #21.1 size 8.28
> surface dust #21.1 size 15.28
> surface dust #21.1 size 20.28
> surface dust #21.1 size 40
> surface dust #21.1 size 90
> surface dust #21.1 size 50
> surface dust #21.1 size 10
> surface dust #21.2 size 10
> surface dust #21.2 size 15
> surface dust #21.2 size 18
> surface dust #21.2 size 10
> tile
2 models tiled
> volume #21.2 level 0.09526
> volume #21.2 level 0.09598
> open /Users/sahtelis/Downloads/cryosparc_P8_J199_005_volume_map.mrc
> /Users/sahtelis/Downloads/cryosparc_P8_J199_005_volume_mask_refine.mrc
Opened cryosparc_P8_J199_005_volume_map.mrc as #7.1, grid size 384,384,384,
pixel 0.828, shown at level 0.0375, step 2, values float32
Opened cryosparc_P8_J199_005_volume_mask_refine.mrc as #7.2, grid size
384,384,384, pixel 0.828, shown at level 1, step 2, values float32
> volume #7.1 level 0.09574
> surface dust #21.1 size 8.28
> surface dust #21.2 size 8.28
> surface dust #7.1 size 8.28
> surface dust #7.2 size 8.28
> tile
2 models tiled
> surface dust #21.1 size 8.28
> surface dust #21.2 size 8.28
> surface dust #7.1 size 8.28
> surface dust #7.2 size 8.28
> volume #7.1 level 0.1021
> ui mousemode right "move picked models"
> view matrix models
> #7.1,1,6.8348e-16,-2.1094e-15,4.2512,1.87e-15,1,-4.2327e-16,-121.61,4.996e-16,-3.4694e-17,1,-5.7056
> tile
3 models tiled
> view
> view matrix models
> #7.1,1,5.1695e-16,-2.2204e-15,-55.681,1.759e-15,1,-7.0083e-16,-15.525,8.6042e-16,-6.4532e-16,1,46.855
> hide #!15 models
> view matrix models
> #21.1,0.11386,0.51881,0.84728,-39.859,-0.44657,-0.73509,0.51012,182.98,0.88748,-0.43645,0.14799,71.335
> view matrix models
> #21.2,0.1664,-0.57234,0.80295,208.18,0.14557,0.81964,0.55407,-114.98,-0.97525,0.024691,0.21971,274.59
> volume #21.1 level 0.06591
> volume #21.2 level 0.09742
> volume #21.2 level 0.08737
> view matrix models
> #21.2,0.1664,-0.57234,0.80295,213.76,0.14557,0.81964,0.55407,-122.09,-0.97525,0.024691,0.21971,266.88
> show #!22 models
> hide #!22 models
> show #!18 models
> select add #18
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> view matrix models
> #18,-0.43736,0.55389,-0.70847,539.11,0.41115,-0.5775,-0.7053,114.74,-0.7998,-0.59976,0.024842,246.11
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.73158,-0.67613,-0.087413,557.01,0.036646,0.089032,-0.99535,122.7,0.68077,-0.73138,-0.040357,198.03
> view matrix models
> #18,0.12344,-0.96733,-0.22144,526.84,-0.27607,0.18087,-0.94397,133.74,0.95318,0.17766,-0.24472,187.94
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.04713, steps = 324
shifted from previous position = 44.9
rotated from previous position = 18.5 degrees
atoms outside contour = 6599, contour level = 0.087374
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
-0.97973109 -0.08044360 0.18345540 212.18777012
-0.16526003 0.84215941 -0.51328034 31.64448848
-0.11320858 -0.53319454 -0.83838384 365.92560057
Axis -0.06440714 0.95948028 -0.27431607
Axis point 121.05478299 0.00000000 179.10593878
Rotation angle (degrees) 171.10662321
Shift along axis -83.68341846
> select subtract #18
Nothing selected
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.04957, steps = 116
shifted from previous position = 10
rotated from previous position = 9.48 degrees
atoms outside contour = 6706, contour level = 0.087374
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.81524682 0.02039119 -0.57875460 148.90297619
0.44198240 -0.66766425 0.59906266 27.78081073
-0.37419815 -0.74418325 -0.55332369 372.45362983
Axis -0.94419534 -0.14378696 0.29634518
Axis point 0.00000000 87.18300348 204.53716043
Rotation angle (degrees) 134.65776440
Shift along axis -34.21317582
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.04957, steps = 48
shifted from previous position = 0.0122
rotated from previous position = 0.0231 degrees
atoms outside contour = 6707, contour level = 0.087374
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.81514886 0.02072144 -0.57888083 148.89943657
0.44232223 -0.66753163 0.59895962 27.76522631
-0.37400996 -0.74429309 -0.55330319 372.45790749
Axis -0.94416395 -0.14400246 0.29634057
Axis point 0.00000000 87.16619874 204.54366986
Rotation angle (degrees) 134.65554307
Shift along axis -34.20935343
> surface dust #21.2 size 10
> surface dust #21.2 size 20
> surface dust #21.2 size 30
> surface dust #21.2 size 50
> surface dust #21.2 size 90
> surface dust #21.2 size 100
> surface dust #21.2 size 10
> hide #!18 models
> show #!18 models
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.04227, steps = 80
shifted from previous position = 5.2
rotated from previous position = 2.35 degrees
atoms outside contour = 6948, contour level = 0.087374
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.85534107 0.19541492 0.47979655 173.48125930
-0.51632523 0.39739580 0.75860720 64.44925257
-0.04242596 -0.89659893 0.44080659 380.85813540
Axis -0.88235346 0.27838517 -0.37941280
Axis point 0.00000000 283.15384549 37.35121031
Rotation angle (degrees) 69.71001443
Shift along axis -279.63252359
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.04227, steps = 44
shifted from previous position = 0.0186
rotated from previous position = 0.029 degrees
atoms outside contour = 6946, contour level = 0.087374
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.85537981 0.19495489 0.47991462 173.48931886
-0.51622105 0.39757089 0.75858635 64.44248444
-0.04290997 -0.89662146 0.44071391 380.88655955
Axis -0.88237543 0.27871278 -0.37912108
Axis point 0.00000000 283.31610395 37.34380710
Rotation angle (degrees) 69.70631383
Shift along axis -279.52389104
> select add #18
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> view matrix models
> #18,-0.46989,-0.83874,-0.27517,533.96,0.50174,-0.51025,0.6985,135.66,-0.72627,0.19015,0.66059,199.67
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05285, steps = 76
shifted from previous position = 2.71
rotated from previous position = 9.72 degrees
atoms outside contour = 6533, contour level = 0.087374
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
-0.73134073 0.62150361 -0.28084526 211.75658908
0.67878276 0.70332638 -0.21115399 9.01733307
0.06629290 -0.34505843 -0.93623714 351.03187321
Axis -0.35570111 -0.92213096 0.15215520
Axis point 85.82756580 0.00000000 186.60971510
Rotation angle (degrees) 169.15072286
Shift along axis -30.22589056
> select subtract #18
Nothing selected
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05285, steps = 56
shifted from previous position = 1.56
rotated from previous position = 0.0155 degrees
atoms outside contour = 6533, contour level = 0.087374
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
-0.35586392 0.92831372 0.10767801 209.32764542
0.91603208 0.32367797 0.23689206 8.96411255
0.18505713 0.18293784 -0.96555044 349.14684496
Axis -0.56717217 -0.81341711 -0.12910591
Axis point 96.75476635 0.00000000 175.50446104
Rotation angle (degrees) 177.27374154
Shift along axis -171.09329780
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05285, steps = 40
shifted from previous position = 0.0248
rotated from previous position = 0.0377 degrees
atoms outside contour = 6535, contour level = 0.087374
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
-0.35539105 0.92850938 0.10755273 209.29225135
0.91627087 0.32331645 0.23646184 8.93181225
0.18478345 0.18258385 -0.96566985 349.15455217
Axis -0.56738189 -0.81330635 -0.12888204
Axis point 96.75381532 0.00000000 175.50893099
Rotation angle (degrees) 177.27860345
Shift along axis -171.01268199
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05285, steps = 28
shifted from previous position = 0.0195
rotated from previous position = 0.0256 degrees
atoms outside contour = 6535, contour level = 0.087374
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
-0.35570374 0.92838408 0.10760065 209.31653899
0.91610510 0.32355664 0.23677537 8.95645278
0.18500357 0.18279538 -0.96558768 349.14603195
Axis -0.56724257 -0.81337972 -0.12903220
Axis point 96.74922176 -0.00000000 175.50555246
Rotation angle (degrees) 177.27277721
Shift along axis -171.06932869
> transparency #18#21.2#!7,21 50
> transparency #18#21.2#!7,21 30
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> lighting simple
> lighting full
> hide #!18 models
> show #!18 models
> transparency #18#21.2#!7,21 20
> lighting shadows false
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05285, steps = 84
shifted from previous position = 3.29
rotated from previous position = 0.0112 degrees
atoms outside contour = 6536, contour level = 0.087374
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.59188793 0.80507367 -0.03905249 174.13283803
0.79869095 -0.57929783 0.16280915 6.64013675
0.10845032 -0.12755564 -0.98588443 349.66573409
Axis -0.89138795 -0.45281739 -0.01959425
Axis point 0.00000000 -24.97778936 176.05113698
Rotation angle (degrees) 170.62634639
Shift along axis -165.07812139
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05285, steps = 40
shifted from previous position = 0.00934
rotated from previous position = 0.011 degrees
