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Opened 4 months ago
Closed 4 months ago
#18075 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.7.4-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 0x00000001fbbccf80 (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, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.mask._mask, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 64)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 4660,
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"codeSigningMonitor" : 1,
"incident" : "F31A3DA0-EAF8-407A-9121-F7CFEF3F2B2B",
"pid" : 86927,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-10 15:09:36.7797 +0200",
"procStartAbsTime" : 23106988048768,
"procExitAbsTime" : 30636279096270,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"3C3BAEBA-B56F-523A-AB34-8947360B3FDD","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "7F15F153-7C73-5EBF-0D45-3C57AF040D9C",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 2,
"sleepWakeUUID" : "6D99AFF6-D1BC-45E5-A7AB-6F4A06BFE638",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4330471063\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1021dc000-1021e0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":86927},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4330471063\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1021dc000-1021e0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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],
"experiments" : [
]
}
}
===== 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/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/LookingForDrug.cxs
> format session
Opened cryosparc_P37_J481_011_volume_map_sharp.mrc masked as #8, grid size
82,93,134, pixel 0.836, shown at level 0.2, step 1, values float32
Opened cryosparc_P37_J170_012_volume_map_sharp.mrc masked as #9, grid size
135,75,92, pixel 0.836, shown at level 0.2, step 1, values float32
Opened cryosparc_P37_J485_009_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 0.836, shown at level 0.2, step 1, values float32
Opened cryosparc_P37_J516_009_volume_map_sharp.mrc as #3, grid size
300,300,300, pixel 0.836, shown at level 0.2, step 2, values float32
opened ChimeraX session
> open "/Users/Celine/Seafile/TASK-1/ExpDataFiles/StructuralAnalysis/4.TASK
> structures/TASK-1/9g9x_emd_51160.map"
Opened 9g9x_emd_51160.map as #6, grid size 256,256,256, pixel 0.832, shown at
level 0.0855, step 1, values float32
> volume #6 level 0.2
> select add #6
4 models selected
> ui tool show "Side View"
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.45098,0.28884,-0.84451,101.62,0.41957,0.76652,0.48622,-62.373,0.78777,-0.5736,0.22449,45.067
> view matrix models
> #6,-0.31922,0.36127,-0.87612,178.7,-0.63111,0.60863,0.48092,66.799,0.70697,0.70644,0.033717,-65.951
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.31922,0.36127,-0.87612,189.29,-0.63111,0.60863,0.48092,62.151,0.70697,0.70644,0.033717,-38.099
> fitmap #6 inMap #8
Fit map 9g9x_emd_51160.map in map cryosparc_P37_J481_011_volume_map_sharp.mrc
masked using 46839 points
correlation = 0.2975, correlation about mean = 0.09011, overlap = 1682
steps = 88, shift = 4.47, angle = 4.73 degrees
Position of 9g9x_emd_51160.map (#6) relative to
cryosparc_P37_J481_011_volume_map_sharp.mrc masked (#8) coordinates:
Matrix rotation and translation
0.92190164 0.36246578 -0.13680619 -14.78536678
-0.28945808 0.87912020 0.37863135 14.32369105
0.25750999 -0.30946121 0.91538100 20.38888311
Axis -0.67024645 -0.38408935 -0.63501580
Axis point -0.00000000 51.81542283 -12.62577391
Rotation angle (degrees) 30.88476637
Shift along axis -8.53900054
> view matrix models
> #6,-0.28893,0.30467,-0.90758,197.6,-0.68044,0.60152,0.41855,83.01,0.67344,0.73848,0.033507,-43.063
> fitmap #6 inMap #8
Fit map 9g9x_emd_51160.map in map cryosparc_P37_J481_011_volume_map_sharp.mrc
masked using 46839 points
correlation = 0.2876, correlation about mean = 0.05038, overlap = 1660
steps = 124, shift = 3.54, angle = 6.93 degrees
Position of 9g9x_emd_51160.map (#6) relative to
cryosparc_P37_J481_011_volume_map_sharp.mrc masked (#8) coordinates:
Matrix rotation and translation
0.89728358 0.40558600 -0.17430488 -17.71593385
-0.34759367 0.89250737 0.28741823 26.91495191
0.27214120 -0.19730839 0.94181133 1.87635110
Axis -0.48435052 -0.44609968 -0.75259527
Axis point 51.86622400 62.59292493 0.00000000
Rotation angle (degrees) 30.02568952
Shift along axis -4.83816256
> view matrix models
> #6,-0.30323,0.19131,-0.93352,204.18,-0.72004,0.59568,0.35596,59.058,0.62418,0.7801,-0.042879,-20.007
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.13527,-0.05992,-0.98899,189.09,0.39848,-0.9106,0.10967,121.91,-0.90715,-0.40893,-0.099303,274.64
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.13527,-0.05992,-0.98899,199.02,0.39848,-0.9106,0.10967,151.51,-0.90715,-0.40893,-0.099303,259.51
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.16773,-0.023058,-0.98556,191.33,0.59595,-0.79401,0.12,117.16,-0.78531,-0.60747,-0.11944,269.44
