![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 months ago
Closed 4 months ago
#18174 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-15.5-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: Segmentation fault
Current thread 0x00000001f6bc1f00 (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, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.graphics._graphics, PIL._imagingmath, chimerax.segment._segment, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, _pyKVFinder, chimerax.mlp._mlp, chimerax.coulombic._esp (total: 67)
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
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"modelCode" : "Mac16,11",
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"captureTime" : "2025-07-10 05:50:28.2091 -0400",
"codeSigningMonitor" : 2,
"incident" : "475D8A60-87B2-4CE4-BBA7-B72BEAD72E63",
"pid" : 32065,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-21 11:40:40.1972 -0400",
"procStartAbsTime" : 32880142488177,
"procExitAbsTime" : 71774005649593,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "2BF2C7CA-DE88-462B-A148-96695BEB4A6D",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "2912C302-1DBF-406E-934D-8C694610AFC4",
"sip" : "enabled",
"vmRegionInfo" : "0x2b4fb23494a8 is not in any region. Bytes after previous region: 47140255863977 Bytes before following region: 57931824065368\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00002b4fb23494a8","rawCodes":[1,47621292201128],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00002b4fb23494a8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":32065},
"ktriageinfo" : "CL - (arg = 0x0) cluster_pagein past EOF\nAPFS - (arg = 0x3b12001600200040) cluster_pagein() failed\nVM - (arg = 0x1900000016) Filesystem pagein returned an error in vnode_pagein\nVM - (arg = 0x0) Page has error bit set\nCL - (arg = 0x0) cluster_pagein past EOF\n",
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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
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> #2,0.87313,0.48696,-0.022539,-145.38,0.48618,-0.87324,-0.032677,611.53,-0.035595,0.017573,-0.99921,870.34
> view matrix models
> #2,0.94879,0.31429,-0.031821,-99.587,0.31394,-0.94931,-0.015756,711.19,-0.03516,0.0049594,-0.99937,875.66
> view matrix models
> #2,0.94962,0.31341,-0.0016287,-112.59,0.31341,-0.94961,0.0032983,703.32,-0.00051288,-0.0036426,-0.99999,864.71
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit map cryosparc_P1_J1907_002_volume_map_sharp.mrc in map
cryosparc_P1_J1887_002_volume_map_sharp.mrc using 3409335 points
correlation = 0.9655, correlation about mean = 0.681, overlap = 5.946e+04
steps = 52, shift = 1.89, angle = 0.265 degrees
Position of cryosparc_P1_J1907_002_volume_map_sharp.mrc (#2) relative to
cryosparc_P1_J1887_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.94871396 0.31613578 0.00000312 -114.08324092
0.31613577 -0.94871395 0.00007177 703.13445484
0.00002564 -0.00006710 -1.00000000 861.04540718
Axis -0.98709520 -0.16013454 -0.00000789
Axis point 0.00000000 360.83631836 430.51063307
Rotation angle (degrees) 179.99596981
Shift along axis 0.00811541
> fitmap #2 inMap #1
Fit map cryosparc_P1_J1907_002_volume_map_sharp.mrc in map
cryosparc_P1_J1887_002_volume_map_sharp.mrc using 3409335 points
correlation = 0.9655, correlation about mean = 0.681, overlap = 5.946e+04
steps = 44, shift = 0.0153, angle = 0.00412 degrees
Position of cryosparc_P1_J1907_002_volume_map_sharp.mrc (#2) relative to
cryosparc_P1_J1887_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.94871435 0.31613460 0.00000003 -114.07729970
0.31613460 -0.94871435 0.00000000 703.17950787
0.00000003 0.00000001 -1.00000000 861.02842044
Axis 0.98771899 0.15491141 -0.02033825
Axis point 0.00000000 360.53555470 429.33972022
Rotation angle (degrees) 179.99999988
Shift along axis -21.25759849
> fitmap #2 inMap #1
Fit map cryosparc_P1_J1907_002_volume_map_sharp.mrc in map
cryosparc_P1_J1887_002_volume_map_sharp.mrc using 3409335 points
correlation = 0.9655, correlation about mean = 0.681, overlap = 5.946e+04
steps = 60, shift = 0.0165, angle = 0.00103 degrees
Position of cryosparc_P1_J1907_002_volume_map_sharp.mrc (#2) relative to
cryosparc_P1_J1887_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.94871947 0.31611924 -0.00000002 -114.06844125
0.31611924 -0.94871947 -0.00000781 703.20747080
-0.00000249 0.00000740 -1.00000000 861.02524262
Axis 0.98709685 0.16012438 -0.00000614
Axis point 0.00000000 360.85400291 430.51363929
Rotation angle (degrees) 179.99955836
Shift along axis -0.00122738
> select subtract #2
Nothing selected
> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Borrelia_Burgdorferi/Motor/Local_NU/cryosparc_P1_J1887_002_volume_map_sharp.mrc
Opened cryosparc_P1_J1887_002_volume_map_sharp.mrc as #3, grid size
640,640,640, pixel 1.35, shown at level 0.111, step 4, values float32
> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Borrelia_Burgdorferi/Motor/Local_NU/cryosparc_P1_J1907_002_volume_map_sharp.mrc
Opened cryosparc_P1_J1907_002_volume_map_sharp.mrc as #4, grid size
640,640,640, pixel 1.35, shown at level 0.102, step 4, values float32
> hide #!3 models
> close #3-4
> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Borrelia_Burgdorferi/Motor/Masks/collar_mask-1.mrc
Opened collar_mask-1.mrc as #3, grid size 356,356,106, pixel 2.75,2.75,2.75,
shown at level 0.0641, step 1, values float32
> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Borrelia_Burgdorferi/Motor/Masks/collar_mask-2.mrc
Opened collar_mask-2.mrc as #4, grid size 356,356,106, pixel 2.75,2.75,2.75,
shown at level 0.0545, step 1, values float32
> select add #3
2 models selected
> select add #4
4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,1,0,0,512.06,0,1,0,287.72,0,0,1,25.504,#4,1,0,0,512.06,0,1,0,287.72,0,0,1,25.504
> view matrix models
> #3,1,0,0,516,0,1,0,244.23,0,0,1,25.219,#4,1,0,0,516,0,1,0,244.23,0,0,1,25.219
> volume #3 level 0.03937
> volume #4 level 0.0319
> fitmap #3 inMap #1
Fit map collar_mask-1.mrc in map cryosparc_P1_J1887_002_volume_map_sharp.mrc
using 413637 points
correlation = 0.5734, correlation about mean = 0.07412, overlap = 1234
steps = 136, shift = 29.5, angle = 1.77 degrees
Position of collar_mask-1.mrc (#3) relative to
cryosparc_P1_J1887_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99952203 -0.03090869 0.00060360 541.25732977
0.03090817 0.99952187 0.00085205 242.37647415
-0.00062964 -0.00083299 0.99999945 3.78167466
Axis -0.02724308 0.01993855 0.99942997
Axis point -7573.15909979 17623.19794212 0.00000000
Rotation angle (degrees) 1.77221529
Shift along axis -6.13336205
> fitmap #4 inMap #1
Fit map collar_mask-2.mrc in map cryosparc_P1_J1887_002_volume_map_sharp.mrc
using 492842 points
correlation = 0.5724, correlation about mean = 0.09506, overlap = 1196
steps = 140, shift = 29.2, angle = 1.76 degrees
Position of collar_mask-2.mrc (#4) relative to
cryosparc_P1_J1887_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99952763 -0.03072152 0.00084482 541.10817581
0.03072022 0.99952688 0.00151417 242.09110672
-0.00089093 -0.00148750 0.99999850 4.29197497
Axis -0.04877639 0.02820544 0.99841140
Axis point -7621.84806887 17706.26118355 0.00000000
Rotation angle (degrees) 1.76325505
Shift along axis -15.27985929
> select subtract #3
2 models selected
> select subtract #4
Nothing selected
> volume #3 level 0.01287
> volume #4 level 0.01081
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> volume #1 step 2
> volume #1 level 0.1223
> volume #3 level 0.04191
> ui mousemode right "rotate selected models"
> select add #3
2 models selected
> view matrix models
> #3,0.99239,-0.12003,-0.027399,570.37,0.11574,0.9854,-0.12488,311.47,0.041989,0.12076,0.99179,-11.262
> view matrix models
> #3,0.99457,-0.082144,-0.063961,580.07,0.072395,0.9872,-0.14214,314.48,0.074818,0.13674,0.98778,-9.0423
> view matrix models
> #3,0.99543,-0.081376,-0.049969,573.62,0.083444,0.99568,0.040799,230.35,0.046433,-0.044782,0.99792,18.073
> view matrix models
> #3,0.99875,-0.0085541,-0.049248,559.7,0.010832,0.99887,0.046184,219.66,0.048798,-0.04666,0.99772,18.771
> fitmap #3 inMap #1
Fit map collar_mask-1.mrc in map cryosparc_P1_J1887_002_volume_map_sharp.mrc
using 374896 points
correlation = 0.5789, correlation about mean = 0.06772, overlap = 1170
steps = 140, shift = 1.06, angle = 4.04 degrees
Position of collar_mask-1.mrc (#3) relative to
cryosparc_P1_J1887_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99952436 -0.03083596 0.00044276 541.31462458
0.03083553 0.99952404 0.00092966 242.34489586
-0.00047121 -0.00091556 0.99999947 3.73120216
Axis -0.02990346 0.01481174 0.99944304
Axis point -7590.89467594 17663.14455798 0.00000000
Rotation angle (degrees) 1.76802320
Shift along axis -8.86850794
> volume #3 level 0.0319
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.99952,-0.030836,0.00044276,562.01,0.030836,0.99952,0.00092966,237.94,-0.00047121,-0.00091556,1,2.1609
> hide #!3 models
> volume #1 level 0.1173
> volume #1 step 1
> volume #1 level 0.1073
> show #!3 models
> view matrix models