atoms outside contour = 6533, contour level = 0.087374
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.59187513 0.80508930 -0.03892408 174.14097388
0.79867456 -0.57928102 0.16294928 6.64744309
0.10864073 -0.12753330 -0.98586636 349.65373350
Axis -0.89138369 -0.45282186 -0.01968447
Axis point 0.00000000 -24.97142100 176.03809861
Rotation angle (degrees) 170.62246424
Shift along axis -165.11928120
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05285, steps = 40
shifted from previous position = 0.00656
rotated from previous position = 0.00849 degrees
atoms outside contour = 6532, contour level = 0.087374
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.59195771 0.80502418 -0.03901500 174.13062004
0.79862753 -0.57935911 0.16290217 6.64839525
0.10853647 -0.12758966 -0.98587055 349.65956458
Axis -0.89140700 -0.45277838 -0.01962885
Axis point 0.00000000 -24.96252504 176.04566580
Rotation angle (degrees) 170.62241064
Shift along axis -165.09491964
> transparency #18#21.2#!7,21 40
> hide #!18 models
> transparency #21.2#!7,21 0
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> lighting full
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting shadows false
> volume #21.2 level 0.09014
> volume #21.2 level 0.1113
> volume #21.2 level 0.08922
> surface dust #21.2 size 20
> surface dust #21.2 size 10
> surface dust #21.2 size 16
> volume #21.2 level 0.08553
> lighting simple
> lighting full
> lighting simple
> lighting soft
> surface dust #21.2 size 16
> surface dust #21.2 size 18
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> surface dust #21.2 size 15
> surface dust #21.2 size 10
> surface dust #21.2 size 8
> surface dust #21.2 size 8.28
> surface dust #21.2 size 15
> lighting full
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting simple
> graphics silhouettes true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> show #!18 models
> transparency #18#21.2#!7,21 30
> lighting full
> graphics silhouettes true
> hide #!18 models
> transparency #21.2#!7,21 0
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> volume #21.2 level 0.05237
> volume #21.2 level 0.08277
> volume #21.2 level 0.0883
> volume #21.2 level 0.1067
> volume #21.2 level 0.09014
> volume #21.2 level 0.08645
> surface dust #21.2 size 15
> surface dust #21.2 size 16
> surface dust #21.2 size 17
> surface dust #21.2 size 15
> volume #21.2 level 0.08553
> volume #21.2 level 0.06527
> volume #21.2 level 0.08553
> volume #21.2 color #ffd479
> volume #21.2 color #d4fb79
> volume #21.2 color #fffc79
> volume #21.2 color #ffd479
> volume #21.2 color #ff9300
> volume #21.2 color #ffd479
> volume #21.2 color #ffd47900
> volume #21.2 color #ffd47980
> volume #21.2 color #73fcd6
> volume #21.2 color #76d6ff
> volume #21.2 color #0096ff
> volume #21.2 color #00fdff
> volume #21.2 color #73fdff
> volume #21.2 color #73fcd6
> volume #21.2 color #76d6ff
> volume #21.2 color #73fdff
> volume #21.2 color #fdc30c
> volume #21.2 color #fdd70c
> volume #21.2 color #fdd35f
> volume #21.2 color #fde97d
> volume #21.2 color #fdee94
> volume #21.2 color #fdeb9c
> volume #21.2 color #fde396
> volume #21.2 color #fdd694
> lighting soft
> graphics silhouettes false
> lighting full
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting soft
> volume #21.2 color #699ef9
> volume #21.2 color #5c91f9
> volume #21.2 color #7394f9
> volume #21.2 color #91b3f9
> volume #21.2 color #82baf9
> volume #21.2 color #77baf9
> volume #21.2 color #68b9f9
> volume #21.2 color #5fabf9
> volume #21.2 color #22c1f9
> volume #21.2 color #52c3f9
> volume #21.2 color #72e0f9
> volume #21.2 color #86e6f9
> volume #21.2 color #61cff9
> volume #21.2 color #5fccf5
> volume #21.2 color #72c9f5
> volume #21.2 color #ace4f3
> volume #21.2 color #a0dcf3
> volume #21.2 color #90d3f3
> volume #21.2 color #7dd3f3
> volume #21.2 color #7cc3f3
> volume #21.2 color #81bcf3
> volume #21.2 color #66ccf3
> volume #21.2 color #f3f3ee
> volume #21.2 color #e9c3f3
> volume #21.2 color #f3d7bb
> volume #21.2 color #82c8f3
> volume #21.2 color #67b7f3
> volume #21.2 color #7eb5f3
> volume #21.2 color #51aff3
> volume #21.2 color #5fb6f3
> volume #21.2 color #6dc2f3
> volume #21.2 color #76d0f3
> set bgColor gray
> set bgColor black
> set bgColor transparent
> lighting soft
> lighting full
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> set bgColor white
> set bgColor #ffffff00
> set bgColor gray
> set bgColor #80808000
> surface dust #21.2 size 15
> surface dust #21.2 size 8.28
> surface dust #21.2 size 10
> surface dust #21.2 size 16
> surface dust #21.2 size 12
> surface dust #21.2 size 15
> surface dust #21.2 size 18
> surface dust #21.2 size 15
> surface dust #21.2 size 16
> surface dust #21.2 size 17
> surface dust #21.2 size 18
> surface dust #21.2 size 17
> surface dust #21.2 size 18
> surface dust #21.2 size 19
> surface dust #21.2 size 20
> graphics silhouettes false
> graphics silhouettes true
> save /Users/sahtelis/Desktop/image1.png supersample 3
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250514.cxs includeMaps true
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!18 models
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.04748, steps = 164
shifted from previous position = 5.78
rotated from previous position = 23 degrees
atoms outside contour = 6576, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.66641990 -0.25762288 0.69965349 180.36346905
0.39479975 -0.67411176 -0.62426477 4.61963299
0.63246952 0.69224548 -0.34753204 352.13110535
Axis 0.89507417 0.04567730 0.44357166
Axis point 0.00000000 -53.99744133 128.95021996
Rotation angle (degrees) 132.65731305
Shift along axis 317.84507440
> hide #!21.2 models
> open /Users/sahtelis/Downloads/cryosparc_P8_J200_005_volume_map_sharp.mrc
Opened cryosparc_P8_J200_005_volume_map_sharp.mrc as #8, grid size
384,384,384, pixel 0.828, shown at level 0.0375, step 2, values float32
> hide #!18 models
> show #!20 models
> hide #!20 models
> select add #8
2 models selected
> select subtract #8
Nothing selected
> select add #8
2 models selected
> view matrix models
> #8,-0.94149,0.24009,0.23654,233.86,-0.32259,-0.43868,-0.83874,409.86,-0.097603,-0.86598,0.49047,232.07
> view matrix models
> #8,-0.021423,-0.82117,0.57029,204.63,-0.205,-0.55469,-0.80641,404.6,0.97853,-0.13419,-0.15646,44.817
> view matrix models
> #8,0.82264,0.56765,-0.032277,-57.049,0.033546,-0.10513,-0.99389,324.23,-0.56758,0.81653,-0.10552,131.58
> ui mousemode right "move picked models"
> view matrix models
> #8,0.82264,0.56765,-0.032277,290.83,0.033546,-0.10513,-0.99389,326.44,-0.56758,0.81653,-0.10552,131.58
> select subtract #8
Nothing selected
> volume #8 level 0.109
> surface dust #8 size 8.28
> show #!21.2 models
> tile
2 models tiled
> select add #8
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.51993,0.85412,-0.012123,442.31,0.85222,-0.5177,0.075541,48.344,0.058245,-0.049607,-0.99707,326.73
> view matrix models
> #8,0.50115,0.86531,-0.0088655,442.99,0.85348,-0.49594,-0.16007,82.693,-0.14291,0.072653,-0.98707,337.66
> view matrix models
> #8,0.51383,0.85185,0.10166,425.29,0.85777,-0.50813,-0.077668,70.656,-0.014504,0.12711,-0.99178,309.35
> ui mousemode right "move picked models"
> view matrix models
> #8,0.49217,0.86322,-0.11237,378.93,0.86604,-0.4986,-0.037028,70.972,-0.08799,-0.079092,-0.99298,354
> view matrix models
> #8,0.48285,0.86851,0.112,293.14,0.8712,-0.48938,0.039043,72.341,0.088717,0.078718,-0.99294,300.82
> select subtract #8
Nothing selected
> fitmap #8 inMap #21.2
Fit map cryosparc_P8_J200_005_volume_map_sharp.mrc in map
cryosparc_P8_J200_005_volume_map.mrc using 10980 points
correlation = 0.9814, correlation about mean = 0.8246, overlap = 257
steps = 76, shift = 0.82, angle = 5.35 degrees
Position of cryosparc_P8_J200_005_volume_map_sharp.mrc (#8) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.25121709 -0.00512177 0.96791721 -7.85634398
0.49873465 -0.85633780 -0.13397492 110.95583099
0.82955028 0.51639065 -0.21257229 194.61850335
Axis 0.77957050 0.16585560 0.60395510
Axis point 0.00000000 40.02544271 112.88603336
Rotation angle (degrees) 155.34643122
Shift along axis 129.81890897
> show #!18 models
> hide #!18 models
> hide #!21.2 models
> show #!21.2 models
> tile
2 models tiled
> view matrix models
> #8,-0.9676,0.11119,0.22669,741.27,0.23928,0.11714,0.96386,-98.242,0.080619,0.98687,-0.13995,20.123
> select add #8
2 models selected
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> select subtract #8
Nothing selected
> volume #8 level 0.1078
> volume #8 level 0.1102
> volume #8 level 0.1022
> volume #8 level 0.09905
> surface dust #8 size 20
> volume #8 level 0.09111
> volume #8 level 0.08952
> volume #8 color #81a8e6
> volume #8 color #6a9ee6
> volume #8 color #5c94e6
> volume #8 color #61abe6
> volume #8 color #70b5e6
> volume #8 color #66bfe6
> volume #8 color #6fc5e6
> volume #8 level 0.09111
> volume #8 level 0.1006
> volume #8 level 0.09111
> surface dust #8 size 20
> surface dust #8 size 22
> surface dust #8 size 25