> fitmap #6 inMap #8
Fit map 9g9x_emd_51160.map in map cryosparc_P37_J481_011_volume_map_sharp.mrc
masked using 46839 points
correlation = 0.9065, correlation about mean = 0.7086, overlap = 7640
steps = 112, shift = 2.7, angle = 16.7 degrees
Position of 9g9x_emd_51160.map (#6) relative to
cryosparc_P37_J481_011_volume_map_sharp.mrc masked (#8) coordinates:
Matrix rotation and translation
-0.91162515 -0.41101500 -0.00250033 247.98714767
0.41101553 -0.91162828 0.00031782 160.25390928
-0.00241000 -0.00073794 0.99999682 5.68150888
Axis -0.00128433 -0.00010988 0.99999917
Axis point 106.76919908 106.78765202 0.00000000
Rotation angle (degrees) 155.73135044
Shift along axis 5.34539736
> ui mousemode right "rotate selected models"
> ui mousemode right select
> select clear
> hide #!3 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> open "/Users/Celine/Downloads/cryosparc_P37_J494_010_volume_map_sharp
> (1).mrc"
Opened cryosparc_P37_J494_010_volume_map_sharp (1).mrc as #7, grid size
300,300,300, pixel 0.836, shown at level 0.0722, step 2, values float32
> volume #7 level 0.2
> open /Users/Celine/Downloads/cryosparc_P37_J294_009_volume_map.mrc
Opened cryosparc_P37_J294_009_volume_map.mrc as #10, grid size 300,300,300,
pixel 0.836, shown at level 0.0575, step 2, values float32
> close #10
> show #!4 models
> hide #!4 models
> fitmap #6 inMap #7
Fit map 9g9x_emd_51160.map in map cryosparc_P37_J494_010_volume_map_sharp
(1).mrc using 46839 points
correlation = 0.2668, correlation about mean = 0.044, overlap = 1176
steps = 144, shift = 2.47, angle = 6.17 degrees
Position of 9g9x_emd_51160.map (#6) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc (#7) coordinates:
Matrix rotation and translation
0.08493191 0.00685174 -0.99636319 198.89242649
0.72459733 -0.68680768 0.05704306 96.58096621
-0.68391905 -0.72680689 -0.06329664 265.96871307
Axis -0.70757930 -0.28204251 0.64790706
Axis point 0.00000000 64.85424924 203.15423371
Rotation angle (degrees) 146.36532799
Shift along axis 4.35090597
> select add #6
4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.98045,-0.14719,-0.13061,44.156,0.12774,0.98092,-0.14653,0.35446,0.14969,0.12698,0.98055,-5.0922
> view matrix models
> #6,0.85392,0.507,-0.11732,-13.203,-0.51614,0.85391,-0.066616,75.458,0.066404,0.11744,0.99086,3.8912
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.85392,0.507,-0.11732,-4.3496,-0.51614,0.85391,-0.066616,90.149,0.066404,0.11744,0.99086,4.6116
> fitmap #6 inMap #7
Fit map 9g9x_emd_51160.map in map cryosparc_P37_J494_010_volume_map_sharp
(1).mrc using 46839 points
correlation = 0.2437, correlation about mean = 0.04358, overlap = 1556
steps = 64, shift = 2.57, angle = 4.47 degrees
Position of 9g9x_emd_51160.map (#6) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc (#7) coordinates:
Matrix rotation and translation
0.85368355 0.51561701 -0.07323578 -7.11750378
-0.51716967 0.85587880 -0.00264310 85.37965449
0.06131812 0.04013170 0.99731114 13.49843197
Axis 0.04103520 -0.12908176 -0.99078454
Axis point 144.22416737 52.76558331 0.00000000
Rotation angle (degrees) 31.41253869
Shift along axis -24.68706220
> view matrix models
> #6,0.85368,0.51562,-0.073236,-15.199,-0.51717,0.85588,-0.0026431,87.852,0.061318,0.040132,0.99731,10.919
> fitmap #6 inMap #7
Fit map 9g9x_emd_51160.map in map cryosparc_P37_J494_010_volume_map_sharp
(1).mrc using 46839 points
correlation = 0.9058, correlation about mean = 0.6931, overlap = 8983
steps = 80, shift = 2.7, angle = 8.23 degrees
Position of 9g9x_emd_51160.map (#6) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc (#7) coordinates:
Matrix rotation and translation
0.91257323 0.40891211 0.00097934 -15.32510247
-0.40890497 0.91253679 0.00856280 70.44940328
0.00260775 -0.00821464 0.99996284 23.91322648
Axis -0.02051055 -0.00199075 -0.99978765
Axis point 156.73372548 72.17840112 0.00000000
Rotation angle (degrees) 24.14174273
Shift along axis -23.73406951
> select subtract #6
Nothing selected
> hide #!5 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> show #!6 models
> show #!5 models
> select add #5
4267 atoms, 4368 bonds, 2 pseudobonds, 529 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.32398,-0.73699,-0.5932,99.885,0.9447,0.21839,0.24464,111.97,-0.050747,-0.63965,0.76699,60.118
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.32398,-0.73699,-0.5932,117.28,0.9447,0.21839,0.24464,129.62,-0.050747,-0.63965,0.76699,67.95
> fitmap #5 inMap #7
Fit molecule TASK1_6rv3.pdb (#5) to map
cryosparc_P37_J494_010_volume_map_sharp (1).mrc (#7) using 4267 atoms
average map value = 0.3467, steps = 116
shifted from previous position = 3.47
rotated from previous position = 14.5 degrees
atoms outside contour = 1686, contour level = 0.2
Position of TASK1_6rv3.pdb (#5) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc (#7) coordinates:
Matrix rotation and translation
0.12530637 -0.67259226 -0.72932706 119.84290876
0.99041420 0.04173848 0.13167238 125.85874867
-0.05812082 -0.73883527 0.67137502 67.89749265
Axis -0.43668127 -0.33670376 0.83423021