> #3,0.99952,-0.030836,0.00044276,544.66,0.030836,0.99952,0.00092966,245.49,-0.00047121,-0.00091556,1,2.5358
> fitmap #3 inMap #1
Fit map collar_mask-1.mrc in map cryosparc_P1_J1887_002_volume_map_sharp.mrc
using 543348 points
correlation = 0.5557, correlation about mean = 0.09128, overlap = 1409
steps = 72, shift = 4.93, angle = 0.0331 degrees
Position of collar_mask-1.mrc (#3) relative to
cryosparc_P1_J1887_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99952305 -0.03087098 0.00080619 541.14431021
0.03086985 0.99952246 0.00137780 242.16836733
-0.00084834 -0.00135226 0.99999873 4.38536621
Axis -0.04415914 0.02676214 0.99866599
Axis point -7583.42885635 17627.73615206 0.00000000
Rotation angle (degrees) 1.77138955
Shift along axis -13.03600805
> volume #3 level 0.01251
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> volume sel showOutlineBox true
> hide #!1 models
> show #!1 models
> select subtract #3
Nothing selected
> volume #!1,3 showOutlineBox false
> volume #!1,3 showOutlineBox true
> volume resample #3 onGrid #1
Opened collar_mask-1.mrc resampled as #5, grid size 640,640,640, pixel 1.35,
shown at step 1, values float32
> volume #5 level 0.009129
> save
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Borrelia_Burgdorferi/Motor/Masks/collar_mask-3_resampled.mrc
> models #5
> hide #!5 models
> volume #!1 showOutlineBox false
> show #!2 models
> hide #!1 models
> lighting soft
> show #!1 models
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> volume #2 level 0.1
> volume #1 level 0.1
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> volume #2 level 0.07844
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #2
2 models selected
> view matrix models
> #2,0.94872,0.31612,-2.3367e-08,-113.76,0.31612,-0.94872,-7.8126e-06,703.01,-2.4919e-06,7.4046e-06,-1,858.46
> view matrix models
> #2,0.94872,0.31612,-2.3367e-08,-113.42,0.31612,-0.94872,-7.8126e-06,702.77,-2.4919e-06,7.4046e-06,-1,857.97
> hide #!2 models
> show #!2 models
> ui tool show "Side View"
> view matrix models
> #2,0.94872,0.31612,-2.3367e-08,-113.73,0.31612,-0.94872,-7.8126e-06,702.29,-2.4919e-06,7.4046e-06,-1,858.89
> fitmap #2 inMap #1
Fit map cryosparc_P1_J1907_002_volume_map_sharp.mrc in map
cryosparc_P1_J1887_002_volume_map_sharp.mrc using 4407872 points
correlation = 0.9611, correlation about mean = 0.7055, overlap = 6.621e+04
steps = 52, shift = 2.32, angle = 0.00411 degrees
Position of cryosparc_P1_J1907_002_volume_map_sharp.mrc (#2) relative to
cryosparc_P1_J1887_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.94874041 0.31605637 0.00002080 -114.06143013
0.31605637 -0.94874041 -0.00002538 703.23886887
0.00001171 0.00003065 -1.00000000 860.98009194
Axis 0.98710199 0.16009270 0.00000674
Axis point 0.00000000 360.86274647 430.49549043
Rotation angle (degrees) 179.99837379
Shift along axis -0.00105673
> select add #2
3 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.1
> volume #1 level 0.06907
> volume #2 level 0.05478
> volume #2 level 0.07
> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Borrelia_Burgdorferi/Motor/Local_NU/cryosparc_P1_J1917_004_volume_map_sharp.mrc
Opened cryosparc_P1_J1917_004_volume_map_sharp.mrc as #6, grid size
640,640,640, pixel 1.35, shown at level 0.145, step 4, values float32
> hide #!2 models
> hide #!1 models
> volume #6 step 1
> surface dust #6 size 13.5
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!6 models
> ui tool show "Side View"
> ui tool show "Segment Map"
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
Segmenting collar_mask-1.mrc, density threshold 0.012510
Only showing 4 of 416 regions.
Showing 4 of 416 region surfaces
898 watershed regions, grouped to 416 regions
Showing collar_mask-1.seg - 416 regions, 4 surfaces
> hide #7.1 models
> show #7.1 models
> hide #7.2 models
> show #7.2 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> close #7
Segmenting collar_mask-1.mrc, density threshold 0.012510
Only showing 50 of 416 regions.
Showing 50 of 416 region surfaces
898 watershed regions, grouped to 416 regions
Showing collar_mask-1.seg - 416 regions, 50 surfaces
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> close #7
Segmenting collar_mask-1.mrc, density threshold 0.012510
Showing 499 region surfaces
898 watershed regions, grouped to 499 regions
Showing collar_mask-1.seg - 499 regions, 499 surfaces
Segmenting collar_mask-1.mrc, density threshold 0.012510
Only showing 100 of 499 regions.
Showing 100 of 499 region surfaces
898 watershed regions, grouped to 499 regions
Showing collar_mask-1.seg - 499 regions, 100 surfaces
Segmenting collar_mask-1.mrc, density threshold 0.012510
Only showing 100 of 416 regions.
Showing 100 of 416 region surfaces
898 watershed regions, grouped to 416 regions
Showing collar_mask-1.seg - 416 regions, 100 surfaces
> close #7
> close #1-6
> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Borrelia_Burgdorferi/Motor/Masks/collar_mask-1.mrc
Opened collar_mask-1.mrc as #1, grid size 356,356,106, pixel 2.75,2.75,2.75,
shown at level 0.0641, step 1, values float32
> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Borrelia_Burgdorferi/Motor/Masks/collar_mask-2.mrc
Opened collar_mask-2.mrc as #2, grid size 356,356,106, pixel 2.75,2.75,2.75,
shown at level 0.0545, step 1, values float32
> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Borrelia_Burgdorferi/Motor/Masks/collar_mask-3_resampled.mrc
Opened collar_mask-3_resampled.mrc as #3, grid size 640,640,640, pixel 1.35,
shown at level 0.046, step 4, values float32
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Borrelia_Burgdorferi/Motor/Local_NU/cryosparc_P1_J1887_002_volume_map_sharp.mrc
Opened cryosparc_P1_J1887_002_volume_map_sharp.mrc as #4, grid size
640,640,640, pixel 1.35, shown at level 0.111, step 4, values float32
> volume #4 step 1
> volume #3 step 1
> volume #1 level 0.01437
> surface dust #1 size 27.5
> surface dust #2 size 27.5
> surface dust #3 size 13.5
> surface dust #4 size 13.5
> hide #!2 models
> hide #!3 models
Segmenting collar_mask-1.mrc, density threshold 0.014367
Only showing 100 of 416 regions.
Showing 100 of 416 region surfaces
898 watershed regions, grouped to 416 regions
Showing collar_mask-1.seg - 416 regions, 100 surfaces
> hide #!1 models
> show #!1 models
> ui tool show "Side View"
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> ui mousemode right select
> select #5.31
1 model selected
> select add #5.60
2 models selected
Grouped 2 regions
> select add #5.52
2 models selected
> select add #5.26
3 models selected
> select clear
> select add #5.26
1 model selected
> select add #5.52
2 models selected
Grouped 2 regions
> select add #5.53
2 models selected
> select add #5.23
3 models selected
Grouped 3 regions
> select add #5.66
2 models selected
> select add #5.30
3 models selected
> select clear
> select #5.23
1 model selected
Ungrouped to 3 regions
> select clear
> select #5.26
1 model selected
> select add #5.52
2 models selected
Grouped 2 regions
> select clear
> select #5.66
1 model selected
> select add #5.30
2 models selected
Grouped 2 regions
> select #5.64
1 model selected
> select clear
> select #5.64
1 model selected
> select add #5.32
2 models selected
> select add #5.97
3 models selected
Grouped 3 regions
> select #5.59
1 model selected
> select add #5.25
2 models selected
> select add #5.100
3 models selected
Grouped 3 regions
> select clear
> select add #5.58
1 model selected
> select add #5.18
2 models selected
> select add #5.99
3 models selected
Grouped 3 regions
> select clear
> select #5.51
1 model selected
> select add #5.21
2 models selected
> select add #5.98
3 models selected
Grouped 3 regions
> select clear
> select #5.63
1 model selected
> select add #5.17
2 models selected
Grouped 2 regions
> select clear
> select add #5.48
1 model selected
> select add #5.27
2 models selected
Grouped 2 regions
> select clear
> select #5.57
1 model selected
> select add #5.22
2 models selected
Grouped 2 regions
> select clear
> select add #5.65
1 model selected
> select add #5.28
2 models selected
Grouped 2 regions
> select clear
> select add #5.54
1 model selected
> select add #5.24
2 models selected
Grouped 2 regions
> select clear
> select add #5.19
1 model selected
> select add #5.61
2 models selected
Grouped 2 regions
> select clear
> select add #5.56
1 model selected
> select add #5.29
2 models selected
Grouped 2 regions
> select clear
> select add #5.55
1 model selected
> select add #5.20
2 models selected
Grouped 2 regions
> select add #5.31
2 models selected
> select add #5.53
3 models selected
> select add #5.23
4 models selected
> select add #5.26
5 models selected
> select add #5.30
6 models selected
> select add #5.25
7 models selected
> select add #5.18
8 models selected
> select add #5.21
9 models selected
> select add #5.17
10 models selected
> select add #5.27
11 models selected
> select add #5.22
12 models selected
> select add #5.28
13 models selected
> select add #5.24
14 models selected
> select add #5.19
15 models selected
> select add #5.29
16 models selected
Grouped 16 regions
Grouped 64 regions
> select clear
> select #5.1
1 model selected
Saving 1 regions to mrc file...