> surface dust #8 size 8
> surface dust #8 size 35
> surface dust #8 size 15
> surface dust #8 size 18
> surface dust #8 size 20
> surface dust #8 size 25
> surface dust #8 size 35
> volume #8 level 0.09587
> volume #8 level 0.09111
> view matrix models
> #21.2,0.1664,-0.57234,0.80295,190.8,0.14557,0.81964,0.55407,-123.33,-0.97525,0.024691,0.21971,328.28
> save /Users/sahtelis/Desktop/image2.png supersample 3
> show #!18 models
> select add #18
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> view matrix models
> #18,0.59782,-0.62169,-0.50608,558.8,0.76612,0.62891,0.13241,110.59,0.23596,-0.46687,0.85226,174.12
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.43362,0.010557,-0.90103,585.29,0.13391,0.98958,-0.052848,127.85,0.89109,-0.14357,-0.43052,129.91
> ui mousemode right "move picked models"
> view matrix models
> #18,-0.43362,0.010557,-0.90103,578.48,0.13391,0.98958,-0.052848,116.95,0.89109,-0.14357,-0.43052,129.91
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.04531, steps = 84
shifted from previous position = 2.36
rotated from previous position = 4.18 degrees
atoms outside contour = 6716, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
-0.92142258 0.24322744 0.30301955 295.03962548
0.35993631 0.82807006 0.42982071 -31.28715280
-0.14637723 0.50511424 -0.85054884 401.80549607
Axis 0.16007313 0.95541209 0.24812162
Axis point 173.40724560 0.00000000 187.71963315
Rotation angle (degrees) 166.39748431
Shift along axis 117.03242146
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.04531, steps = 48
shifted from previous position = 0.00552
rotated from previous position = 0.00641 degrees
atoms outside contour = 6718, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
-0.92138651 0.24323366 0.30312422 295.04149531
0.35999670 0.82804697 0.42981462 -31.29410429
-0.14645571 0.50514911 -0.85051462 401.81109355
Axis 0.16009384 0.95540541 0.24813396
Axis point 173.41936732 0.00000000 187.71618715
Rotation angle (degrees) 166.39173731
Shift along axis 117.03874713
> view matrix models
> #18,-0.51676,-0.00011569,-0.85613,591.83,-0.29028,-0.94074,0.17534,130.13,-0.80542,0.33912,0.48611,200.26
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05026, steps = 156
shifted from previous position = 5.76
rotated from previous position = 10.7 degrees
atoms outside contour = 6384, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.56750650 -0.41815504 -0.70928326 227.50968740
0.19159655 -0.77072629 0.60767734 -31.35618750
-0.80076660 -0.48075706 -0.35727512 432.65043938
Axis -0.87009189 0.07313157 0.48743398
Axis point 0.00000000 80.18702369 286.53965753
Rotation angle (degrees) 141.28323799
Shift along axis 10.64106471
> select subtract #18
Nothing selected
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05026, steps = 64
shifted from previous position = 0.95
rotated from previous position = 0.00923 degrees
atoms outside contour = 6387, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.83147713 -0.43731737 -0.34263579 226.62773315
-0.03607024 -0.65793416 0.75221112 -21.70946662
-0.55438679 -0.61308739 -0.56283136 421.26621354
Axis -0.94897608 0.14718146 0.27889427
Axis point 0.00000000 107.22365639 245.47315263
Rotation angle (degrees) 133.99887077
Shift along axis -100.77079582
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05026, steps = 48
shifted from previous position = 0.00469
rotated from previous position = 0.00774 degrees
atoms outside contour = 6388, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.83141133 -0.43741884 -0.34266594 226.63032724
-0.03613768 -0.65794571 0.75219778 -21.70618242
-0.55448107 -0.61300261 -0.56283083 421.27356604
Axis -0.94895681 0.14723363 0.27893230
Axis point 0.00000000 107.22796227 245.48107107
Rotation angle (degrees) 134.00193021
Shift along axis -100.75146677
> select add #18
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.63682,0.65812,-0.40167,602.67,-0.74873,-0.6522,0.11845,140.17,-0.18402,0.37618,0.90809,188.96
> view matrix models
> #18,-0.37864,-0.11475,0.9184,617.74,-0.80479,-0.44924,-0.38794,132.8,0.4571,-0.88601,0.077748,149.7
> view matrix models
> #18,-0.511,-0.070146,0.85672,620.84,-0.5576,0.78556,-0.26827,130.52,-0.65419,-0.61479,-0.44053,175.42
> view matrix models
> #18,0.22018,-0.36965,0.90271,597.97,-0.75546,0.52081,0.39753,148.75,-0.61709,-0.76949,-0.16458,179.11
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.04321, steps = 88
shifted from previous position = 2.44
rotated from previous position = 5.5 degrees
atoms outside contour = 6886, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.45658608 0.81306377 0.36118757 256.64987270
-0.78666821 0.55857623 -0.26295573 -12.83981552
-0.41555056 -0.16407286 0.89464955 445.07278661
Axis 0.05551852 0.43610538 -0.89818138
Axis point 285.52536639 -151.53187962 0.00000000
Rotation angle (degrees) 62.94111832
Shift along axis -391.10678149
> view matrix models
> #18,-0.10309,-0.98274,0.15364,590.99,-0.47703,-0.086691,-0.8746,115.17,0.87282,-0.16345,-0.45985,126.59
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.04747, steps = 72
shifted from previous position = 1.59
rotated from previous position = 1.17 degrees
atoms outside contour = 6604, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
-0.93690001 0.00016727 0.34959738 296.53978696
-0.30327014 0.49707634 -0.81298359 -38.64211824
-0.17391258 -0.86770679 -0.46566011 409.87794334
Axis -0.09007014 0.86165687 -0.49943449
Axis point 171.31607975 0.00000000 169.12326252
Rotation angle (degrees) 162.31515923
Shift along axis -264.71280925
> select subtract #18
Nothing selected
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.04901, steps = 92
shifted from previous position = 4.36
rotated from previous position = 5.89 degrees
atoms outside contour = 6484, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.90728307 -0.04845439 -0.41771949 225.21575697
-0.01211435 0.98991552 -0.14113993 -31.61704338
0.42034587 0.13311427 0.89754662 423.54804234
Axis 0.31075302 -0.94959838 0.04117631
Axis point -840.52541037 0.00000000 638.34392278
Rotation angle (degrees) 26.18516980
Shift along axis 117.45011273
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.04901, steps = 44
shifted from previous position = 0.018
rotated from previous position = 0.0144 degrees
atoms outside contour = 6488, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.90735684 -0.04846165 -0.41755838 225.23247319
-0.01201155 0.98993772 -0.14099292 -31.61748421
0.42018954 0.13294641 0.89764469 423.54528969
Axis 0.31053514 -0.94966343 0.04131950
Axis point -840.87472278 0.00000000 638.60632003
Rotation angle (degrees) 26.17256923
Shift along axis 117.46924421
> transparency #18#21.2#!7,21 50
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05318, steps = 84
shifted from previous position = 4.2
rotated from previous position = 9.61 degrees
atoms outside contour = 6404, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.73497752 -0.37167713 -0.56715441 225.05221862
0.58566286 -0.07361452 0.80720499 -35.87559709
-0.34177043 -0.92543880 0.16357248 427.31016347
Axis -0.86965994 -0.11312620 0.48051437
Axis point 0.00000000 189.00159580 293.90826402
Rotation angle (degrees) 95.02165568
Shift along axis 13.66824510
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05318, steps = 40
shifted from previous position = 0.00537
rotated from previous position = 0.013 degrees
atoms outside contour = 6403, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.73497623 -0.37171573 -0.56713079 225.05756453
0.58572316 -0.07340125 0.80718065 -35.87876277
-0.34166985 -0.92544024 0.16377434 427.31065626
Axis -0.86963259 -0.11316277 0.48055525
Axis point 0.00000000 189.04232920 293.92173054
Rotation angle (degrees) 95.00975436
Shift along axis 13.68912544
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05318, steps = 72
shifted from previous position = 1.26
rotated from previous position = 0.0112 degrees
atoms outside contour = 6400, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.66414688 -0.38006183 -0.64378715 225.65068014
0.41895683 -0.52400034 0.74155160 -34.29108532
-0.61918015 -0.76221822 -0.18878370 429.49231069
Axis -0.88298924 -0.01444883 0.46917079
Axis point 0.00000000 116.45913184 285.52976592
Rotation angle (degrees) 121.62238246
Shift along axis 2.75358994
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05318, steps = 64
shifted from previous position = 0.0147
rotated from previous position = 0.0195 degrees
atoms outside contour = 6407, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.66406936 -0.38001490 -0.64389480 225.63687507
0.41885572 -0.52428869 0.74140490 -34.29270777
-0.61933168 -0.76204331 -0.18899265 429.49708075
Axis -0.88298397 -0.01442607 0.46918141
Axis point 0.00000000 116.40706742 285.52641226
Rotation angle (degrees) 121.64172288
Shift along axis 2.77301054
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05318, steps = 28
shifted from previous position = 0.0142
rotated from previous position = 0.0228 degrees