Axis point 15.20976471 133.68483590 0.00000000
Rotation angle (degrees) 94.63397991
Shift along axis -38.06812863
> close #4
> show #!1 models
> select add #1
8597 atoms, 8788 bonds, 6 pseudobonds, 1075 residues, 4 models selected
> select subtract #5
4330 atoms, 4420 bonds, 4 pseudobonds, 546 residues, 2 models selected
> view matrix models
> #1,0.053082,0.76022,-0.64749,160.31,0.81418,0.34248,0.46885,106.91,0.57818,-0.55206,-0.60078,103.8
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.16142,0.51148,0.844,91.089,-0.98597,-0.046736,-0.16026,103.51,-0.042523,-0.85802,0.51185,44.219
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.16142,0.51148,0.844,128.85,-0.98597,-0.046736,-0.16026,116.91,-0.042523,-0.85802,0.51185,67.417
> fitmap #1 inMap #7
Fit molecule TASK1-AF.pdb (#1) to map cryosparc_P37_J494_010_volume_map_sharp
(1).mrc (#7) using 4330 atoms
average map value = 0.05458, steps = 64
shifted from previous position = 2.62
rotated from previous position = 5.05 degrees
atoms outside contour = 3790, contour level = 0.2
Position of TASK1-AF.pdb (#1) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc (#7) coordinates:
Matrix rotation and translation
-0.08870828 0.47733554 0.87423203 128.45177223
-0.99440731 0.00806294 -0.10530486 117.79947867
-0.05731463 -0.87868413 0.47395069 69.64435627
Axis -0.40581144 0.48880583 -0.77226028
Axis point 112.87037787 29.42141174 0.00000000
Rotation angle (degrees) 107.65876225
Shift along axis -48.32969644
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.2623,0.61038,0.74742,139.03,-0.95705,-0.26367,-0.12054,105.12,0.1235,-0.74694,0.65332,70.199
> view matrix models
> #1,0.0066146,0.68501,0.7285,144.59,-0.99977,-0.010269,0.018734,112.21,0.020314,-0.72846,0.68479,69.482
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.0066146,0.68501,0.7285,133.44,-0.99977,-0.010269,0.018734,125.42,0.020314,-0.72846,0.68479,67.267
> fitmap #1 inMap #7
Fit molecule TASK1-AF.pdb (#1) to map cryosparc_P37_J494_010_volume_map_sharp
(1).mrc (#7) using 4330 atoms
average map value = 0.3271, steps = 108
shifted from previous position = 4.75
rotated from previous position = 8.48 degrees
atoms outside contour = 1848, contour level = 0.2
Position of TASK1-AF.pdb (#1) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc (#7) coordinates:
Matrix rotation and translation
-0.12753611 0.67355124 0.72805445 131.33928965
-0.99102456 -0.05688982 -0.12097063 123.15230888
-0.04006103 -0.73694796 0.67476132 67.99393820
Axis -0.31850399 0.39717021 -0.86070380
Axis point 117.36602458 25.80311221 0.00000000
Rotation angle (degrees) 104.76364847
Shift along axis -51.44230077
> close #3
> show #!7 models
> close #9
> show #!8 models
> hide #!8 models
> show #!2 models
> hide #!2 models
> close #2
> show #!8 models
> open /Users/Celine/Downloads/cryosparc_P37_J535_010_volume_map_sharp.mrc
Opened cryosparc_P37_J535_010_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 0.836, shown at level 0.081, step 1, values float32
> volume #1-9 step 1 level 0.2
> hide #!8 models
> select add #2
4330 atoms, 4420 bonds, 4 pseudobonds, 546 residues, 6 models selected
> select subtract #1
4 models selected
> view matrix models #2,1,0,0,19.748,0,1,0,18.132,0,0,1,19.505
> hide #!2,5-7 target m
> fitmap #2 inMap #7
Fit map cryosparc_P37_J535_010_volume_map_sharp.mrc in map
cryosparc_P37_J494_010_volume_map_sharp (1).mrc using 39143 points
correlation = 0.9428, correlation about mean = 0.7454, overlap = 6022
steps = 56, shift = 1.86, angle = 0.198 degrees
Position of cryosparc_P37_J535_010_volume_map_sharp.mrc (#2) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc (#7) coordinates:
Matrix rotation and translation
0.99999415 0.00329464 -0.00092113 18.14222419
-0.00329504 0.99999448 -0.00043312 18.73134557
0.00091970 0.00043616 0.99999948 18.09345232
Axis 0.12603819 -0.26690434 -0.95544568
Axis point 4075.15937866 -6264.46995590 0.00000000
Rotation angle (degrees) 0.19758393
Shift along axis -20.00017523
> show #!2 models
> select add #2
3 models selected
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> select subtract #2
Nothing selected
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!2 models
> hide #!7 models
> show #!2 models
> color #2 #009193ff models
> color #6 #ebebebff models
> open /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/masks/J294_map15.mrc
Opened J294_map15.mrc as #3, grid size 150,150,150, pixel 1.67, shown at level
0.0365, step 1, values float32
> vop mask #3 surfaces 6
> volume mask #3 surfaces 6
Invalid "surfaces" argument: invalid surfaces specifier
> vop mask #3 surfaces #6
Opened J294_map15.mrc masked as #4, grid size 41,38,48, pixel 1.67, shown at
step 1, values float32
> close #4
> vop mask #6 surfaces #3
Opened 9g9x_emd_51160.map masked as #4, grid size 69,95,143, pixel 0.832,
shown at step 1, values float32
> vop mask #2 surfaces #3
Opened cryosparc_P37_J535_010_volume_map_sharp.mrc masked as #9, grid size
77,88,142, pixel 0.836, shown at step 1, values float32
> hide #!4 models
> show #!4 models
> hide #!9 models