Opened collar_mask-1_region_1.mrc as #6, grid size 195,196,76, pixel
2.75,2.75,2.75, shown at step 1, values float32
Wrote collar_mask-1_region_1.mrc
> select clear
> select add #5
3 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> volume #6 level 0.01504
> volume #6 level 0.004558
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> close #6
> show #!5 models
Segmenting collar_mask-1.mrc, density threshold 0.014367
Only showing 150 of 416 regions.
Showing 150 of 416 region surfaces
898 watershed regions, grouped to 416 regions
Showing collar_mask-1.seg - 416 regions, 150 surfaces
> hide #!1 models
> show #!1 models
Segmenting collar_mask-1.mrc, density threshold 0.014367
Only showing 200 of 416 regions.
Showing 200 of 416 region surfaces
898 watershed regions, grouped to 416 regions
Showing collar_mask-1.seg - 416 regions, 200 surfaces
> select #1
2 models selected
> select clear
Segmenting collar_mask-1.mrc, density threshold 0.014367
Only showing 300 of 416 regions.
Showing 300 of 416 region surfaces
898 watershed regions, grouped to 416 regions
Showing collar_mask-1.seg - 416 regions, 300 surfaces
> select #5.9
1 model selected
> select clear
Segmenting collar_mask-1.mrc, density threshold 0.014367
Only showing 250 of 416 regions.
Showing 250 of 416 region surfaces
898 watershed regions, grouped to 416 regions
Showing collar_mask-1.seg - 416 regions, 250 surfaces
> select #1
2 models selected
> select clear
Segmenting collar_mask-1.mrc, density threshold 0.014367
Only showing 280 of 416 regions.
Showing 280 of 416 region surfaces
898 watershed regions, grouped to 416 regions
Showing collar_mask-1.seg - 416 regions, 280 surfaces
Segmenting collar_mask-1.mrc, density threshold 0.014367
Only showing 280 of 416 regions.
Showing 280 of 416 region surfaces
898 watershed regions, grouped to 416 regions
Showing collar_mask-1.seg - 416 regions, 280 surfaces
> select #1
2 models selected
> select clear
Segmenting collar_mask-1.mrc, density threshold 0.014367
Only showing 300 of 416 regions.
Showing 300 of 416 region surfaces
898 watershed regions, grouped to 416 regions
Showing collar_mask-1.seg - 416 regions, 300 surfaces
> select #1
2 models selected
> select clear
> hide #!1 models
Drag select of 1289, 278 of 11064 triangles, 1265, 7169 of 10984 triangles,
1292, 7514 of 11024 triangles, 1279, 7824 of 9304 triangles, 1339, 7920 of
9212 triangles, 1275, 1047, 4943 of 6564 triangles, 1095, 3043 of 6464
triangles, 88, 85 of 7052 triangles, 992, 800 of 6612 triangles, 930, 2296 of
5964 triangles
> select clear
> select #5.107
1 model selected
> select #5.105
1 model selected
> select #5.109
1 model selected
> select add #5.105
2 models selected
> select add #5.107
3 models selected
> select add #5.98
4 models selected
> select add #5.99
5 models selected
> select add #5.100
6 models selected
> select add #5.97
7 models selected
> select add #5.102
8 models selected
> select add #5.101
9 models selected
> select add #5.106
10 models selected
> select add #5.111
11 models selected
> select add #5.110
12 models selected
> select add #5.112
13 models selected
> select add #5.103
14 models selected
> open
> "/Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Treponema_Denticola/Sheath_Asymmetry/Alignment/J1898/cryosparc_P1_J1898_map_aligned_1
> (1).mrc"
Opened cryosparc_P1_J1898_map_aligned_1 (1).mrc as #6, grid size 144,144,144,
pixel 2.67, shown at level 0.36, step 1, values float32
[deleted to fit within ticket limits]
> fitmap #16.19 inMap #103
Fit molecule FlaA1_sheath_sym_part b (#16.19) to map sheath_masked_map (#103)
using 2616 atoms
average map value = 0.1163, steps = 40
shifted from previous position = 0.96
rotated from previous position = 1.97 degrees
atoms outside contour = 1247, contour level = 0.11
Position of FlaA1_sheath_sym_part b (#16.19) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
0.96799671 -0.25067740 -0.01196615 54.17122891
-0.25044950 -0.96796612 0.01779389 426.04158336
-0.01604336 -0.01422751 -0.99977006 372.24428918
Axis -0.99196637 0.12630467 0.00705984
Axis point 0.00000000 217.98376246 184.58315002
Rotation angle (degrees) 179.07518506
Shift along axis 2.70298966
> fitmap #16.20 inMap #103
Fit molecule FlaA1_sheath_sym_part c (#16.20) to map sheath_masked_map (#103)
using 2616 atoms
average map value = 0.1216, steps = 52
shifted from previous position = 0.918
rotated from previous position = 1.09 degrees
atoms outside contour = 1181, contour level = 0.11
Position of FlaA1_sheath_sym_part c (#16.20) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
0.97124264 -0.23797666 -0.00740366 50.50658875
-0.23796629 -0.97127077 0.00226369 425.72519708
-0.00772966 -0.00043677 -0.99997002 368.31113901
Axis -0.99278447 0.11985181 0.00381426
Axis point 0.00000000 216.03738634 184.10688286
Rotation angle (degrees) 179.92207523
Shift along axis 2.28661617
> fitmap #16.21 inMap #103
Fit molecule FlaA1_sheath_sym_part d (#16.21) to map sheath_masked_map (#103)
using 2616 atoms
average map value = 0.1152, steps = 52
shifted from previous position = 1.36
rotated from previous position = 0.81 degrees
atoms outside contour = 1225, contour level = 0.11
Position of FlaA1_sheath_sym_part d (#16.21) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
0.97223261 -0.23328418 -0.01849904 51.59597791
-0.23365549 -0.97208421 -0.02138651 428.78580212
-0.01299350 0.02511506 -0.99960011 364.62319854
Axis 0.99303295 -0.11756996 -0.00792926
Axis point 0.00000000 215.29776353 185.04400461
Rotation angle (degrees) 178.65835913
Shift along axis -2.06701852
> fitmap #16.22 inMap #103
Fit molecule FlaA1_sheath_sym_part e (#16.22) to map sheath_masked_map (#103)
using 2616 atoms
average map value = 0.1131, steps = 56
shifted from previous position = 1.39
rotated from previous position = 2.41 degrees
atoms outside contour = 1282, contour level = 0.11
Position of FlaA1_sheath_sym_part e (#16.22) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
0.97056670 -0.24081291 0.00306796 49.70568777
-0.24081615 -0.97027416 0.02399207 423.68227169
-0.00280084 -0.02402472 -0.99970743 371.86579060
Axis -0.99261331 0.12132111 -0.00006709
Axis point 0.00000000 217.14439836 183.35137297
Rotation angle (degrees) 178.61404870
Shift along axis 2.03812687
> fitmap #16.23 inMap #103
Fit molecule FlaA1_sheath_sym_part f (#16.23) to map sheath_masked_map (#103)
using 2616 atoms
average map value = 0.1204, steps = 48
shifted from previous position = 0.619
rotated from previous position = 1.01 degrees
atoms outside contour = 1166, contour level = 0.11
Position of FlaA1_sheath_sym_part f (#16.23) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
0.97374953 -0.22739367 -0.01019532 48.27721058
-0.22757340 -0.97349063 -0.02294180 427.74795004
-0.00470823 0.02465976 -0.99968481 363.10558865
Axis 0.99341477 -0.11451211 -0.00375093
Axis point 0.00000000 214.46691265 184.22169909
Rotation angle (degrees) 178.62714468
Shift along axis -2.38501202
> fitmap #16.24 inMap #103
Fit molecule FlaA1_sheath_sym_part g (#16.24) to map sheath_masked_map (#103)
using 2616 atoms
average map value = 0.09811, steps = 68
shifted from previous position = 0.697
rotated from previous position = 2.1 degrees
atoms outside contour = 1506, contour level = 0.11
Position of FlaA1_sheath_sym_part g (#16.24) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
0.97445387 -0.22373755 -0.01952271 49.34342177
-0.22441244 -0.97344105 -0.04529418 432.04691186
-0.00887021 0.04851823 -0.99878290 359.22716714
Axis 0.99358937 -0.11282322 -0.00714791
Axis point 0.00000000 214.55574216 184.92287872
Rotation angle (degrees) 177.29412681
Shift along axis -2.28555026
> color #103 #fff6b6ff models
> color #103 #fff6b6c8 models
> color #103 #fff6b64e models
> color #103 #fff6b64c models
> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Treponema_Denticola/T.Denticola_WT/FlaA1_real_space_refined-1.pdb
Chain information for FlaA1_real_space_refined-1.pdb #19
---
Chain | Description
A | No description available
> rename #19 AF_FlaA1_TDE1712_J2116map_related
> rename #19 AF_FlaA1_TDE1712_J2116map_related.pdb
> rename #19 id #55
> rename #55.6 id #49
> color #103 #fff6b6ff models