atoms outside contour = 6400, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.66417218 -0.38013748 -0.64371637 225.65033188
0.41889326 -0.52395555 0.74161916 -34.28632756
-0.61919602 -0.76221128 -0.18875968 429.49318583
Axis -0.88299479 -0.01439746 0.46916192
Axis point -0.00000000 116.47722848 285.52780413
Rotation angle (degrees) 121.61921612
Shift along axis 2.74741791
> hide #!18 models
> show #!18 models
> volume flip z-axis #21.2
Missing or invalid "volumes" argument: invalid density maps specifier
> volume flip #21.2 z-axis
Expected a keyword
> volume flip #21.2 z-axis
Expected a keyword
> vop zflip #21.2
> volume zflip #21.2
Expected a density maps specifier or a keyword
> hide #!21.2 models
> show #!21.2 models
> hide #!18 models
> hide #!21 models
> show #!21 models
> select add #21.2
2 models selected
> vop zflip #21.2
> volume zflip #21.2
Expected a density maps specifier or a keyword
> volume flip #21.2 axis z
Opened cryosparc_P8_J200_005_volume_map.mrc z flip as #9, grid size
384,384,384, pixel 0.828, shown at step 1, values float32
> view matrix models
> #21.2,0.1664,-0.57234,0.80295,190.8,0.14557,0.81964,0.55407,-123.33,-0.97525,0.024691,0.21971,328.28
> hide #!9 models
> show #!9 models
> select add #9
4 models selected
> ui mousemode right "move picked models"
> view matrix models
> #9,-0.49806,0.086549,-0.86281,788.32,0.1705,0.98536,0.00042112,-31.569,0.85021,-0.1469,-0.50553,178.48
> select subtract #9
2 models selected
> volume #9 level 0.1177
> surface dust #9 size 8.28
> volume #9 level 0.09431
> view matrix models
> #9,-0.92885,-0.14789,-0.33965,808.16,0.31078,0.18791,-0.93172,187.55,0.20162,-0.97099,-0.12858,353.81
> surface dust #9 size 25
> graphics silhouettes false
> graphics silhouettes true
> show #!18 models
> select subtract #21.2
Nothing selected
> fitmap #18 inMap #9
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
z flip (#9) using 8232 atoms
average map value = 0.03683, steps = 324
shifted from previous position = 34.3
rotated from previous position = 21.3 degrees
atoms outside contour = 7496, contour level = 0.094314
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.15167976 0.56042598 -0.81419649 173.75920114
-0.29932432 -0.81109261 -0.50252728 170.68355467
-0.94201812 0.16748560 0.29077547 188.13251619
Axis 0.61051038 0.11647005 -0.78339760
Axis point 193.22110565 63.68680723 0.00000000
Rotation angle (degrees) 146.71994892
Shift along axis -21.42124562
> fitmap #18 inMap #9
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
z flip (#9) using 8232 atoms
average map value = 0.03683, steps = 84
shifted from previous position = 0.000599
rotated from previous position = 0.00232 degrees
atoms outside contour = 7496, contour level = 0.094314
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.15169808 0.56045338 -0.81417422 173.76068075
-0.29932140 -0.81107823 -0.50255223 170.68351656
-0.94201610 0.16746356 0.29079470 188.13266366
Axis 0.61050007 0.11648602 -0.78340326
Axis point 193.22077895 63.68780515 0.00000000
Rotation angle (degrees) 146.71915046
Shift along axis -21.42059150
> select add #18
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> view matrix models
> #18,0.075099,-0.94797,0.30938,584.89,0.79499,0.24421,0.5553,108.94,-0.60196,0.20425,0.77196,227.33
> fitmap #18 inMap #9
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
z flip (#9) using 8232 atoms
average map value = 0.03797, steps = 128
shifted from previous position = 2.6
rotated from previous position = 7.78 degrees
atoms outside contour = 6985, contour level = 0.094314
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.21691369 0.56834828 -0.79368044 159.06516470
-0.40525214 -0.79209635 -0.45645811 164.49350542
-0.88809858 0.22262870 0.40214091 177.96138226
Axis 0.57028447 0.07929060 -0.81761153
Axis point 175.47545880 53.95464709 0.00000000
Rotation angle (degrees) 143.45934362
Shift along axis -41.74809637
> fitmap #18 inMap #9
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
z flip (#9) using 8232 atoms
average map value = 0.03797, steps = 40
shifted from previous position = 0.0212
rotated from previous position = 0.0304 degrees
atoms outside contour = 6983, contour level = 0.094314
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.21649144 0.56839167 -0.79376465 159.05441676
-0.40501494 -0.79206997 -0.45671436 164.47980070
-0.88830979 0.22261180 0.40168350 177.93787327
Axis 0.57049115 0.07939804 -0.81745691
Axis point 175.49880167 53.96425757 0.00000000
Rotation angle (degrees) 143.45976611
Shift along axis -41.65803145
> fitmap #18 inMap #9
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
z flip (#9) using 8232 atoms
average map value = 0.04135, steps = 68
shifted from previous position = 3.67
rotated from previous position = 5.34 degrees
atoms outside contour = 6835, contour level = 0.094314
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.27912529 0.55876143 -0.78094475 154.17335794
-0.45604828 -0.79283496 -0.40426803 161.21104217
-0.84504969 0.24330708 0.47612248 179.56973982
Axis 0.53717063 0.05317575 -0.84179573
Axis point 167.11581601 49.18273785 0.00000000
Rotation angle (degrees) 142.93182842
Shift along axis -59.77112308
> fitmap #18 inMap #9
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
z flip (#9) using 8232 atoms
average map value = 0.04135, steps = 44
shifted from previous position = 0.00171
rotated from previous position = 0.0067 degrees
atoms outside contour = 6833, contour level = 0.094314
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.27909255 0.55868383 -0.78101196 154.16962741
-0.45598948 -0.79288717 -0.40423195 161.20907275
-0.84509223 0.24331512 0.47604287 179.56832394
Axis 0.53720583 0.05316107 -0.84177420
Axis point 167.11446103 49.18536446 0.00000000
Rotation angle (degrees) 142.93653849
Shift along axis -59.76511374
> show #!21.2 models
> select subtract #18
Nothing selected
> hide #!21.2 models
> hide #!18 models
> show #!21.2 models
> hide #!21.2 models
> show #!21.2 models
> tile
2 models tiled
> open /Users/sahtelis/Downloads/cryosparc_P8_J203_005_volume_map.mrc
> /Users/sahtelis/Downloads/cryosparc_P8_J203_005_volume_map_sharp.mrc
Opened cryosparc_P8_J203_005_volume_map.mrc as #13.1, grid size 384,384,384,
pixel 0.828, shown at level 0.0325, step 2, values float32
Opened cryosparc_P8_J203_005_volume_map_sharp.mrc as #13.2, grid size
384,384,384, pixel 0.828, shown at level 0.0345, step 2, values float32
> view matrix models
> #13.1,1,4.1633e-17,5.5511e-17,270.19,6.9389e-18,1,5.5511e-17,-44.088,0,0,1,72.532
> view matrix models
> #13.2,1,5.1348e-16,-6.6613e-16,265.81,-9.0206e-17,1,-3.6082e-16,-176.32,-2.7756e-16,5.5511e-16,1,31.964
> volume #13.1 level 0.09755
> volume #13.2 level 0.1682
> view matrix models
> #13.1,1,-1.1727e-15,-1.9429e-16,322.97,-4.8052e-16,1,-2.2204e-16,-96.874,6.245e-17,1.3587e-31,1,89.175
> view matrix models
> #13.1,1,-1.5977e-15,-3.1919e-16,339.13,-9.8879e-17,1,-1.6653e-16,-93.135,-4.1633e-17,2.2204e-16,1,88.696
> view matrix models
> #13.1,1,-1.7087e-15,-4.4409e-16,324.55,-4.3368e-17,1,-1.1102e-16,-70.578,4.576e-31,2.6368e-16,1,44.282
> volume #13.1 level 0.06024
> view matrix models
> #13.2,1,2.2204e-16,-6.6613e-16,270.1,-1.0408e-16,1,-4.8919e-16,-158.82,-2.3592e-16,8.318e-16,1,93.425
> volume #13.2 level 0.09926
> surface dust #21.2 size 8.28
> surface dust #9 size 8.28
> surface dust #13.1 size 8.28
> surface dust #13.2 size 8.28
> volume #13.2 level 0.08254
> volume #13.2 level 0.1264
> volume #13.1 level 0.08476
> view matrix models
> #13.1,1,-2.4303e-15,-1.2143e-15,322.55,6.7828e-16,1,2.498e-16,-69.979,-2.7756e-17,-2.7756e-17,1,69.194
> volume #13.1 level 0.06557
> surface dust #21.2 size 20
> surface dust #21.2 size 18
> surface dust #21.2 size 19
> surface dust #21.2 size 20
> view matrix models
> #21.2,0.1664,-0.57234,0.80295,186.25,0.14557,0.81964,0.55407,-126.21,-0.97525,0.024691,0.21971,327.95
> open /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250324.cxs
Opened cryosparc_P7_J67_004_volume_map_sharp.mrc as #1, grid size 192,192,192,
pixel 1.84, shown at level 1.62, step 1, values float32
Opened cryosparc_P7_J67_004_volume_map_sharp.mrc 0 as #3.1, grid size
192,192,192, pixel 1.84, shown at level 1.17, step 1, values float32
Opened cryosparc_P7_J67_004_volume_map_sharp.mrc 1 as #3.2, grid size
192,192,192, pixel 1.84, shown at level 1.17, step 1, values float32
Opened cryosparc_P7_J67_004_volume_map_sharp.mrc 2 as #3.3, grid size
192,192,192, pixel 1.84, shown at level 1.17, step 1, values float32
Opened cryosparc_P7_J67_004_volume_map_sharp.mrc 3 as #3.4, grid size
192,192,192, pixel 1.84, shown at level 1.17, step 1, values float32
Opened cryosparc_P7_J67_004_volume_map_sharp.mrc 4 as #3.5, grid size
192,192,192, pixel 1.84, shown at level 1.17, step 1, values float32
Opened cryosparc_P7_J67_004_volume_map_sharp.mrc 5 as #3.6, grid size
192,192,192, pixel 1.84, shown at level 1.17, step 1, values float32
Opened cryosparc_P7_J67_004_volume_map_sharp.mrc 6 as #3.7, grid size