> show #!9 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!1 models
> volume #9 level 0.0958
> volume #9 level 0.06219
> volume #9 level -0.001678
> volume #9 level 0.01849
> hide #!9 models
> show #!2 models
> volume #2 level 0.06219
> volume #2 level 0.116
> hide #!2 models
> show #!9 models
> hide #!4 models
> show #!4 models
> volume #9 level 0.2
> hide #!4 models
> hide #!1 models
> volume #9 level 0.25
> volume #9 level 0.2
> hide #!9 models
> show #!7 models
> color #7 #009193ff models
> show #!4 models
> hide #!7 models
> show #!7 models
> vop mask #7 surfaces #3
Opened cryosparc_P37_J494_010_volume_map_sharp (1).mrc masked as #10, grid
size 77,88,141, pixel 0.836, shown at step 1, values float32
> hide #!4 models
> show #!8 models
> hide #!8 models
> close #8
> show #!9 models
> hide #!10 models
> color #10 #d6d6d6ff models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> color #10 #009193ff models
> show #!4 models
> volume #10 level 0.1934
> volume #10 level 0.2
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> hide #!10 models
> show #!4 models
> open /Users/Celine/Downloads/emd_48216.map
Opened emd_48216.map as #8, grid size 384,384,384, pixel 0.725, shown at level
0.121, step 2, values float32
> open /Users/Celine/Downloads/emd_48217.map
Opened emd_48217.map as #11, grid size 384,384,384, pixel 0.725, shown at
level 0.0847, step 2, values float32
> open /Users/Celine/Downloads/9mel.cif
9mel.cif title:
Structure of the human TWIK-2 potassium channel in complex with pimozide [more
info...]
Chain information for 9mel.cif #12
---
Chain | Description | UniProt
A B | Potassium channel subfamily K member 6 | KCNK6_HUMAN 1-313
Non-standard residues in 9mel.cif #12
---
1II —
3-[1-[4,4-bis(4-fluorophenyl)butyl]piperidin-4-yl]-1~{H}-benzimidazol-2-one
K — potassium ion
44 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/Celine/Downloads/9mek.cif
9mek.cif title:
Structure of the human TWIK-2 potassium channel [more info...]
Chain information for 9mek.cif #13
---
Chain | Description | UniProt
A B | Potassium channel subfamily K member 6 | KCNK6_HUMAN 1-313
Non-standard residues in 9mek.cif #13
---
HP6 — heptane
K — potassium ion
> volume #1-9 step 1 level 0.2
> volume #1-11 step 1 level 0.2
> hide #!4 models
> hide #!8 models
> hide #!12 models
> hide #!13 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!10 models
> select add #11
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.33123,0.93885,0.094034,-50.178,0.9391,-0.33769,0.063654,46.966,0.091516,0.067223,-0.99353,244.67
> volume #11 level 0.2771
> volume #11 level 0.5196
> view matrix models
> #11,0.92666,0.31319,0.20788,-61.656,0.33151,-0.9416,-0.059157,232.53,0.17721,0.12373,-0.97636,222.5
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.92666,0.31319,0.20788,-82.475,0.33151,-0.9416,-0.059157,220.29,0.17721,0.12373,-0.97636,199.4
> fitmap #11 inMap #10
Fit map emd_48217.map in map cryosparc_P37_J494_010_volume_map_sharp (1).mrc
masked using 51457 points
correlation = 0.2691, correlation about mean = 0.03752, overlap = 3705
steps = 96, shift = 1.19, angle = 6.29 degrees
Position of emd_48217.map (#11) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc masked (#10) coordinates:
Matrix rotation and translation
0.90873941 0.32047226 0.26737652 -87.88247416
0.36603599 -0.91975640 -0.14165389 224.00372599
0.20052513 0.22659590 -0.95312327 178.59384292
Axis 0.97670719 0.17730965 0.12084847
Axis point 0.00000000 111.13887927 105.85221761
Rotation angle (degrees) 169.13380998
Shift along axis -24.53462962
> view matrix models
> #11,0.90874,0.32047,0.26738,-84.975,0.36604,-0.91976,-0.14165,221.28,0.20053,0.2266,-0.95312,180.71
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.95754,0.19253,0.21461,-66.688,0.21553,-0.97241,-0.089272,242.34,0.1915,0.13174,-0.97261,197.86
> fitmap #11 inMap #10
Fit map emd_48217.map in map cryosparc_P37_J494_010_volume_map_sharp (1).mrc
masked using 51457 points
correlation = 0.3248, correlation about mean = 0.08683, overlap = 4970
steps = 132, shift = 2.13, angle = 8.27 degrees
Position of emd_48217.map (#11) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc masked (#10) coordinates:
Matrix rotation and translation
0.98843219 0.11403267 0.09999178 -44.10633461
0.12225284 -0.98924254 -0.08033334 258.40633980
0.08975550 0.09162834 -0.99173998 219.65849212
Axis 0.99709844 0.05935381 0.04766362
Axis point 0.00000000 125.73917117 116.50409815
Rotation angle (degrees) 175.05318131
Shift along axis -18.17123626
> view matrix models
> #11,-0.80456,-0.59208,-0.046087,323.9,-0.58903,0.80548,-0.065133,105.5,0.075687,-0.025257,-0.99681,238.59
> fitmap #11 inMap #10
Fit map emd_48217.map in map cryosparc_P37_J494_010_volume_map_sharp (1).mrc
masked using 51457 points
correlation = 0.7063, correlation about mean = 0.4702, overlap = 1.392e+04
steps = 112, shift = 3.03, angle = 17 degrees
Position of emd_48217.map (#11) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc masked (#10) coordinates:
Matrix rotation and translation
-0.94085710 -0.33879760 -0.00202454 303.88306663