> color #103 #fff6b6ec models
> color #103 #fff6b6be models
> preset "overall look" interactive
Using preset: Overall Look / Interactive
> set bgColor transparent
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
> set bgColor #ffffff00
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select add #49
2616 atoms, 2669 bonds, 328 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #49,1,0,0,-42.627,0,1,0,-43.977,0,0,1,18.247
> view matrix models #49,1,0,0,-110,0,1,0,45.325,0,0,1,-4.847
> view matrix models #49,1,0,0,-130.14,0,1,0,49.526,0,0,1,42.599
> view matrix models #49,1,0,0,-64.95,0,1,0,130.73,0,0,1,13.374
> ui mousemode right "rotate selected models"
> view matrix models
> #49,0.6483,0.67122,0.3594,-167.61,0.74065,-0.66536,-0.093386,249.49,0.17645,0.32674,-0.9285,321.64
> view matrix models
> #49,0.95365,0.29361,0.065942,-108.08,0.28219,-0.94865,0.14292,307.62,0.10452,-0.11768,-0.98754,400.16
> ui mousemode right "translate selected models"
> view matrix models
> #49,0.95365,0.29361,0.065942,-66.291,0.28219,-0.94865,0.14292,265.42,0.10452,-0.11768,-0.98754,459.27
> view matrix models
> #49,0.95365,0.29361,0.065942,-47.999,0.28219,-0.94865,0.14292,278.96,0.10452,-0.11768,-0.98754,442.12
> fitmap #49 inMap #103
Fit molecule AF_FlaA1_TDE1712_J2116map_related.pdb (#49) to map
sheath_masked_map (#103) using 2616 atoms
average map value = 0.04067, steps = 140
shifted from previous position = 2.74
rotated from previous position = 5.85 degrees
atoms outside contour = 2116, contour level = 0.11
Position of AF_FlaA1_TDE1712_J2116map_related.pdb (#49) relative to
sheath_masked_map (#103) coordinates:
Matrix rotation and translation
0.94495457 0.30025714 0.13002505 -61.56523770
0.29401992 -0.95357108 0.06522639 293.87346972
0.14357282 -0.02340602 -0.98936293 426.68413434
Axis -0.98613558 -0.15073418 -0.06939619
Axis point 0.00000000 156.49509621 212.18124374
Rotation angle (degrees) 177.42430246
Shift along axis -13.19535754
> view matrix models
> #49,0.94495,0.30026,0.13003,-58.113,0.29402,-0.95357,0.065226,297.65,0.14357,-0.023406,-0.98936,425.92
> view matrix models
> #49,0.94495,0.30026,0.13003,-71.942,0.29402,-0.95357,0.065226,307.52,0.14357,-0.023406,-0.98936,420.4
> view matrix models
> #49,0.94495,0.30026,0.13003,-71.157,0.29402,-0.95357,0.065226,304.06,0.14357,-0.023406,-0.98936,376.56
> fitmap #49 inMap #103
Fit molecule AF_FlaA1_TDE1712_J2116map_related.pdb (#49) to map
sheath_masked_map (#103) using 2616 atoms
average map value = 0.1326, steps = 100
shifted from previous position = 4.49
rotated from previous position = 8.45 degrees
atoms outside contour = 1041, contour level = 0.11
Position of AF_FlaA1_TDE1712_J2116map_related.pdb (#49) relative to
sheath_masked_map (#103) coordinates:
Matrix rotation and translation
0.95458754 0.29791989 0.00252510 -50.67425979
0.29793059 -0.95455380 -0.00802625 321.03075399
0.00001916 0.00841406 -0.99996461 394.82521485
Axis 0.98858149 0.15068585 0.00064336
Axis point 0.00000000 163.54717396 198.10463163
Rotation angle (degrees) 179.52357452
Shift along axis -1.46682864
> view matrix models
> #49,0.95459,0.29792,0.0025251,-49.407,0.29793,-0.95455,-0.0080262,326.74,1.9162e-05,0.0084141,-0.99996,442.49
> fitmap #49 inMap #103
Fit molecule AF_FlaA1_TDE1712_J2116map_related.pdb (#49) to map
sheath_masked_map (#103) using 2616 atoms
average map value = 0.1257, steps = 92
shifted from previous position = 6.28
rotated from previous position = 2 degrees
atoms outside contour = 1111, contour level = 0.11
Position of AF_FlaA1_TDE1712_J2116map_related.pdb (#49) relative to
sheath_masked_map (#103) coordinates:
Matrix rotation and translation
0.96200717 0.27262565 0.01474691 -49.50796978
0.27247967 -0.96209662 0.01117708 323.71631382
0.01723511 -0.00673420 -0.99982879 446.71296586
Axis -0.99045606 -0.13759224 -0.00807277
Axis point 0.00000000 166.31648790 222.81914070
Rotation angle (degrees) 179.48192795
Shift along axis 0.88840515
> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Treponema_Denticola/T.Denticola_WT/FlaA1_real_space_refined-1.pdb
Chain information for FlaA1_real_space_refined-1.pdb #19
---
Chain | Description
A | No description available
> rename #19 FlaA1_sheath_sym_part h
Expected a keyword
> rename #19 FlaA1_sheath_sym_part_h
> rename #19 id #16.25
> mmaker #16.25 to #49
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF_FlaA1_TDE1712_J2116map_related.pdb, chain A (#49) with
FlaA1_sheath_sym_part_h, chain A (#16.25), sequence alignment score = 1665.1
RMSD between 328 pruned atom pairs is 0.000 angstroms; (across all 328 pairs:
0.000)
> select subtract #49
Nothing selected
> hide #49 models
> color #16.25 #cafac5ff
> color #16.25 #a9fab5ff
> hide #!16 models
> show #!16 models
> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Treponema_Denticola/T.Denticola_WT/FlaA1_real_space_refined-1.pdb
Chain information for FlaA1_real_space_refined-1.pdb #19
---
Chain | Description
A | No description available
> select add #19
2616 atoms, 2669 bonds, 328 residues, 1 model selected
> view matrix models #19,1,0,0,-69.463,0,1,0,170.32,0,0,1,6.8273
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.94496,0.25246,-0.20813,-52.662,0.015051,-0.66897,-0.74314,524.31,-0.32685,0.6991,-0.63595,285.9
> view matrix models
> #19,0.86229,-0.020301,-0.506,52.269,-0.29945,-0.82622,-0.47716,539.25,-0.40838,0.56298,-0.71853,331.39
> view matrix models
> #19,0.94591,-0.30312,-0.11559,-0.47949,-0.32364,-0.85717,-0.40065,531.85,0.022363,0.41639,-0.90891,322.88
> mmaker #119 to #16.25
No molecules/chains to match specified
> mmaker #19 to #16.25
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FlaA1_sheath_sym_part_h, chain A (#16.25) with
FlaA1_real_space_refined-1.pdb, chain A (#19), sequence alignment score =
1665.1
RMSD between 328 pruned atom pairs is 0.000 angstroms; (across all 328 pairs:
0.000)
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.96201,0.27263,0.014747,-3.267,0.27248,-0.9621,0.011177,329.14,0.017235,-0.0067342,-0.99983,466.46
> view matrix models
> #19,0.96201,0.27263,0.014747,-8.274,0.27248,-0.9621,0.011177,336.64,0.017235,-0.0067342,-0.99983,458.92
> view matrix models
> #19,0.96201,0.27263,0.014747,-6.5037,0.27248,-0.9621,0.011177,336.5,0.017235,-0.0067342,-0.99983,468.26
> view matrix models
> #19,0.96201,0.27263,0.014747,-2.2049,0.27248,-0.9621,0.011177,342.81,0.017235,-0.0067342,-0.99983,466.86
> view matrix models
> #19,0.96201,0.27263,0.014747,-7.9531,0.27248,-0.9621,0.011177,346.51,0.017235,-0.0067342,-0.99983,466.15
> view matrix models
> #19,0.96201,0.27263,0.014747,-6.3655,0.27248,-0.9621,0.011177,346.74,0.017235,-0.0067342,-0.99983,463.27
> fitmap #19 inMap #103
Fit molecule FlaA1_real_space_refined-1.pdb (#19) to map sheath_masked_map
(#103) using 2616 atoms
average map value = 0.05001, steps = 152
shifted from previous position = 4.84
rotated from previous position = 12.8 degrees
atoms outside contour = 2083, contour level = 0.11
Position of FlaA1_real_space_refined-1.pdb (#19) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
0.97005089 0.16438854 0.17882298 -24.71484896
0.18456394 -0.97744555 -0.10264657 380.67473421
0.15791581 0.13257667 -0.97851214 424.81718816
Axis 0.99245781 0.08821188 0.08512438
Axis point 0.00000000 178.82475313 224.75291638
Rotation angle (degrees) 173.19414632
Shift along axis 45.21388974
> color #103 #fff6b6d8 models
> color #103 #fff6b6ff models
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.97824,0.20485,0.03299,-2.6305,0.20741,-0.96985,-0.12795,381.24,0.0057843,0.13201,-0.99123,450.04
> fitmap #19 inMap #103
Fit molecule FlaA1_real_space_refined-1.pdb (#19) to map sheath_masked_map
(#103) using 2616 atoms
average map value = 0.05001, steps = 108
shifted from previous position = 0.602
rotated from previous position = 8.84 degrees
atoms outside contour = 2083, contour level = 0.11
Position of FlaA1_real_space_refined-1.pdb (#19) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
0.97004490 0.16441663 0.17882964 -24.71854322
0.18458570 -0.97744629 -0.10260041 380.65857034
0.15792716 0.13253640 -0.97851576 424.82287563
Axis 0.99245632 0.08822439 0.08512884
Axis point 0.00000000 178.82146272 224.75132722