192,192,192, pixel 1.84, shown at level 1.17, step 1, values float32
Opened micelle-gaussian.mrc as #4, grid size 192,192,192, pixel 1.84, shown at
level 0.514, step 1, values float32
Opened cryosparc_P7_J193_006_volume_map_sharp.mrc as #5, grid size
192,192,192, pixel 1.84, shown at level 1.65, step 1, values float32
Opened micelle-gaussian.mrc as #7, grid size 192,192,192, pixel 1.84, shown at
level 0.552, step 1, values float32
> set bgColor transparent
opened ChimeraX session
> open /Users/sahtelis/Downloads/cryosparc_P8_J200_005_volume_map.mrc
Opened cryosparc_P8_J200_005_volume_map.mrc as #8, grid size 384,384,384,
pixel 0.828, shown at level 0.037, step 2, values float32
> volume #8 level 0.1095
> surface dust #5 size 18.4
> surface dust #7 size 18.4
> surface dust #8 size 8.28
> select add #8
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.11764,-0.16736,0.97885,9.1846,-0.46012,0.86432,0.20308,62.001,-0.88003,-0.47428,0.024679,372.43
> view matrix models
> #8,-0.79227,-0.55646,0.25032,333.06,-0.60845,0.75127,-0.2557,177.46,-0.045777,-0.35489,-0.93379,375.23
> view matrix models
> #8,-0.81535,-0.57803,0.03293,375.18,-0.55237,0.75961,-0.34333,181.34,0.17344,-0.29813,-0.93864,332.14
> ui mousemode right "move picked models"
> view matrix models
> #8,-0.81535,-0.57803,0.03293,373.66,-0.55237,0.75961,-0.34333,189.42,0.17344,-0.29813,-0.93864,360.89
> view matrix models
> #8,-0.81535,-0.57803,0.03293,383.98,-0.55237,0.75961,-0.34333,201.22,0.17344,-0.29813,-0.93864,354.14
> view matrix models
> #8,-0.81535,-0.57803,0.03293,384.89,-0.55237,0.75961,-0.34333,194.56,0.17344,-0.29813,-0.93864,357.54
> ui tool show "Fit in Map"
> fitmap #8 inMap #5
Fit map cryosparc_P8_J200_005_volume_map.mrc in map
cryosparc_P7_J193_006_volume_map_sharp.mrc using 7032 points
correlation = 0.4725, correlation about mean = 0.06496, overlap = 925
steps = 80, shift = 4.71, angle = 8.2 degrees
Position of cryosparc_P8_J200_005_volume_map.mrc (#8) relative to
cryosparc_P7_J193_006_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.52013255 -0.85382228 -0.02120499 392.48773376
0.85408183 -0.51989666 -0.01586478 126.23344513
0.00252130 -0.02636259 0.99964927 7.69782291
Axis -0.00614589 -0.01389045 0.99988464
Axis point 160.79035219 173.43982809 0.00000000
Rotation angle (degrees) 121.34499517
Shift along axis 3.53130805
> select subtract #8
Nothing selected
> surface dust #8 size 20
> hide #!5 models
> fitmap #6 inMap #8
Fit molecule cx45hexamer.pdb (#6) to map cryosparc_P8_J200_005_volume_map.mrc
(#8) using 8232 atoms
average map value = 0.04922, steps = 104
shifted from previous position = 4.33
rotated from previous position = 9.71 degrees
atoms outside contour = 7238, contour level = 0.10953
Position of cx45hexamer.pdb (#6) relative to
cryosparc_P8_J200_005_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.02016435 0.99891469 -0.04198623 162.18961652
0.57851763 0.04590788 0.81437695 156.02813809
0.81542059 -0.00786839 -0.57881547 123.66777502
Axis -0.65250014 -0.68040285 -0.33360984
Axis point -3.93186728 0.00000000 22.78656629
Rotation angle (degrees) 140.94449726
Shift along axis -253.24752440
> select add #6
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.5659,-0.13732,-0.81296,173.03,-0.21141,-0.9289,0.30407,185.31,-0.79691,0.34394,0.49663,222.26
> view matrix models
> #6,-0.37997,0.54064,-0.75056,170.14,-0.57429,-0.77397,-0.26677,186.22,-0.72513,0.32968,0.60457,222.03
> fitmap #6 inMap #8
Fit molecule cx45hexamer.pdb (#6) to map cryosparc_P8_J200_005_volume_map.mrc
(#8) using 8232 atoms
average map value = 0.05026, steps = 116
shifted from previous position = 4.04
rotated from previous position = 8.74 degrees
atoms outside contour = 7140, contour level = 0.10953
Position of cx45hexamer.pdb (#6) relative to
cryosparc_P8_J200_005_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.59271501 0.25600248 0.76364367 157.23888875
0.05852677 -0.95932362 0.27617531 158.15364261
0.80328297 -0.11899965 -0.58358851 127.09392055
Axis -0.89094896 -0.08936953 -0.44522247
Axis point 0.00000000 73.28497413 15.48081243
Rotation angle (degrees) 167.18687082
Shift along axis -210.81100867
> open /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250514.cxs
Opened cryosparc_P8_J146_006_volume_map.mrc as #1, grid size 384,384,384,
pixel 0.828, shown at level 0.0784, step 2, values float32
Opened cryosparc_P8_J146_006_volume_map_36_regions.mrc as #4, grid size
97,103,84, pixel 0.828, shown at level 0.0822, step 1, values float32
Opened J146_resampled_mask.mrc as #5, grid size 384,384,384, pixel 0.828,
shown at level 0.0684, step 1, values float32
Opened cryosparc_P8_J167_mask.mrc as #6, grid size 384,384,384, pixel 0.828,
shown at level 0.378, step 2, values float32
Opened cryosparc_P8_J173_mask.mrc as #10, grid size 384,384,384, pixel 0.828,
shown at level 0.152, step 2, values float32
Opened cryosparc_P8_J176_mask.mrc as #12, grid size 384,384,384, pixel 0.828,
shown at level 0.527, step 2, values float32
Opened cryosparc_P7_mask_resampled.mrc as #14, grid size 192,192,192, pixel
1.84, shown at level 0.349, step 1, values float32
Opened cryosparc_P8_J178_mask.mrc as #15, grid size 384,384,384, pixel 0.92,
shown at level 0.0533, step 2, values float32
Opened cryosparc_P8_J170_004_volume_map.mrc as #11, grid size 384,384,384,
pixel 0.828, shown at level 0.0989, step 2, values float32
Opened cryosparc_P8_J177_005_volume_map_sharp.mrc as #16.1, grid size
384,384,384, pixel 0.828, shown at level 0.172, step 2, values float32
Opened cryosparc_P8_J177_005_volume_map.mrc as #16.2, grid size 384,384,384,
pixel 0.828, shown at level 0.119, step 2, values float32
Opened cryosparc_P8_J179_006_volume_map.mrc as #17, grid size 384,384,384,
pixel 0.828, shown at level 0.0837, step 2, values float32
Opened cryosparc_P8_J187_class_00_00120_volume.mrc as #2, grid size
384,384,384, pixel 0.828, shown at level 0.0365, step 2, values float32
Opened cryosparc_P8_J185_class_00_00120_volume.mrc as #3, grid size
384,384,384, pixel 0.828, shown at level 0.0873, step 2, values float32
Opened cryosparc_P8_J201_005_volume_map.mrc as #21.1, grid size 384,384,384,
pixel 0.828, shown at level 0.0659, step 2, values float32
Opened cryosparc_P8_J200_005_volume_map.mrc as #21.2, grid size 384,384,384,
pixel 0.828, shown at level 0.0855, step 2, values float32
Opened cryosparc_P8_J198_006_volume_map_sharp.mrc as #21.3, grid size
384,384,384, pixel 0.828, shown at level 0.135, step 2, values float32
Opened cryosparc_P8_J198_006_volume_map.mrc as #21.4, grid size 384,384,384,
pixel 0.828, shown at level 0.0951, step 2, values float32
Opened cryosparc_P8_J197_class_00_final_volume.mrc as #21.5, grid size
192,192,192, pixel 1.66, shown at level 0.132, step 1, values float32
Opened cryosparc_P8_J201_005_volume_map_sharp.mrc as #20, grid size
384,384,384, pixel 0.828, shown at level 0.152, step 2, values float32
Opened cryosparc_P8_J201_005_volume_mask_refine.mrc as #22, grid size
384,384,384, pixel 0.828, shown at level 0.447, step 2, values float32
Opened cryosparc_P8_J198_006_volume_mask_refine.mrc as #23, grid size
384,384,384, pixel 0.828, shown at level 0.889, step 2, values float32
Opened cryosparc_P8_J199_005_volume_map.mrc as #7.1, grid size 384,384,384,
pixel 0.828, shown at level 0.102, step 2, values float32
Opened cryosparc_P8_J199_005_volume_mask_refine.mrc as #7.2, grid size
384,384,384, pixel 0.828, shown at level 1, step 2, values float32
> set bgColor #80808000
opened ChimeraX session
> close #6
> close #10
> close #12
> close #14
> close #15
> close #11
> close #16.1
> close #16.2
> close #17
> close #2
> close #3
> close #21.3
> close #21.4
> close #21.5
> close #23
> close #7.1
> close #7.2
> close #5
> hide #7 models
> show #!18 models
> ui tool show "Fit in Map"
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.04656, steps = 220
shifted from previous position = 6.16
rotated from previous position = 13.2 degrees
atoms outside contour = 6709, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.57191492 -0.19097013 0.79777426 182.69156717
0.57313355 -0.60275667 -0.55515974 1.54909274
0.58688267 0.77473533 -0.23527414 352.99955404
Axis 0.85898946 0.13621650 0.49354045
Axis point 0.00000000 -65.98618677 111.98956679
Rotation angle (degrees) 129.27609403
Shift along axis 331.36070051
> select add #21.2
2 models selected
> view matrix models
> #21.2,0.28155,-0.51796,0.80775,186.04,-0.028919,0.83684,0.54669,-95.892,-0.95911,-0.17728,0.22063,296.27
> view matrix models
> #21.2,0.25856,-0.56756,0.78168,201.78,0.0001456,0.80922,0.58751,-102.7,-0.96599,-0.15179,0.20932,295.14
> view matrix models
> #21.2,0.2095,-0.54688,0.81058,201.63,-0.034154,0.82437,0.56501,-96.033,-0.97721,-0.14606,0.15403,304.92
> view matrix models
> #21.2,0.17625,-0.53856,0.82395,203.44,-0.056777,0.83009,0.55473,-91.687,-0.98271,-0.14455,0.11572,311.73
> fitmap #18 inMap #21.2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
(#21.2) using 8232 atoms
average map value = 0.05285, steps = 148
shifted from previous position = 2.7