-0.33877492 0.94083834 -0.00740040 42.03685853
0.00441201 -0.00627685 -0.99997057 246.70563336
Axis 0.17195601 -0.98509851 0.00347138
Axis point 155.40594187 0.00000000 123.67716354
Rotation angle (degrees) 179.81281685
Shift along axis 11.70048235
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.94086,-0.3388,-0.0020245,303.53,-0.33877,0.94084,-0.0074004,41.362,0.004412,-0.0062769,-0.99997,250.34
> view matrix models
> #11,-0.94086,-0.3388,-0.0020245,301.26,-0.33877,0.94084,-0.0074004,42.292,0.004412,-0.0062769,-0.99997,249.64
> fitmap #11 inMap #10
Fit map emd_48217.map in map cryosparc_P37_J494_010_volume_map_sharp (1).mrc
masked using 51457 points
correlation = 0.3096, correlation about mean = 0.07579, overlap = 4746
steps = 92, shift = 1.24, angle = 4.45 degrees
Position of emd_48217.map (#11) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc masked (#10) coordinates:
Matrix rotation and translation
-0.94584685 -0.31863980 0.06198715 290.87294906
-0.32165568 0.94570097 -0.04676846 45.43390052
-0.04371902 -0.06417433 -0.99698059 264.72572704
Axis -0.16241041 0.98632194 -0.02814052
Axis point 152.77149629 0.00000000 129.07924028
Rotation angle (degrees) 176.92827489
Shift along axis -9.87786175
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.99623,-0.035637,-0.079105,0.58176,-0.042777,-0.99498,-0.090486,282.78,-0.075484,0.093528,-0.99275,246.61
> fitmap #11 inMap #10
Fit map emd_48217.map in map cryosparc_P37_J494_010_volume_map_sharp (1).mrc
masked using 51457 points
correlation = 0.226, correlation about mean = 0.02187, overlap = 3165
steps = 196, shift = 1.71, angle = 8.19 degrees
Position of emd_48217.map (#11) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc masked (#10) coordinates:
Matrix rotation and translation
0.99175953 0.01469099 -0.12726827 0.09429834
0.01845106 -0.99942588 0.02841609 257.75112926
-0.12677774 -0.03053017 -0.99146120 271.76551669
Axis -0.99793731 -0.00830447 0.06365664
Axis point 0.00000000 130.87924566 133.97738166
Rotation angle (degrees) 178.30757746
Shift along axis 15.06509054
> view matrix models
> #11,0.90444,0.41676,-0.091142,-48.696,0.41484,-0.90901,-0.039966,199.41,-0.099506,-0.0016633,-0.99504,264.44
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.90444,0.41676,-0.091142,-44.885,0.41484,-0.90901,-0.039966,195.48,-0.099506,-0.0016633,-0.99504,262.75
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.92568,0.37747,-0.025231,-51.454,0.37823,-0.92201,0.08266,185.49,0.0079379,-0.08606,-0.99626,259.71
> fitmap #11 inMap #10
Fit map emd_48217.map in map cryosparc_P37_J494_010_volume_map_sharp (1).mrc
masked using 51457 points
correlation = 0.3599, correlation about mean = 0.1268, overlap = 5670
steps = 380, shift = 4.64, angle = 9.83 degrees
Position of emd_48217.map (#11) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc masked (#10) coordinates:
Matrix rotation and translation
0.89172249 0.45012110 0.04713811 -67.83040533
0.45215628 -0.89055682 -0.04963110 192.37790719
0.01963916 0.06557096 -0.99765462 239.00358386
Axis 0.97252953 0.23214463 0.01718093
Axis point 0.00000000 100.63798460 123.09337301
Rotation angle (degrees) 176.60449530
Shift along axis -17.20126952
> hide #!11 models
> hide #!10 models
> show #!5 models
> show #!12 models
> show #!13 models
> ui tool show Matchmaker
> matchmaker #!5 to #12
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 9mel.cif, chain A (#12) with TASK1_6rv3.pdb, chain B (#5), sequence
alignment score = 478.7
RMSD between 127 pruned atom pairs is 1.044 angstroms; (across all 220 pairs:
4.397)
> matchmaker #!5 to #1
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 TASK1-AF.pdb, chain A (#1) with TASK1_6rv3.pdb, chain B (#5),
sequence alignment score = 1330.7
RMSD between 258 pruned atom pairs is 0.414 angstroms; (across all 259 pairs:
0.437)
> matchmaker #!12 to #1
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 TASK1-AF.pdb, chain A (#1) with 9mel.cif, chain A (#12), sequence
alignment score = 472
RMSD between 130 pruned atom pairs is 0.961 angstroms; (across all 221 pairs:
7.073)
> matchmaker #!13 to #1
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 TASK1-AF.pdb, chain A (#1) with 9mek.cif, chain A (#13), sequence
alignment score = 476.8
RMSD between 138 pruned atom pairs is 0.945 angstroms; (across all 220 pairs:
6.464)
> matchmaker #!13 to #12
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 9mel.cif, chain A (#12) with 9mek.cif, chain A (#13), sequence
alignment score = 1499.8
RMSD between 238 pruned atom pairs is 0.368 angstroms; (across all 238 pairs:
0.368)
> matchmaker #!13 to #12
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 9mel.cif, chain A (#12) with 9mek.cif, chain A (#13), sequence
alignment score = 1499.8
RMSD between 238 pruned atom pairs is 0.368 angstroms; (across all 238 pairs:
0.368)
> show #!11 models
> hide #!13 models
> view matrix models
> #11,0.9822,0.17799,0.060061,-44.324,0.18198,-0.98086,-0.06928,245.26,0.04658,0.078977,-0.99579,233.13
> fitmap #11 inMap #10