Rotation angle (degrees) 173.19664879
Shift along axis 45.21597424
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.97004,0.16442,0.17883,-28.361,0.18459,-0.97745,-0.1026,377.42,0.15793,0.13254,-0.97852,431.97
> fitmap #19 inMap #103
Fit molecule FlaA1_real_space_refined-1.pdb (#19) to map sheath_masked_map
(#103) using 2616 atoms
average map value = 0.04549, steps = 68
shifted from previous position = 1.04
rotated from previous position = 5.95 degrees
atoms outside contour = 2162, contour level = 0.11
Position of FlaA1_real_space_refined-1.pdb (#19) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
0.98599399 0.08826079 0.14151276 -14.32389738
0.09737446 -0.99350854 -0.05881299 384.48018664
0.13540325 0.07176899 -0.98818781 444.27844280
Axis 0.99648857 0.04662244 0.06954767
Axis point 0.00000000 185.30382075 228.93944412
Rotation angle (degrees) 176.24322837
Shift along axis 34.55033595
> fitmap #19 inMap #103
Fit molecule FlaA1_real_space_refined-1.pdb (#19) to map sheath_masked_map
(#103) using 2616 atoms
average map value = 0.04549, steps = 44
shifted from previous position = 0.0175
rotated from previous position = 0.0165 degrees
atoms outside contour = 2162, contour level = 0.11
Position of FlaA1_real_space_refined-1.pdb (#19) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
0.98602218 0.08836988 0.14124804 -14.27955647
0.09746613 -0.99349907 -0.05882111 384.45821929
0.13513178 0.07176582 -0.98822520 444.33554796
Axis 0.99649565 0.04667253 0.06941252
Axis point 0.00000000 185.29097412 228.96523238
Rotation angle (degrees) 176.24311251
Shift along axis 34.55657220
> view matrix models
> #19,0.98602,0.08837,0.14125,-16.532,0.097466,-0.9935,-0.058821,384.42,0.13513,0.071766,-0.98823,443.47
> fitmap #19 inMap #103
Fit molecule FlaA1_real_space_refined-1.pdb (#19) to map sheath_masked_map
(#103) using 2616 atoms
average map value = 0.04549, steps = 56
shifted from previous position = 2.4
rotated from previous position = 0.011 degrees
atoms outside contour = 2160, contour level = 0.11
Position of FlaA1_real_space_refined-1.pdb (#19) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
0.98601029 0.08826368 0.14139739 -14.30211280
0.09736439 -0.99351149 -0.05877980 384.47817598
0.13529181 0.07172456 -0.98820630 444.30384826
Axis 0.99649267 0.04662038 0.06949033
Axis point 0.00000000 185.30622682 228.94713890
Rotation angle (degrees) 176.24547990
Shift along axis 34.54739114
> view matrix models
> #19,0.98601,0.088264,0.1414,-16.21,0.097364,-0.99351,-0.05878,386.49,0.13529,0.071725,-0.98821,388.47
> fitmap #19 inMap #103
Fit molecule FlaA1_real_space_refined-1.pdb (#19) to map sheath_masked_map
(#103) using 2616 atoms
average map value = 0.1261, steps = 120
shifted from previous position = 6.48
rotated from previous position = 23.9 degrees
atoms outside contour = 1110, contour level = 0.11
Position of FlaA1_real_space_refined-1.pdb (#19) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
0.95774354 -0.28737144 -0.01203959 63.91447537
-0.28740218 -0.95780959 -0.00086852 433.34391123
-0.01128205 0.00429202 -0.99992713 420.73431959
Axis 0.98937948 -0.14523605 -0.00589333
Axis point 0.00000000 221.08586934 210.84287741
Rotation angle (degrees) 179.85057434
Shift along axis -2.18101607
> view matrix models
> #19,0.95774,-0.28737,-0.01204,68.009,-0.2874,-0.95781,-0.00086852,431.89,-0.011282,0.004292,-0.99993,475.33
> fitmap #19 inMap #103
Fit molecule FlaA1_real_space_refined-1.pdb (#19) to map sheath_masked_map
(#103) using 2616 atoms
average map value = 0.1109, steps = 60
shifted from previous position = 3.14
rotated from previous position = 1.95 degrees
atoms outside contour = 1305, contour level = 0.11
Position of FlaA1_real_space_refined-1.pdb (#19) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
0.95008875 -0.31197374 -0.00193400 67.98777048
-0.31188314 -0.94993059 0.01899379 432.31384124
-0.00776272 -0.01744260 -0.99981772 476.28080698
Axis -0.98744228 0.15796114 0.00245517
Axis point 0.00000000 223.81985440 236.20707491
Rotation angle (degrees) 178.94283961
Shift along axis 2.32413863
> select subtract #19
Nothing selected
> rename #19 id #16.26
> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Treponema_Denticola/T.Denticola_WT/FlaA1_real_space_refined-1.pdb
Chain information for FlaA1_real_space_refined-1.pdb #19
---
Chain | Description
A | No description available
> mmaker #19 to #16.25
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FlaA1_sheath_sym_part_h, chain A (#16.25) with
FlaA1_real_space_refined-1.pdb, chain A (#19), sequence alignment score =
1665.1
RMSD between 328 pruned atom pairs is 0.000 angstroms; (across all 328 pairs:
0.000)
> select add #19
2616 atoms, 2669 bonds, 328 residues, 1 model selected
> view matrix models
> #19,0.96201,0.27263,0.014747,-66.705,0.27248,-0.9621,0.011177,277.89,0.017235,-0.0067342,-0.99983,476.4
> view matrix models
> #19,0.96201,0.27263,0.014747,-74.275,0.27248,-0.9621,0.011177,279.74,0.017235,-0.0067342,-0.99983,473.89
> view matrix models
> #19,0.96201,0.27263,0.014747,-70.358,0.27248,-0.9621,0.011177,282.34,0.017235,-0.0067342,-0.99983,477.59
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.74688,0.66074,0.074764,-99.155,0.66343,-0.74806,-0.016306,202.34,0.045155,0.061779,-0.99707,464.22
> fitmap #19 inMap #103
Fit molecule FlaA1_real_space_refined-1.pdb (#19) to map sheath_masked_map
(#103) using 2616 atoms
average map value = 0.1129, steps = 100
shifted from previous position = 4.3
rotated from previous position = 8.71 degrees
atoms outside contour = 1280, contour level = 0.11
Position of FlaA1_real_space_refined-1.pdb (#19) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
0.65154525 0.75824668 0.02346832 -84.86370931
0.75751528 -0.65195502 0.03354487 166.84040646
0.04073558 -0.00407839 -0.99916164 470.46895898
Axis -0.90871005 -0.41705393 -0.01766537
Axis point 0.00000000 105.57403615 235.11089394
Rotation angle (degrees) 178.81380877
Shift along axis -0.77594775
> select subtract #19
Nothing selected
> rename #19 id #16.27
> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Treponema_Denticola/T.Denticola_WT/FlaA1_real_space_refined-1.pdb
Chain information for FlaA1_real_space_refined-1.pdb #19
---
Chain | Description
A | No description available
> mmaker #19 to #16.25
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FlaA1_sheath_sym_part_h, chain A (#16.25) with
FlaA1_real_space_refined-1.pdb, chain A (#19), sequence alignment score =
1665.1
RMSD between 328 pruned atom pairs is 0.000 angstroms; (across all 328 pairs:
0.000)
> select add #19
2616 atoms, 2669 bonds, 328 residues, 1 model selected
> view matrix models
> #19,0.6464,-0.76081,-0.057824,142.55,-0.75653,-0.64892,0.081074,423.76,-0.099205,-0.0086602,-0.99503,463.37
> mmaker #19 to #16.25
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FlaA1_sheath_sym_part_h, chain A (#16.25) with
FlaA1_real_space_refined-1.pdb, chain A (#19), sequence alignment score =
1665.1
RMSD between 328 pruned atom pairs is 0.000 angstroms; (across all 328 pairs:
0.000)
> mmaker #19 to #16.26
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FlaA1_real_space_refined-1.pdb, chain A (#16.26) with
FlaA1_real_space_refined-1.pdb, chain A (#19), sequence alignment score =
1665.1
RMSD between 328 pruned atom pairs is 0.000 angstroms; (across all 328 pairs:
0.000)
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.95009,-0.31197,-0.001934,197.5,-0.31188,-0.94993,0.018994,301.88,-0.0077627,-0.017443,-0.99982,455.38
> view matrix models
> #19,0.95009,-0.31197,-0.001934,228.51,-0.31188,-0.94993,0.018994,326.39,-0.0077627,-0.017443,-0.99982,421.57
> view matrix models
> #19,0.95009,-0.31197,-0.001934,172.72,-0.31188,-0.94993,0.018994,426.41,-0.0077627,-0.017443,-0.99982,465.54
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.19704,-0.97853,-0.06039,380.74,-0.97749,-0.20082,0.064698,421.81,-0.075437,0.046283,-0.99608,466.82
> view matrix models
> #19,0.18685,-0.98217,0.020938,366.87,-0.9799,-0.18785,-0.067209,446.24,0.069944,-0.0079596,-0.99752,452.31
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.18685,-0.98217,0.020938,346.07,-0.9799,-0.18785,-0.067209,431.21,0.069944,-0.0079596,-0.99752,471.62