rotated from previous position = 21.9 degrees
atoms outside contour = 6454, contour level = 0.085532
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc (#21.2) coordinates:
Matrix rotation and translation
0.62344960 -0.26244458 0.73650083 179.88884950
0.35976669 -0.74004094 -0.56824937 10.34456267
0.69417472 0.61924331 -0.36695939 350.08506068
Axis 0.88533175 0.03155611 0.46388782
Axis point 0.00000000 -41.68066485 127.95427866
Rotation angle (degrees) 137.88286978
Shift along axis 321.98794017
> transparency #21.2 50
> select subtract #21.2
Nothing selected
> volume flip #21.2 axis y
Opened cryosparc_P8_J200_005_volume_map.mrc y flip as #2, grid size
384,384,384, pixel 0.828, shown at step 1, values float32
> select add #2
2 models selected
> view matrix models
> #2,0.28805,-0.53402,0.79489,189.63,-0.043544,0.82191,0.56796,-94.628,-0.95663,-0.19821,0.21349,300.32
> ui mousemode right "move picked models"
> view matrix models
> #2,0.28805,-0.53402,0.79489,227,-0.043544,0.82191,0.56796,-106.42,-0.95663,-0.19821,0.21349,225.07
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.82472,-0.47067,0.31353,209.23,-0.39691,-0.086795,0.91374,37.742,-0.40286,-0.87803,-0.2584,320.59
> volume #2 level 0.102
> surface dust #2 size 8.28
> view matrix models
> #2,0.76439,-0.62341,-0.16453,319.95,-0.19827,-0.47009,0.86006,75.425,-0.61351,-0.6248,-0.48294,350.18
> ui mousemode right "move picked models"
> view matrix models
> #2,0.76439,-0.62341,-0.16453,336.43,-0.19827,-0.47009,0.86006,24.915,-0.61351,-0.6248,-0.48294,407.84
> view matrix models
> #2,0.76439,-0.62341,-0.16453,340.01,-0.19827,-0.47009,0.86006,14.381,-0.61351,-0.6248,-0.48294,418.87
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.5968,-0.78849,-0.14872,390.22,-0.069677,-0.23557,0.96936,-60.75,-0.79936,-0.56815,-0.19553,393.18
> ui mousemode right "move picked models"
> view matrix models
> #2,0.5968,-0.78849,-0.14872,417.03,-0.069677,-0.23557,0.96936,-20.261,-0.79936,-0.56815,-0.19553,463.19
> view matrix models
> #2,0.5968,-0.78849,-0.14872,431.82,-0.069677,-0.23557,0.96936,-8.2864,-0.79936,-0.56815,-0.19553,496.68
> view matrix models
> #2,0.5968,-0.78849,-0.14872,500.48,-0.069677,-0.23557,0.96936,26.703,-0.79936,-0.56815,-0.19553,509.62
> view matrix models
> #2,0.5968,-0.78849,-0.14872,550.08,-0.069677,-0.23557,0.96936,47.505,-0.79936,-0.56815,-0.19553,519.66
> view matrix models
> #2,0.5968,-0.78849,-0.14872,594.67,-0.069677,-0.23557,0.96936,57.723,-0.79936,-0.56815,-0.19553,507.35
> view matrix models
> #2,0.5968,-0.78849,-0.14872,580.26,-0.069677,-0.23557,0.96936,41.593,-0.79936,-0.56815,-0.19553,413.89
> view matrix models
> #2,0.5968,-0.78849,-0.14872,580.5,-0.069677,-0.23557,0.96936,29.792,-0.79936,-0.56815,-0.19553,415.26
> fitmap #18 inMap #2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
y flip (#2) using 8232 atoms
average map value = 0.04255, steps = 64
shifted from previous position = 0.687
rotated from previous position = 4.79 degrees
atoms outside contour = 7148, contour level = 0.10199
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc y flip (#2) coordinates:
Matrix rotation and translation
0.66638139 0.22004773 0.71240078 153.29799664
-0.16796619 -0.88659611 0.43096950 168.00077819
0.72644560 -0.40684930 -0.55385056 125.05358550
Axis -0.90730626 -0.01520968 -0.42019522
Axis point 0.00000000 88.57483368 4.77465630
Rotation angle (degrees) 152.50270590
Shift along axis -194.19038817
> select subtract #2
Nothing selected
> fitmap #18 inMap #2
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
y flip (#2) using 8232 atoms
average map value = 0.04254, steps = 44
shifted from previous position = 0.0147
rotated from previous position = 0.0228 degrees
atoms outside contour = 7150, contour level = 0.10199
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc y flip (#2) coordinates:
Matrix rotation and translation
0.66629300 0.22014482 0.71245346 153.30635783
-0.16766358 -0.88673670 0.43079805 167.97387708
0.72659657 -0.40649022 -0.55391618 125.05253918
Axis -0.90728805 -0.01532551 -0.42023033
Axis point 0.00000000 88.54493507 4.79016734
Rotation angle (degrees) 152.52099085
Shift along axis -194.21818151
> volume flip #21.2 axis y
Opened cryosparc_P8_J200_005_volume_map.mrc y flip as #3, grid size
384,384,384, pixel 0.828, shown at step 1, values float32
> volume flip #21.2 axis x
Opened cryosparc_P8_J200_005_volume_map.mrc x flip as #5, grid size
384,384,384, pixel 0.828, shown at step 1, values float32
> close #3
> volume #5 level 0.1115
> surface dust #2 size 8.28
> surface dust #5 size 8.28
> volume #5 level 0.09593
> volume #5 level 0.08726
> volume #5 color #9bc5f280
> volume #5 color #85b4f280
> volume #5 color #78a0f280
> volume #5 color #73acf280
> volume #5 color #8abdf280
> volume #5 color #7598f280
> volume #5 color #69a1f280
> volume #5 color #67b4f280
> select add #5
2 models selected
> view matrix models
> #5,0.17625,-0.53856,0.82395,293.51,-0.056777,0.83009,0.55473,-114.68,-0.98271,-0.14455,0.11572,207.26
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> view matrix models
> #5,0.17625,-0.53856,0.82395,319.19,-0.056777,0.83009,0.55473,-32.799,-0.98271,-0.14455,0.11572,210.85
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.19578,-0.77463,0.60134,389.49,0.069109,0.62258,0.77949,-55.936,-0.97821,-0.11105,0.17543,195.19
> view matrix models
> #5,-0.15865,-0.75203,0.63975,435.77,0.18089,0.61485,0.76762,-70.47,-0.97062,0.2375,0.038488,160.65
> view matrix models
> #5,0.2375,-0.78591,0.57091,389.6,0.012622,0.59017,0.80718,-46.31,-0.97131,-0.1845,0.15008,209.86
> ui mousemode right "move picked models"
> view matrix models
> #5,0.2375,-0.78591,0.57091,396.69,0.012622,0.59017,0.80718,-46.481,-0.97131,-0.1845,0.15008,202.76
> view matrix models
> #5,0.2375,-0.78591,0.57091,473.66,0.012622,0.59017,0.80718,-86.392,-0.97131,-0.1845,0.15008,182
> view matrix models
> #5,0.2375,-0.78591,0.57091,505.53,0.012622,0.59017,0.80718,-93.809,-0.97131,-0.1845,0.15008,179.82
> view matrix models
> #5,0.2375,-0.78591,0.57091,497.82,0.012622,0.59017,0.80718,-148.79,-0.97131,-0.1845,0.15008,225.8
> view matrix models
> #5,0.2375,-0.78591,0.57091,516.06,0.012622,0.59017,0.80718,-136.53,-0.97131,-0.1845,0.15008,332.2
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.17882,-0.98384,0.0087511,647.39,-0.30593,-0.047146,0.95089,-7.9909,-0.93511,-0.17271,-0.30942,398.64
> view matrix models
> #5,0.18931,-0.97762,-0.091744,660.93,-0.37709,-0.15865,0.91249,27.178,-0.90662,-0.13815,-0.39869,403.02
> ui mousemode right "move picked models"
> view matrix models
> #5,0.18931,-0.97762,-0.091744,674.87,-0.37709,-0.15865,0.91249,31.212,-0.90662,-0.13815,-0.39869,412.49
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.19567,-0.97286,-0.12354,678.23,-0.29172,-0.17802,0.93979,16.39,-0.93627,-0.14785,-0.31864,405.82
> ui mousemode right "move picked models"
> view matrix models
> #5,0.19567,-0.97286,-0.12354,669.37,-0.29172,-0.17802,0.93979,61.13,-0.93627,-0.14785,-0.31864,392.87
> hide #!2 models
> fitmap #18 inMap #5
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
x flip (#5) using 8232 atoms
average map value = 0.086, steps = 116
shifted from previous position = 4.76
rotated from previous position = 20.2 degrees
atoms outside contour = 4409, contour level = 0.087265
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc x flip (#5) coordinates:
Matrix rotation and translation
0.53762501 -0.27648145 0.79656600 156.24085414
-0.25625885 -0.95360242 -0.15803111 159.18021928
0.80329992 -0.11916561 -0.58353132 127.46549978
Axis 0.87680336 -0.15191682 0.45622050
Axis point 0.00000000 92.81277452 24.25511474
Rotation angle (degrees) 178.73003941
Shift along axis 170.96272679
> view matrix models
> #5,0.19567,-0.97286,-0.12354,668.35,-0.29172,-0.17802,0.93979,63.622,-0.93627,-0.14785,-0.31864,390.89
> fitmap #18 inMap #5
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
x flip (#5) using 8232 atoms
average map value = 0.086, steps = 64
shifted from previous position = 3.34
rotated from previous position = 0.00534 degrees
atoms outside contour = 4411, contour level = 0.087265
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc x flip (#5) coordinates:
Matrix rotation and translation
0.53768796 -0.27651427 0.79651212 156.23317108
-0.25629358 -0.95359261 -0.15803400 159.18725211
0.80324671 -0.11916796 -0.58360409 127.46559624
Axis 0.87682131 -0.15193298 0.45618062
Axis point 0.00000000 92.81671580 24.26156508
Rotation angle (degrees) 178.73004790
Shift along axis 170.95011545
> select subtract #5
Nothing selected
> surface dust #5 size 20
> save /Users/sahtelis/Desktop/image3.png supersample 3
> save /Users/sahtelis/Desktop/image4.png supersample 3
> save /Users/sahtelis/Desktop/image5.png supersample 3
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250514.cxs includeMaps true
> volume #5 level 0.05867
> ui tool show "Segment Map"
Segmenting cryosparc_P8_J200_005_volume_map.mrc x flip, density threshold
0.058672
Only showing 60 of 105 regions.