Fit map emd_48217.map in map cryosparc_P37_J494_010_volume_map_sharp (1).mrc
masked using 51457 points
correlation = 0.3039, correlation about mean = 0.07341, overlap = 4636
steps = 80, shift = 4.45, angle = 6.43 degrees
Position of emd_48217.map (#11) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc masked (#10) coordinates:
Matrix rotation and translation
0.97287306 0.21490472 0.08563861 -49.32684078
0.22669193 -0.95943161 -0.16763579 252.41476522
0.04613867 0.18250192 -0.98212233 215.01356381
Axis 0.99314123 0.11203883 0.03343361
Axis point 0.00000000 119.35324349 119.69380743
Rotation angle (degrees) 169.84696713
Shift along axis -13.51958361
> view matrix models
> #11,-0.87863,-0.46392,-0.11309,330.28,-0.44985,0.88362,-0.1298,84.823,0.16014,-0.063174,-0.98507,233.75
> fitmap #11 inMap #10
Fit map emd_48217.map in map cryosparc_P37_J494_010_volume_map_sharp (1).mrc
masked using 51457 points
correlation = 0.7063, correlation about mean = 0.47, overlap = 1.392e+04
steps = 96, shift = 5.1, angle = 12.2 degrees
Position of emd_48217.map (#11) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc masked (#10) coordinates:
Matrix rotation and translation
-0.94088371 -0.33872399 -0.00197327 303.86914645
-0.33870244 0.94086588 -0.00721435 41.99817408
0.00430025 -0.00611952 -0.99997202 246.70263832
Axis 0.17191746 -0.98510554 0.00338420
Axis point 155.39994195 0.00000000 123.66738490
Rotation angle (degrees) 179.81755929
Shift along axis 11.70266833
> hide #!12 models
> show #!10 models
> select subtract #11
Nothing selected
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!8 models
> volume #8 level 0.7446
> select add #8
4 models selected
> view matrix models
> #8,0.92453,0.37757,0.051748,-49.24,0.37397,-0.92497,0.067628,206.51,0.0734,-0.043173,-0.99637,273.06
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.92453,0.37757,0.051748,-65.687,0.37397,-0.92497,0.067628,191.7,0.0734,-0.043173,-0.99637,242.58
> fitmap #8 inMap #10
Fit map emd_48216.map in map cryosparc_P37_J494_010_volume_map_sharp (1).mrc
masked using 34828 points
correlation = 0.7267, correlation about mean = 0.3997, overlap = 1.424e+04
steps = 92, shift = 3.28, angle = 5.76 degrees
Position of emd_48216.map (#8) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc masked (#10) coordinates:
Matrix rotation and translation
0.93951352 0.34251181 -0.00003450 -52.96901462
0.34249240 -0.93946133 -0.01055258 209.35520111
-0.00364680 0.00990248 -0.99994431 245.62092561
Axis 0.98476185 0.17390578 -0.00093448
Axis point 0.00000000 108.70709121 123.34466555
Rotation angle (degrees) 179.40492729
Shift along axis -15.98331272
> select subtract #8
Nothing selected
> hide #!5 models
> hide #!11 models
> show #!11 models
> hide #!8 models
> show #!8 models
> show #!12 models
> hide #!11 models
> show #!13 models
> hide #!12 models
> volume #11 level 0.2
> volume #8 level 0.2
> volume #8 level 0.5403
> volume #8 level 0.554
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!7 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!8 models
> hide #!7 models
> color #8 #ffd479ff models
> color #8 #d783ffff models
> color #8 #ff85ffff models
> color #8 #ff8ad8ff models
> color #8 #ffd479ff models
> color #8 #7a81ffff models
> color #13 #ff85ffff
> color #13 #0433ffff
> color #8 #7a81ffdd models
> color #8 #7a81ffbc models
> color #8 #7a81ffcc models
> hide #!8 models
> color #11 #7a81ffff models
> hide #!13 models
> show #!13 models
> show #!11 models
> hide #!13 models
> show #!12 models
> color #12 #0433ffff
> color #11 #7a81ffcc models
> color #11 #7a81ffec models
> color #11 #7a81ffe6 models
> volume #8 level 0.5
> volume #11 level 0.5
> show #!12 cartoons
> hide #!12 atoms
> show #!12 cartoons
> show #!12 atoms
> hide #!12 atoms
> hide #12.2.1 models
> hide #!12.2 models
> select add #12
3545 atoms, 3627 bonds, 26 pseudobonds, 480 residues, 4 models selected
> hide #!12 target m
> show #!9 target m
> hide #!8 target m
> show #!10 target m
> hide #!9 target m
> show #!11 target m
> hide #!10 target m
> show #!10 target m
> hide #!11 target m
> hide #!10 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13.2 models
> hide #12.1 models
> show #12.1 models
> hide #12.1 models
> show #12.1 models
> hide #12.1 models
> show sel atoms
> ui mousemode right select
> select down
3545 atoms, 3627 bonds, 26 pseudobonds, 480 residues, 4 models selected
> select down
3545 atoms, 3627 bonds, 26 pseudobonds, 480 residues, 4 models selected
> select down
3545 atoms, 3627 bonds, 26 pseudobonds, 480 residues, 4 models selected
> select up
3545 atoms, 3627 bonds, 26 pseudobonds, 480 residues, 4 models selected
> select up
3545 atoms, 3627 bonds, 26 pseudobonds, 480 residues, 4 models selected
> select #13/A:248
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/B:401@C17
1 atom, 1 residue, 1 model selected
> select #12/B:401@C17
1 atom, 1 residue, 1 model selected
> select #13/B:131
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
262 atoms, 265 bonds, 36 residues, 1 model selected
> select up
457 atoms, 468 bonds, 61 residues, 1 model selected