> view matrix models
> #19,0.18685,-0.98217,0.020938,344.2,-0.9799,-0.18785,-0.067209,430.16,0.069944,-0.0079596,-0.99752,458.41
> fitmap #19 inMap #103
Fit molecule FlaA1_real_space_refined-1.pdb (#19) to map sheath_masked_map
(#103) using 2616 atoms
average map value = 0.1036, steps = 64
shifted from previous position = 2.95
rotated from previous position = 6.98 degrees
atoms outside contour = 1406, contour level = 0.11
Position of FlaA1_real_space_refined-1.pdb (#19) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
0.12675724 -0.99192467 0.00425155 355.55701053
-0.99130237 -0.12652249 0.03621746 401.84377004
-0.03538709 -0.00880540 -0.99933499 474.37409458
Axis -0.75051998 0.66076634 0.01037365
Axis point 0.00000000 362.18037648 235.65220599
Rotation angle (degrees) 178.28118707
Shift along axis 3.59318587
> rename #19 id #16.28
> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Treponema_Denticola/T.Denticola_WT/FlaA1_real_space_refined-1.pdb
Chain information for FlaA1_real_space_refined-1.pdb #19
---
Chain | Description
A | No description available
> mmaker #19 to #16.28
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FlaA1_real_space_refined-1.pdb, chain A (#16.28) with
FlaA1_real_space_refined-1.pdb, chain A (#19), sequence alignment score =
1665.1
RMSD between 328 pruned atom pairs is 0.000 angstroms; (across all 328 pairs:
0.000)
> select subtract #16.28
Nothing selected
> select add #19
2616 atoms, 2669 bonds, 328 residues, 1 model selected
> view matrix models
> #19,0.12676,-0.99192,0.0042515,253.72,-0.9913,-0.12652,0.036217,224.96,-0.035387,-0.0088054,-0.99933,467.67
> view matrix models
> #19,0.12676,-0.99192,0.0042515,366.89,-0.9913,-0.12652,0.036217,331.99,-0.035387,-0.0088054,-0.99933,419.25
> view matrix models
> #19,0.12676,-0.99192,0.0042515,364.69,-0.9913,-0.12652,0.036217,317.15,-0.035387,-0.0088054,-0.99933,472.37
> ui mousemode right "rotate selected models"
> view matrix models
> #19,-0.47706,-0.87837,0.029742,435.32,-0.87723,0.47383,-0.077206,246.22,0.053723,-0.062922,-0.99657,465.41
> fitmap #19 inMap #103
Fit molecule FlaA1_real_space_refined-1.pdb (#19) to map sheath_masked_map
(#103) using 2616 atoms
average map value = 0.1021, steps = 156
shifted from previous position = 5.73
rotated from previous position = 28.8 degrees
atoms outside contour = 1454, contour level = 0.11
Position of FlaA1_real_space_refined-1.pdb (#19) relative to sheath_masked_map
(#103) coordinates:
Matrix rotation and translation
-0.83512323 -0.54995056 0.01111617 454.02491958
-0.54971312 0.83514232 0.01878281 133.87955403
-0.01961320 0.00957526 -0.99976179 464.10942626
Axis -0.28701805 0.95789658 0.00740161
Axis point 249.01283593 0.00000000 229.63504426
Rotation angle (degrees) 179.08093485
Shift along axis 1.36457672
> rename #19 id #16.29
> select subtract #16.29
Nothing selected
> rename #16.26 FlaA1_sheath_sym_part_i
> rename #16.27 FlaA1_sheath_sym_part_j
> rename #16.28 FlaA1_sheath_sym_part_k
> rename #16.29 FlaA1_sheath_sym_part_l
> color #16.26 #fff6b6ff
> color #16.26 #a9fab5ff
> color #16.27 #a9fab5ff
> color #16.28 #58ac5aff
> color #16.28 #a9fab5ff
> color #16.29 #a9fab5ff
> hide #!103 models
> show #!103 models
> show #!55 models
> show #!56 models
> show #!57 models
> show #!58 models
> hide
> #16.1-29#58.1-5#56.1.3.1-7#56.5.2.1-12#!55.1-5#!56.1-5#!57.1-5#!56.1.2.1-7#!56.4.2.1-5
> surfaces
> show
> #16.1-29#58.1-5#56.1.3.1-7#56.5.2.1-12#!55.1-5#!56.1-5#!57.1-5#!56.1.2.1-7#!56.4.2.1-5
> cartoons
> hide
> #16.1-29#58.1-5#56.1.3.1-7#56.5.2.1-12#!55.1-5#!56.1-5#!57.1-5#!56.1.2.1-7#!56.4.2.1-5
> atoms
> close #56.1.2
> close #56.1.3
> close #56.4.2
> close #56.5.2
> fitmap #55.1 inMap #103
Fit molecule Asym_part_1 A (#55.1) to map sheath_masked_map (#103) using 1624
atoms
average map value = 0.09951, steps = 44
shifted from previous position = 1.08
rotated from previous position = 1.96 degrees
atoms outside contour = 954, contour level = 0.11
Position of Asym_part_1 A (#55.1) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.85520454 0.51800792 0.01711716 -78.70791176
-0.51745894 0.85523664 -0.02839942 135.33865809
-0.02935035 0.01542989 0.99945009 26.36346556
Axis 0.04224776 0.04479077 -0.99810266
Axis point 205.54278711 207.47464708 0.00000000
Rotation angle (degrees) 31.24627079
Shift along axis -23.57675566
> fitmap #55.2 inMap #103
Fit molecule Asym_part_1 B (#55.2) to map sheath_masked_map (#103) using 1611
atoms
average map value = 0.113, steps = 68
shifted from previous position = 1.37
rotated from previous position = 3.02 degrees
atoms outside contour = 787, contour level = 0.11
Position of Asym_part_1 B (#55.2) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.87512486 0.48384751 0.00693286 -74.52868979
-0.48377326 0.87513517 -0.01009284 122.60672956
-0.01095059 0.00547856 0.99992503 24.34667727
Axis 0.01608763 0.01847634 -0.99969986
Axis point 201.35683337 205.22735307 0.00000000
Rotation angle (degrees) 28.94407150
Shift along axis -23.27303692
> fitmap #55.3 inMap #103
Fit molecule Asym_part_1 C (#55.3) to map sheath_masked_map (#103) using 1579
atoms
average map value = 0.1062, steps = 40
shifted from previous position = 0.833
rotated from previous position = 1.39 degrees
atoms outside contour = 845, contour level = 0.11
Position of Asym_part_1 C (#55.3) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.84672406 0.53197255 0.00797322 -76.85347785
-0.53164939 0.84658811 -0.02524873 136.87209131
-0.02018167 0.01713975 0.99964940 23.43737015
Axis 0.03980742 0.02644052 -0.99885748
Axis point 200.70338976 200.58711768 0.00000000
Rotation angle (degrees) 32.16906134
Shift along axis -22.85096119
> fitmap #55.4 inMap map #103
Invalid "inMap" argument: invalid density map specifier
> fitmap #55.4 inMap #103
Fit molecule Asym_part_1 D (#55.4) to map sheath_masked_map (#103) using 1624
atoms
average map value = 0.08559, steps = 68
shifted from previous position = 1.21
rotated from previous position = 1.57 degrees
atoms outside contour = 1106, contour level = 0.11
Position of Asym_part_1 D (#55.4) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.84394019 0.53524507 -0.03574468 -64.92272182
-0.53607674 0.84394119 -0.01962104 138.70451738
0.01966434 0.03572087 0.99916832 14.23308998
Axis 0.05152014 -0.05158260 -0.99733891
Axis point 204.39627095 178.51353224 0.00000000
Rotation angle (degrees) 32.48577143
Shift along axis -24.69478220
> fitmap #55.5 inMap #103
Fit molecule Asym_part_1 E (#55.5) to map sheath_masked_map (#103) using 1611
atoms
average map value = 0.09144, steps = 44
shifted from previous position = 1.11
rotated from previous position = 1.94 degrees
atoms outside contour = 1017, contour level = 0.11
Position of Asym_part_1 E (#55.5) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.86583177 0.50023550 -0.00998981 -72.40692566
-0.50024232 0.86588318 0.00198325 121.87612857
0.00964210 0.00328017 0.99994813 20.21225629
Axis 0.00129604 -0.01961875 -0.99980669
Axis point 190.27106194 195.71950915 0.00000000
Rotation angle (degrees) 30.02220748
Shift along axis -22.69324861
> fitmap #56.1 inMap #103
Fit molecule Asym_part_2 A (#56.1) to map sheath_masked_map (#103) using 1624
atoms
average map value = 0.1202, steps = 52
shifted from previous position = 0.735
rotated from previous position = 2.61 degrees
atoms outside contour = 749, contour level = 0.11
Position of Asym_part_2 A (#56.1) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.86632228 0.49868652 0.02823929 -79.31014804
-0.49864154 0.86676036 -0.00911574 124.70081241
-0.02902260 -0.00618411 0.99955963 -21.78793378
Axis 0.00293464 0.05732065 -0.99835151
Axis point 190.59317837 210.29711652 0.00000000
Rotation angle (degrees) 29.96609458
Shift along axis 28.66720205
> fitmap #56.2 inMap #103
Fit molecule Asym_part_2 B (#56.2) to map sheath_masked_map (#103) using 1611
atoms
average map value = 0.1373, steps = 68
shifted from previous position = 0.796
rotated from previous position = 4.04 degrees
atoms outside contour = 622, contour level = 0.11
Position of Asym_part_2 B (#56.2) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.88793637 0.45954087 0.01977838 -75.42945903