Showing 60 of 105 region surfaces
2406 watershed regions, grouped to 105 regions
Showing cryosparc_P8_J200_005_volume_map x flip.seg - 105 regions, 60 surfaces
Segmenting cryosparc_P8_J200_005_volume_map.mrc x flip, density threshold
0.058672
Only showing 60 of 105 regions.
Showing 60 of 105 region surfaces
2406 watershed regions, grouped to 105 regions
Showing cryosparc_P8_J200_005_volume_map x flip.seg - 105 regions, 60 surfaces
> close #2
> close #22
> close #20
> close #21.1
> close #4
> close #1
> close #7
> close #16
> hide #!18 models
> hide #!5 models
> hide #!3 models
> hide #!21 models
> show #!5 models
> show #!3 models
> hide #!5 models
> hide #!3 models
> show #!3 models
> view matrix models #3.42,1,0,0,187.54,0,1,0,-32.27,0,0,1,-62.855
> select add #3
61 models selected
> close #3
> show #!5 models
Segmenting cryosparc_P8_J200_005_volume_map.mrc x flip, density threshold
0.058672
Only showing 60 of 105 regions.
Showing 60 of 105 region surfaces
2406 watershed regions, grouped to 105 regions
Showing cryosparc_P8_J200_005_volume_map x flip.seg - 105 regions, 60 surfaces
> hide #!5 models
> select add #1
61 models selected
> show #!5 models
> view matrix models #1.26,1,0,0,45.566,0,1,0,-7.2951,0,0,1,-7.609
> hide #!5 models
> close #5
> select subtract #1
Nothing selected
> show #!21.2 models
> hide #!21 models
> hide #!21.2 models
> select add #1
61 models selected
> close #1
> show #!21.2 models
> volume flip #21.2 axis x
Opened cryosparc_P8_J200_005_volume_map.mrc x flip as #1, grid size
384,384,384, pixel 0.828, shown at step 1, values float32
> surface dust #1 size 20
> view matrix models
> #1,0.17625,-0.53856,0.82395,145.23,-0.056777,0.83009,0.55473,-81.149,-0.98271,-0.14455,0.11572,206.36
> volume #1 level 0.05342
> transparency #1#!21 0
Segmenting cryosparc_P8_J200_005_volume_map.mrc x flip, density threshold
0.053417
Only showing 60 of 105 regions.
Showing 60 of 105 region surfaces
2576 watershed regions, grouped to 105 regions
Showing cryosparc_P8_J200_005_volume_map x flip.seg - 105 regions, 60 surfaces
> hide #!1 models
> hide #2.1 models
> show #2.1 models
> hide #2.2 models
> show #2.2 models
> hide #2.3 models
> show #2.3 models
> hide #2.5 models
> show #2.5 models
> hide #2.60 models
> show #2.60 models
> hide #2.59 models
> show #2.59 models
> hide #2.58 models
> show #2.58 models
> hide #2.57 models
> show #2.57 models
> hide #2.56 models
> show #2.56 models
> hide #2.55 models
> show #2.55 models
> hide #2.54 models
> show #2.54 models
> hide #2.53 models
> show #2.53 models
> hide #2.52 models
> show #2.52 models
> hide #2.51 models
> show #2.51 models
> hide #2.50 models
> show #2.50 models
> hide #2.52 models
> hide #2.53 models
> show #2.53 models
> show #2.52 models
> hide #2.51 models
> show #2.51 models
> hide #2.55 models
> show #2.55 models
> hide #2.53 models
> hide #2.52 models
> show #2.53 models
> show #2.52 models
> hide #2.51 models
> show #2.51 models
> hide #2.50 models
> show #2.50 models
> hide #2.50 models
> hide #2.49 models
> hide #2.48 models
> show #2.48 models
> hide #2.51 models
> show #2.51 models
> hide #2.47 models
> show #2.47 models
> hide #2.46 models
> show #2.46 models
> select #2.5
1 model selected
> select #2.5
1 model selected
> select #2.18
1 model selected
> select #2.15
1 model selected
> select #2.18
1 model selected
> select #2.19
1 model selected
> select #2.14
1 model selected
> select #2.16
1 model selected
> select #2.20
1 model selected
> select #2.17
1 model selected
> select #2.13
1 model selected
> select #2.23
1 model selected
> select #2.34
1 model selected
> select #2.21
1 model selected
> select #2.36
1 model selected
> select #2.27
1 model selected
> select #2.31
1 model selected
> select #2.38
1 model selected
> select #2.24
1 model selected
> select #2.39
1 model selected
> select #2.25
1 model selected
> select #2.33
1 model selected
> select #2.35
1 model selected
> select #2.22
1 model selected
> select #2.29
1 model selected
> select #2.41
1 model selected
> select #2.28
1 model selected
> select #2.32
1 model selected
> select #2.40
1 model selected
> select #2.26
1 model selected
> select #2.37
1 model selected
> select #2.30
1 model selected
> select #2.42
1 model selected
> select add #2.1
2 models selected
> select add #2.2
3 models selected
> select add #2.3
4 models selected
> select add #2.4
5 models selected
> select add #2.5
6 models selected
> select add #2.6
7 models selected
> select add #2.7
8 models selected
> select add #2.8
9 models selected
> select add #2.9
10 models selected
> select add #2.10
11 models selected
> select add #2.11
12 models selected
> select add #2.12
13 models selected
> select subtract #2.42
12 models selected
> show #2.42 models
> hide #2.42 models
> select add #2.43
13 models selected
> select add #2.44
14 models selected
> select add #2.45
15 models selected
> select add #2.46
16 models selected
> select add #2.47
17 models selected
> select add #2.48
18 models selected
> select add #2.51
19 models selected
> select add #2.52
20 models selected
> select add #2.53
21 models selected
> select add #2.54
22 models selected
> select add #2.55
23 models selected
> select add #2.56
24 models selected
> select add #2.57
25 models selected
> select add #2.58
26 models selected
> select add #2.59
27 models selected
> select add #2.60
28 models selected
> select add #21
31 models selected
> select subtract #21
28 models selected
> hide #!21 models
Saving 28 regions to mrc file...