> select up
1795 atoms, 1835 bonds, 240 residues, 1 model selected
> select up
3594 atoms, 3671 bonds, 484 residues, 1 model selected
> select down
1795 atoms, 1835 bonds, 240 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide #!13 models
> show #!12 cartoons
> hide #!12 atoms
> show #!12 atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
252 atoms, 254 bonds, 35 residues, 1 model selected
> select up
447 atoms, 457 bonds, 60 residues, 1 model selected
> select up
1788 atoms, 1832 bonds, 239 residues, 1 model selected
> select down
447 atoms, 457 bonds, 60 residues, 1 model selected
> hide sel atoms
> select #12/B:246
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
278 atoms, 284 bonds, 34 residues, 1 model selected
> select up
808 atoms, 832 bonds, 106 residues, 1 model selected
> select up
1788 atoms, 1832 bonds, 239 residues, 1 model selected
> select down
808 atoms, 832 bonds, 106 residues, 1 model selected
> hide sel atoms
> select #12/A:14
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
320 atoms, 323 bonds, 45 residues, 1 model selected
> hide sel atoms
> select #12/A:246
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
278 atoms, 284 bonds, 34 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
252 atoms, 254 bonds, 35 residues, 1 model selected
> hide sel atoms
> select #12/B:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
312 atoms, 315 bonds, 44 residues, 1 model selected
> hide sel atoms
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!13 models
> show #!13 atoms
> show #!13 cartoons
> select #13/B:131
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
262 atoms, 265 bonds, 36 residues, 1 model selected
> hide sel atoms
> select #13/A:14
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
336 atoms, 339 bonds, 45 residues, 1 model selected
> hide sel atoms
> select #13/B:246
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
276 atoms, 282 bonds, 35 residues, 1 model selected
> select up
816 atoms, 840 bonds, 106 residues, 1 model selected
> hide sel atoms
> select #13/A:134@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
262 atoms, 265 bonds, 36 residues, 1 model selected
> select up
457 atoms, 468 bonds, 61 residues, 1 model selected
> hide sel atoms
> select #13/A:248
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
276 atoms, 282 bonds, 35 residues, 1 model selected
> select up
816 atoms, 840 bonds, 106 residues, 1 model selected
> hide sel atoms
> select #13/B:14
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
328 atoms, 331 bonds, 44 residues, 1 model selected
> hide sel atoms
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!13 models
> show #!8 models
> color #8 #7a81ffe6 models
> color #13 #941100ff
> color #13 black
> color #13 #ff7e79ff
> color #13 #ffd479ff
> color #13 #ff2600ff
> color #13 #011993ff
> color #13 #0433ffff
> select clear
> color #8 #7a81ffd9 models
> hide #!8 models
> show #!11 models
> show #!12 models
> hide #!13 models
> open /Users/Celine/Downloads/cryosparc_P37_J333_class_04_00162_volume.mrc
Opened cryosparc_P37_J333_class_04_00162_volume.mrc as #14, grid size
128,128,128, pixel 1.67, shown at level 0.134, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J333_class_03_00162_volume.mrc
Opened cryosparc_P37_J333_class_03_00162_volume.mrc as #15, grid size
128,128,128, pixel 1.67, shown at level 0.129, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J333_class_02_00162_volume.mrc
Opened cryosparc_P37_J333_class_02_00162_volume.mrc as #16, grid size
128,128,128, pixel 1.67, shown at level 0.132, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J333_class_01_00162_volume.mrc
Opened cryosparc_P37_J333_class_01_00162_volume.mrc as #17, grid size
128,128,128, pixel 1.67, shown at level 0.171, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J333_class_00_00162_volume.mrc
Opened cryosparc_P37_J333_class_00_00162_volume.mrc as #18, grid size
128,128,128, pixel 1.67, shown at level 0.179, step 1, values float32
> hide #!11 models
> hide #!12 models
> volume #14-18 step 1 level 0.2
Drag select of 14 cryosparc_P37_J333_class_04_00162_volume.mrc , 15
cryosparc_P37_J333_class_03_00162_volume.mrc , 16
cryosparc_P37_J333_class_02_00162_volume.mrc , 17
cryosparc_P37_J333_class_01_00162_volume.mrc , 18
cryosparc_P37_J333_class_00_00162_volume.mrc
> select clear
> color #14 #d6d6d6ff models
> color #15 #d6d6d6ff models
> color #16 #d6d6d6ff models
> color #17 #d6d6d6ff models
> color #18 #d6d6d6ff models
> hide #!18 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> show #!15 models
> hide #!14 models
> show #!16 models
> hide #!15 models
> show #!17 models
> hide #!16 models
> show #!18 models
> hide #!17 models
> open /Users/Celine/Downloads/cryosparc_P37_J378_class_00_00125_volume.mrc
Opened cryosparc_P37_J378_class_00_00125_volume.mrc as #19, grid size
128,128,128, pixel 1.67, shown at level 0.19, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J378_class_01_00125_volume.mrc
Opened cryosparc_P37_J378_class_01_00125_volume.mrc as #20, grid size