-0.45978593 0.88797132 0.01018992 110.69132409
-0.01287995 -0.01814182 0.99975246 -23.15110101
Axis -0.03078390 0.03548496 -0.99889598
Axis point 187.80520493 207.97127654 0.00000000
Rotation angle (degrees) 27.39817067
Shift along axis 29.37543159
> fitmap #56.3 inMap #103
Fit molecule Asym_part_2 C (#56.3) to map sheath_masked_map (#103) using 1579
atoms
average map value = 0.1162, steps = 44
shifted from previous position = 1.29
rotated from previous position = 1.84 degrees
atoms outside contour = 758, contour level = 0.11
Position of Asym_part_2 C (#56.3) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.85928842 0.51116971 0.01813699 -77.49656516
-0.51115136 0.85946989 -0.00598391 125.65227825
-0.01864699 -0.00412884 0.99981760 -24.88854117
Axis 0.00181339 0.03595753 -0.99935167
Axis point 187.83920461 203.41729517 0.00000000
Rotation angle (degrees) 30.76327194
Shift along axis 29.25001936
> fitmap #56.4 inMap #103
Fit molecule Asym_part_2 D (#56.4) to map sheath_masked_map (#103) using 1624
atoms
average map value = 0.1145, steps = 56
shifted from previous position = 1.63
rotated from previous position = 0.47 degrees
atoms outside contour = 757, contour level = 0.11
Position of Asym_part_2 D (#56.4) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.85696460 0.51495106 -0.02090657 -66.57796947
-0.51513448 0.85709904 -0.00420693 128.57831207
0.01575264 0.01437489 0.99977258 -33.06453834
Axis 0.01802476 -0.03556021 -0.99920497
Axis point 199.94662852 185.78246628 0.00000000
Rotation angle (degrees) 31.02770995
Shift along axis 27.26592700
> fitmap #56.5 inMap #103
Fit molecule Asym_part_2 E (#56.5) to map sheath_masked_map (#103) using 1611
atoms
average map value = 0.1204, steps = 56
shifted from previous position = 1.92
rotated from previous position = 2.81 degrees
atoms outside contour = 745, contour level = 0.11
Position of Asym_part_2 E (#56.5) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.87924492 0.47636667 0.00178127 -73.06428590
-0.47631634 0.87908360 0.01829692 111.00275289
0.00715016 -0.01693592 0.99983101 -27.52379108
Axis -0.03695691 -0.00563160 -0.99930099
Axis point 183.24811353 197.53534486 0.00000000
Rotation angle (degrees) 28.46844591
Shift along axis 29.57965877
> fitmap #57.5 inMap #103
Fit molecule Asym_part_3 E (#57.5) to map sheath_masked_map (#103) using 1611
atoms
average map value = 0.1243, steps = 52
shifted from previous position = 0.583
rotated from previous position = 2.07 degrees
atoms outside contour = 723, contour level = 0.11
Position of Asym_part_3 E (#57.5) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.89362675 0.44859665 0.01386618 -74.12681205
-0.44877316 0.89272442 0.04056782 96.61783449
0.00581991 -0.04247526 0.99908057 -74.59447618
Axis -0.09214314 0.00892799 -0.99570575
Axis point 168.62915527 188.39138290 0.00000000
Rotation angle (degrees) 26.78346839
Shift along axis 81.96702914
> fitmap #57.4 inMap #103
Fit molecule Asym_part_3 D (#57.4) to map sheath_masked_map (#103) using 1624
atoms
average map value = 0.126, steps = 52
shifted from previous position = 0.678
rotated from previous position = 1.65 degrees
atoms outside contour = 688, contour level = 0.11
Position of Asym_part_3 D (#57.4) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.87077885 0.49159026 -0.00912166 -67.97056210
-0.49148170 0.87080692 0.01187640 116.76382543
0.01378153 -0.00585859 0.99988787 -80.96581915
Axis -0.01803256 -0.02328746 -0.99956617
Axis point 192.46102475 185.94375686 0.00000000
Rotation angle (degrees) 29.45562395
Shift along axis 79.43724336
> fitmap #57.3 inMap #103
Fit molecule Asym_part_3 C (#57.3) to map sheath_masked_map (#103) using 1579
atoms
average map value = 0.1085, steps = 52
shifted from previous position = 0.921
rotated from previous position = 1.51 degrees
atoms outside contour = 815, contour level = 0.11
Position of Asym_part_3 C (#57.3) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.87563243 0.48168714 0.03528955 -79.73008012
-0.48238578 0.87583848 0.01452271 111.53288768
-0.02391254 -0.02973974 0.99927160 -71.49145486
Axis -0.04577757 0.06122861 -0.99707345
Axis point 168.99824455 201.38623193 0.00000000
Rotation angle (degrees) 28.91105577
Shift along axis 81.76108418
> fitmap #57.2 inMap #103
Fit molecule Asym_part_3 B (#57.2) to map sheath_masked_map (#103) using 1611
atoms
average map value = 0.1388, steps = 56
shifted from previous position = 0.697
rotated from previous position = 3.14 degrees
atoms outside contour = 619, contour level = 0.11
Position of Asym_part_3 B (#57.2) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.90135661 0.43194498 0.03130173 -76.16769267
-0.43280473 0.90099824 0.02970244 97.44949294
-0.01537298 -0.04032003 0.99906855 -70.52107810
Axis -0.08059355 0.05372105 -0.99529831
Axis point 169.33356669 199.78901141 0.00000000
Rotation angle (degrees) 25.74822452
Shift along axis 81.56322352
> fitmap #57.1 inMap #103
Fit molecule Asym_part_3 A (#57.1) to map sheath_masked_map (#103) using 1624
atoms
average map value = 0.1222, steps = 52
shifted from previous position = 0.115
rotated from previous position = 2 degrees
atoms outside contour = 732, contour level = 0.11
Position of Asym_part_3 A (#57.1) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.88231352 0.46877328 0.04212437 -80.89544971
-0.46956832 0.88282859 0.01092075 110.48557909
-0.03206925 -0.02941580 0.99905269 -68.93945798
Axis -0.04281402 0.07875059 -0.99597455
Axis point 169.87573348 207.83401404 0.00000000
Rotation angle (degrees) 28.10358387
Shift along axis 80.82620942
> fitmap #58.1 inMap #103
Fit molecule Asym_part_4 A (#58.1) to map sheath_masked_map (#103) using 1624
atoms
average map value = 0.1037, steps = 52
shifted from previous position = 0.376
rotated from previous position = 1.84 degrees
atoms outside contour = 896, contour level = 0.11
Position of Asym_part_4 A (#58.1) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.89462170 0.44417997 0.04854029 -81.05183893
-0.44577741 0.89467565 0.02894794 97.19998079
-0.03056972 -0.04753562 0.99840165 -117.40294150
Axis -0.08529123 0.08822014 -0.99244275
Axis point 146.58104529 191.90316212 0.00000000
Rotation angle (degrees) 26.63896801
Shift along axis 132.00370500
> fitmap #58.2 inMap #103
Fit molecule Asym_part_4 B (#58.2) to map sheath_masked_map (#103) using 1611
atoms
average map value = 0.1144, steps = 52
shifted from previous position = 0.764
rotated from previous position = 3.31 degrees
atoms outside contour = 805, contour level = 0.11
Position of Asym_part_4 B (#58.2) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.91421622 0.40293798 0.04300787 -77.22055532
-0.40482529 0.91287509 0.05268350 82.29272865
-0.01803263 -0.06557478 0.99768470 -117.25272551
Axis -0.14445474 0.07456214 -0.98669819
Axis point 141.32645025 174.05637544 0.00000000
Rotation angle (degrees) 24.16252871
Shift along axis 132.98384903
> fitmap #58.3 inMap #103
Fit molecule Asym_part_4 C (#58.3) to map sheath_masked_map (#103) using 1579
atoms
average map value = 0.08212, steps = 56
shifted from previous position = 1.22
rotated from previous position = 0.976 degrees
atoms outside contour = 1093, contour level = 0.11
Position of Asym_part_4 C (#58.3) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.88861725 0.45731128 0.03501109 -78.53630790
-0.45842052 0.88799401 0.03629412 97.26675839
-0.01449193 -0.04830138 0.99872767 -120.90733812
Axis -0.09185555 0.05375140 -0.99432054
Axis point 152.12082923 182.13878922 0.00000000
Rotation angle (degrees) 27.41816163
Shift along axis 132.66287024
> fitmap #58.4 inMap #103
Fit molecule Asym_part_4 D (#58.4) to map sheath_masked_map (#103) using 1624
atoms
average map value = 0.114, steps = 68
shifted from previous position = 0.812
rotated from previous position = 1.76 degrees
atoms outside contour = 798, contour level = 0.11
Position of Asym_part_4 D (#58.4) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.88293189 0.46950032 0.00085725 -69.31700480
-0.46925598 0.88241047 0.03392037 102.88120045
0.01516918 -0.03035164 0.99942417 -128.93159108
Axis -0.06829726 -0.01520827 -0.99754909
Axis point 180.07018993 173.36925517 0.00000000
Rotation angle (degrees) 28.06879494