Opened micelle.mrc as #3, grid size 151,149,71, pixel 0.828, shown at step 1,
values float32
Wrote micelle.mrc
> select add #2
61 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> select add #3
2 models selected
> view matrix models
> #3,0.17625,-0.53856,0.82395,135.31,-0.056777,0.83009,0.55473,-52.341,-0.98271,-0.14455,0.11572,294.26
> view matrix models
> #3,0.17625,-0.53856,0.82395,124.46,-0.056777,0.83009,0.55473,-61.916,-0.98271,-0.14455,0.11572,348.77
> volume #3 level 0.06708
> surface dust #3 size 8.28
> volume gaussian #3 sDev 2
Opened micelle.mrc gaussian as #4, grid size 151,149,71, pixel 0.828, shown at
step 1, values float32
> volume #4 level 0.009178
> volume #4 color #e2d8e6
> volume #4 color #cdb3e6
> volume #4 color #dddbe6
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!18 models
> select subtract #3
Nothing selected
> volume #1 level 0.08469
> select add #4
2 models selected
> select subtract #4
Nothing selected
> select add #1
2 models selected
> view matrix models
> #1,0.17625,-0.53856,0.82395,114.93,-0.056777,0.83009,0.55473,-12.56,-0.98271,-0.14455,0.11572,243.83
> view matrix models
> #1,0.17625,-0.53856,0.82395,106.05,-0.056777,0.83009,0.55473,-15.863,-0.98271,-0.14455,0.11572,243.67
> view matrix models
> #1,0.17625,-0.53856,0.82395,100.71,-0.056777,0.83009,0.55473,-17.501,-0.98271,-0.14455,0.11572,243.93
> view matrix models
> #1,0.17625,-0.53856,0.82395,101.25,-0.056777,0.83009,0.55473,-12.583,-0.98271,-0.14455,0.11572,246.54
> show #!2 models
> hide #!2 models
> view matrix models
> #1,0.17625,-0.53856,0.82395,145.8,-0.056777,0.83009,0.55473,-4.1578,-0.98271,-0.14455,0.11572,289.13
> view matrix models
> #1,0.17625,-0.53856,0.82395,171.4,-0.056777,0.83009,0.55473,-24.934,-0.98271,-0.14455,0.11572,345.77
> view matrix models
> #1,0.17625,-0.53856,0.82395,121.59,-0.056777,0.83009,0.55473,-55.183,-0.98271,-0.14455,0.11572,332.81
> volume #4 level 0.004372
> view matrix models
> #1,0.17625,-0.53856,0.82395,118.61,-0.056777,0.83009,0.55473,-55.665,-0.98271,-0.14455,0.11572,333.89
> view matrix models
> #1,0.17625,-0.53856,0.82395,126.65,-0.056777,0.83009,0.55473,-57.057,-0.98271,-0.14455,0.11572,343.23
> view matrix models
> #1,0.17625,-0.53856,0.82395,128.25,-0.056777,0.83009,0.55473,-60.587,-0.98271,-0.14455,0.11572,345.36
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.12776,-0.48949,0.8626,121.89,-0.076019,0.86233,0.5006,-53.947,-0.98889,-0.12953,0.072957,350.84
> ui mousemode right "move picked models"
> select subtract #1
Nothing selected
> select add #1
2 models selected
> view matrix models
> #1,0.12776,-0.48949,0.8626,118.34,-0.076019,0.86233,0.5006,-58.46,-0.98889,-0.12953,0.072957,349.96
> select subtract #1
Nothing selected
> volume #4 level 0.01111
> volume #4 level 0.01184
> volume #4 level 0.01038
> transparency #1,4,18 50
> volume #4 level 0.006558
> set bgColor black
> set bgColor transparent
> transparency #4 75
> transparency #4 90
> transparency #4 0
> volume #4 color #ddeaea
> volume #4 color #eadad5
> volume #4 color #e9eade
> volume #4 color #686863
> transparency #4 75
> volume #4 color #edede640
> transparency #1 40
> transparency #1 0
> graphics drawOrder offset #4 -10
Expected a keyword
> graphics draworder offset #4 -10
Expected a keyword
> move z -1 #4
Expected an integer >= 1 or a keyword
> move z 1 #4
Expected an integer >= 1 or a keyword
> move z -10 models #4
> move z 10 models #4
> hide #!18 models
> show #!18 models
> select add #18
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> view matrix models
> #18,0.25531,0.88832,0.3817,218.63,0.64365,0.13843,-0.75269,92.013,-0.72147,0.43786,-0.53643,123.02
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.8979,-0.089638,0.43098,196.85,0.36515,0.69845,-0.61549,104.83,-0.24585,0.71002,0.65987,131.61
> view matrix models
> #18,0.69911,-0.59995,-0.38898,186.12,0.52699,0.80003,-0.28677,106.28,0.48324,-0.0045064,0.87548,110.97
> ui mousemode right "move picked models"
> view matrix models
> #18,0.69911,-0.59995,-0.38898,183.9,0.52699,0.80003,-0.28677,117.63,0.48324,-0.0045064,0.87548,109.21
> ui tool show "Fit in Map"
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
x flip (#1) using 8232 atoms
average map value = 0.03585, steps = 344
shifted from previous position = 47.5
rotated from previous position = 29.8 degrees
atoms outside contour = 7488, contour level = 0.084687
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc x flip (#1) coordinates:
Matrix rotation and translation
-0.59182300 -0.46888259 -0.65566355 194.35561563
0.06300669 0.78401194 -0.61753984 147.19139501
0.80360172 -0.40678546 -0.43445354 122.88643591
Axis 0.13446015 -0.93100331 0.33934247
Axis point 69.80505654 0.00000000 141.14439518
Rotation angle (degrees) 128.39886790
Shift along axis -69.20200456
> view matrix models
> #18,0.58674,-0.79456,-0.15624,171.52,0.50161,0.50809,-0.70017,127.82,0.63571,0.33244,0.69667,170
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
x flip (#1) using 8232 atoms
average map value = 0.03995, steps = 108
shifted from previous position = 5.06
rotated from previous position = 9.97 degrees
atoms outside contour = 7039, contour level = 0.084687
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc x flip (#1) coordinates:
Matrix rotation and translation
-0.52429738 -0.36896225 -0.76744977 169.02279435
0.19539494 0.82507906 -0.53015599 158.84869394
0.82881427 -0.42791519 -0.36049342 123.18540462
Axis 0.06027725 -0.94109607 0.33272336
Axis point 43.68230496 0.00000000 141.20044849
Rotation angle (degrees) 121.99571687
Shift along axis -98.31699026
> view matrix models
> #4,0.17625,-0.53856,0.82395,126.27,-0.056777,0.83009,0.55473,-70.175,-0.98271,-0.14455,0.11572,371.77
> undo
> view matrix models
> #18,0.55231,-0.82013,-0.1495,181.2,0.62326,0.52533,-0.57929,113.66,0.55363,0.22677,0.80129,177.38
> fitmap #18 inMap #1
Fit molecule cx45hexamer.pdb (#18) to map cryosparc_P8_J200_005_volume_map.mrc
x flip (#1) using 8232 atoms
average map value = 0.08603, steps = 236
shifted from previous position = 10.8
rotated from previous position = 31.9 degrees
atoms outside contour = 4305, contour level = 0.084687
Position of cx45hexamer.pdb (#18) relative to
cryosparc_P8_J200_005_volume_map.mrc x flip (#1) coordinates:
Matrix rotation and translation
-0.49084206 -0.68754531 -0.53512199 159.28748498
-0.33746234 0.71628906 -0.61077752 160.52253517
0.80323923 -0.11921177 -0.58360543 127.46516645
Axis 0.33482440 -0.91160947 0.23845502
Axis point 74.97874372 0.00000000 127.94835312
Rotation angle (degrees) 132.77173121
Shift along axis -62.60581816
> move z 10 models #4
> move z -10 models #4
> move z 10 models #4
> volume #4 level 0.009219
> surface dust #1 20
Expected a keyword
> surface dust #1 size 20
> surface dust #1 size 100
> surface dust #1 size 10
> surface dust #1 size 20
> transparency #1 40
> transparency #1 20
> transparency #1 50
> select subtract #18
Nothing selected
> move z 10 models #4
> move z -10 models #4
> transparency #1 25
> transparency #1 40
> transparency #1 50
> move z 10 models #4
> move z -10 models #4
> volume #4 level 0.006735
> move z 10 models #4
> move z -10 models #4
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250514.cxs
> save /Users/sahtelis/Desktop/image6.png supersample 3
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_micelle_20250415.png width 821 height 627
> supersample 3 transparentBackground true
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_micelle_20250415_2.png width 821 height 627
> supersample 3
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250415.png width 821 height 627 supersample 3
> transparentBackground true
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250415_top.png width 821 height 627
> supersample 3 transparentBackground true
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250415_top-2.png width 821 height 627
> supersample 3 transparentBackground true
> hide #!18 models
> transparency #1 0
> lighting soft
> lighting full
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> volume #1 level 0.09613
> volume #1 level 0.09422
> volume #1 level 0.09518
> save /Users/sahtelis/Desktop/connexin-str_analysis/cx45_map_20250415.png
> width 821 height 627 supersample 3 transparentBackground true
> show #!18 models
> transparency #1 40
> graphics silhouettes false
> lighting full
> lighting simple
> lighting soft
> lighting full
> transparency #1 50
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250415-new.png width 821 height 627
> supersample 3
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250415-new2.png width 821 height 627
> supersample 3 transparentBackground true
> set bgColor white
> set bgColor #ffffff00
> set bgColor gray
> set bgColor #80808000
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250415-new3.png width 821 height 627
> supersample 3
> transparency #1 40
> set bgColor black
> set bgColor transparent
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250415-new4.png width 821 height 627
> supersample 3 transparentBackground true
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250415_top-3.png width 821 height 627
> supersample 3 transparentBackground true
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250415-new5.png width 821 height 627
> supersample 3 transparentBackground true
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250415_top-4.png width 821 height 627
> supersample 3 transparentBackground true
> hide #!18 models
> transparency #1 0
> graphics silhouettes true
> graphics silhouettes false
> save /Users/sahtelis/Desktop/connexin-str_analysis/cx45_map_20250415_new.png
> width 821 height 627 supersample 3 transparentBackground true
> open /Users/sahtelis/Downloads/cryosparc_P8_J203_005_volume_map.mrc
Opened cryosparc_P8_J203_005_volume_map.mrc as #5, grid size 384,384,384,
pixel 0.828, shown at level 0.0325, step 2, values float32
> volume #5 level 0.1193
> close #5
> show #!18 models
> transparency #1 40
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250415_top-5.png width 821 height 627
> supersample 3 transparentBackground true
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,12
Model Number: MC8G4KS/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 22 days, 11 hours, 40 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
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: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
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: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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