Shift along axis 131.78510843
> fitmap #58.5 inMap #103
Fit molecule Asym_part_4 E (#58.5) to map sheath_masked_map (#103) using 1611
atoms
average map value = 0.1037, steps = 64
shifted from previous position = 0.731
rotated from previous position = 2.29 degrees
atoms outside contour = 895, contour level = 0.11
Position of Asym_part_4 E (#58.5) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.90794073 0.41863384 0.01973154 -73.89954073
-0.41902315 0.90587740 0.06169060 81.08140864
0.00795141 -0.06427938 0.99790026 -122.85894981
Axis -0.14869717 0.01390547 -0.98878501
Axis point 152.54001227 162.61641703 0.00000000
Rotation angle (degrees) 25.06074746
Shift along axis 133.59721521
> fitmap #58.5 inMap #103
Fit molecule Asym_part_4 E (#58.5) to map sheath_masked_map (#103) using 1611
atoms
average map value = 0.1036, steps = 40
shifted from previous position = 0.00379
rotated from previous position = 0.00897 degrees
atoms outside contour = 895, contour level = 0.11
Position of Asym_part_4 E (#58.5) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
0.90791857 0.41867925 0.01978761 -73.91155468
-0.41907098 0.90584602 0.06182638 81.05981354
0.00796089 -0.06442573 0.99789075 -122.84041408
Axis -0.14900649 0.01395825 -0.98873770
Axis point 152.46391479 162.51851236 0.00000000
Rotation angle (degrees) 25.06501193
Shift along axis 133.60170227
> combine #55-58
Remapping chain ID 'A' in Asym_part_2 A #56.1 to 'F'
Remapping chain ID 'B' in Asym_part_2 B #56.2 to 'G'
Remapping chain ID 'C' in Asym_part_2 C #56.3 to 'H'
Remapping chain ID 'D' in Asym_part_2 D #56.4 to 'I'
Remapping chain ID 'E' in Asym_part_2 E #56.5 to 'J'
Remapping chain ID 'A' in Asym_part_3 A #57.1 to 'K'
Remapping chain ID 'B' in Asym_part_3 B #57.2 to 'L'
Remapping chain ID 'C' in Asym_part_3 C #57.3 to 'M'
Remapping chain ID 'D' in Asym_part_3 D #57.4 to 'N'
Remapping chain ID 'E' in Asym_part_3 E #57.5 to 'O'
Remapping chain ID 'A' in Asym_part_4 A #58.1 to 'P'
Remapping chain ID 'B' in Asym_part_4 B #58.2 to 'Q'
Remapping chain ID 'C' in Asym_part_4 C #58.3 to 'R'
Remapping chain ID 'D' in Asym_part_4 D #58.4 to 'S'
Remapping chain ID 'E' in Asym_part_4 E #58.5 to 'T'
> hide #19 models
> show #19 models
> select add #19
32196 atoms, 33008 bonds, 3984 residues, 1 model selected
> select subtract #19
Nothing selected
> rename #19 Asym_part_model.pdb
> show #3 models
> hide #3 models
> close #3
> rename #19 id #3
> hide #!55 models
> hide #!56 models
> hide #!57 models
> hide #!58 models
> show #!4 models
> hide #!4 models
> hide #!103 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> close #4
> volume zone #103 nearAtoms #3 range 5 invert false newMap true minimalBounds
> true bondPointSpacing 2
Opened sheath_masked_map zone as #4, grid size 147,99,230, pixel 1.07, shown
at step 1, values float32
> surface dust #4 size 10.7
> rename #4 Asym_part_map_zone
> hide #!4 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> close #8
> volume zone #103 nearAtoms #16 range 5 invert false newMap true
> minimalBounds true bondPointSpacing 2
Opened sheath_masked_map zone as #8, grid size 203,202,264, pixel 1.07, shown
at step 1, values float32
> surface dust #8 size 10.7
> hide #!8 models
> show #!8 models
> color #8 #a9fab5ff models
> rename #8 Sym_part_map_zone
> show #!4 models
> color #4 #d6741dff models
> color #4 #76609fff models
> color #4 #febe0eff models
> color #4 #fdd900ff models
> color #4 #fdf100ff models
> color #4 #fddc00ff models
> color #4 #a89200ff models
> color #4 #a89b45ff models
> color #4 #a89552ff models
> color #4 #c0aa5eff models
> show #!9 models
> hide #!9 models
> close #9-12
> show #5 models
> show #!6 models
> close #6
> show #!103 models
> hide #!8 models
> hide #!16 models
> hide #3 models
> hide #!4 models
> fitmap #5 inMap #103
Fit molecule FlaB1_core_long.pdb (#5) to map sheath_masked_map (#103) using
216018 atoms
average map value = 0.08392, steps = 56
shifted from previous position = 0.667
rotated from previous position = 0.661 degrees
atoms outside contour = 156278, contour level = 0.11
Position of FlaB1_core_long.pdb (#5) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
-0.44913203 0.89343216 -0.00770671 106.45522107
0.89339980 0.44897783 -0.01599060 -62.19268972
-0.01082638 -0.01406706 -0.99984244 381.40647802
Axis 0.52481747 0.85116901 -0.00882835
Axis point 72.60642083 0.00000000 190.32328410
Rotation angle (degrees) 179.89500092
Shift along axis -0.43412162
> fitmap #5 inMap #103
Fit molecule FlaB1_core_long.pdb (#5) to map sheath_masked_map (#103) using
216018 atoms
average map value = 0.08392, steps = 28
shifted from previous position = 0.0197
rotated from previous position = 0.0013 degrees
atoms outside contour = 156277, contour level = 0.11
Position of FlaB1_core_long.pdb (#5) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
-0.44913169 0.89343215 -0.00772768 106.44345783
0.89339999 0.44897714 -0.01599941 -62.18916013
-0.01082484 -0.01408975 -0.99984214 381.42206285
Axis 0.52481764 0.85116881 -0.00883761
Axis point 72.59798923 -0.00000000 190.33117529
Rotation angle (degrees) 179.89575836
Shift along axis -0.44092742
> volume zone #103 nearAtoms #5 range 5 invert false newMap true minimalBounds
> true bondPointSpacing 2
Opened sheath_masked_map zone as #6, grid size 146,146,360, pixel 1.07, shown
at step 1, values float32
> surface dust #6 size 10.7
> show #!35 models
> fitmap #35 inMap #103
Fit map Glycan_all.mrc in map sheath_masked_map using 37363 points
correlation = 0.6469, correlation about mean = 0.2251, overlap = 844.3
steps = 56, shift = 0.717, angle = 0.856 degrees
Position of Glycan_all.mrc (#35) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
-0.12599883 0.99202301 0.00383431 24.14550820
-0.99199110 -0.12602730 0.00841576 404.03671984
0.00883185 -0.00274322 0.99995726 15.60214762
Axis -0.00562434 -0.00251886 -0.99998101
Axis point 189.98996295 191.40403576 0.00000000
Rotation angle (degrees) 97.24049688
Shift along axis -16.75536576
> fitmap #35 inMap #103
Fit map Glycan_all.mrc in map sheath_masked_map using 37363 points
correlation = 0.6469, correlation about mean = 0.2252, overlap = 844.3
steps = 48, shift = 0.00209, angle = 0.00517 degrees
Position of Glycan_all.mrc (#35) relative to sheath_masked_map (#103)
coordinates:
Matrix rotation and translation
-0.12608044 0.99201276 0.00380350 24.16898295
-0.99198058 -0.12610870 0.00843635 404.04800775
0.00884862 -0.00270934 0.99995720 15.59092235
Axis -0.00561770 -0.00254287 -0.99998099
Axis point 189.99184041 191.39999157 0.00000000
Rotation angle (degrees) 97.24520610
Shift along axis -16.75384017
> hide #!35 models
> show #!4 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!13 models
> hide #!13 models
> show #3 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!4 models
> hide #!16 models
> show #!16 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> volume #8 level 0.125
===== Log before crash end =====
Log:
Startup Messages
---
warning | Registration file '/Users/clem/Library/Application Support/ChimeraX/registration' has expired
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
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 M4 Pro
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: Mac mini
Model Identifier: Mac16,11
Model Number: Z1JV000KLLL/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 34 days, 18 hours, 21 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LS32D70xE:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
LG HDR 4K:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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: 3.10.3
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
narwhals: 1.46.0
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: 2.2.6
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
plotly: 6.0.1
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
pyKVFinder: 0.8.1
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
tomlkit: 0.13.2
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 , 4 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 , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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