128,128,128, pixel 1.67, shown at level 0.169, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J378_class_02_00125_volume.mrc
Opened cryosparc_P37_J378_class_02_00125_volume.mrc as #21, grid size
128,128,128, pixel 1.67, shown at level 0.178, step 1, values float32
> close #14
> close #15
> close #16
> close #18
> close #17
> color #19 #d6d6d6ff models
> color #20 #d6d6d6ff models
> color #21 #d6d6d6ff models
> volume #19-21 step 1 level 0.2
> hide #!21 models
> hide #!20 models
> show #!20 models
> hide #!19 models
> show #!21 models
> hide #!20 models
> view clip false
> color #21 #009193ff models
> color #21 #85ab2cff models
> color #21 #85ab2bff models
> color #21 #85ab2cff models
> color #21 #85ac2cff models
> color #21 #85ac2bff models
> color #21 #c2ab85ff models
> color #21 #85ab2cff models
> color #21 #4eaa80ff models
> color #21 #65aaa2ff models
> color #21 #73c2b9ff models
> color #21 #74c3baff models
> color #21 #85c2baff models
> color #21 #85ba5cff models
> color #21 #85c2baff models
> color #21 #85c2abff models
> show #!19 models
> close #19
> close #20
> close #21
> open /Users/Celine/Downloads/cryosparc_P37_J392_009_volume_map_sharp.mrc
Opened cryosparc_P37_J392_009_volume_map_sharp.mrc as #14, grid size
256,256,256, pixel 0.836, shown at level 0.0767, step 1, values float32
> volume #14 level 0.2
> volume #14 level 0.1532
> show #!13 models
> hide #!13 models
> show #!5 models
> select add #14
2 models selected
> hide #!5 models
> select subtract #14
Nothing selected
> select add #14
2 models selected
> select clear
> select add #14
2 models selected
> show #!2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.11128,0.35361,0.92875,-34.176,-0.43689,0.85681,-0.27387,95.531,-0.8926,-0.37529,0.24983,224.49
> view matrix models
> #14,-0.1549,-0.089688,0.98385,37.815,0.04225,0.99436,0.097298,-14.808,-0.98703,0.056639,-0.15024,232.86
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.1549,-0.089688,0.98385,55.455,0.04225,0.99436,0.097298,-4.732,-0.98703,0.056639,-0.15024,235.96
> fitmap #14 inMap #2
Fit map cryosparc_P37_J392_009_volume_map_sharp.mrc in map
cryosparc_P37_J535_010_volume_map_sharp.mrc using 33424 points
correlation = 0.3448, correlation about mean = 0.09546, overlap = 681.5
steps = 116, shift = 3.05, angle = 11.5 degrees
Position of cryosparc_P37_J392_009_volume_map_sharp.mrc (#14) relative to
cryosparc_P37_J535_010_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.18196187 -0.18960927 0.96485139 52.23769793
0.19286442 0.95529115 0.22410293 -46.42584144
-0.96420599 0.22686369 -0.13725768 196.05981960
Axis 0.00140382 0.98090474 0.19448372
Axis point 109.89815247 0.00000000 80.47605170
Rotation angle (degrees) 100.48418990
Shift along axis -7.33555280
> close #14
> open /Users/Celine/Downloads/cryosparc_P37_J458_class_02_00165_volume.mrc
Opened cryosparc_P37_J458_class_02_00165_volume.mrc as #14, grid size
128,128,128, pixel 1.67, shown at level 0.181, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J458_class_01_00165_volume.mrc
Opened cryosparc_P37_J458_class_01_00165_volume.mrc as #15, grid size
128,128,128, pixel 1.67, shown at level 0.172, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J458_class_00_00165_volume.mrc
Opened cryosparc_P37_J458_class_00_00165_volume.mrc as #16, grid size
128,128,128, pixel 1.67, shown at level 0.171, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J456_class_02_00145_volume.mrc
Opened cryosparc_P37_J456_class_02_00145_volume.mrc as #17, grid size
128,128,128, pixel 1.67, shown at level 0.183, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J456_class_01_00145_volume.mrc
Opened cryosparc_P37_J456_class_01_00145_volume.mrc as #18, grid size
128,128,128, pixel 1.67, shown at level 0.154, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J456_class_00_00145_volume.mrc
Opened cryosparc_P37_J456_class_00_00145_volume.mrc as #19, grid size
128,128,128, pixel 1.67, shown at level 0.176, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J460_class_02_00145_volume.mrc
Opened cryosparc_P37_J460_class_02_00145_volume.mrc as #20, grid size
128,128,128, pixel 1.67, shown at level 0.179, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J460_class_01_00145_volume.mrc
Opened cryosparc_P37_J460_class_01_00145_volume.mrc as #21, grid size
128,128,128, pixel 1.67, shown at level 0.185, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J460_class_00_00145_volume.mrc
Opened cryosparc_P37_J460_class_00_00145_volume.mrc as #22, grid size
128,128,128, pixel 1.67, shown at level 0.172, step 1, values float32
> volume #14-22 step 1 level 0.2
> hide #!22 models
> hide #!21 models
> hide #!20 models
> hide #!19 models
> hide #!18 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> color #14 #d6d6d6ff models
> hide #!2 models
> show #!15 models
> color #15 #d6d6d6ff models
> show #!16 models
> color #16 #d6d6d6ff models
> color #15 #85c2abff models
> hide #!15 models
> hide #!16 models
> show #!15 models
> hide #!14 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> color #17 #d6d6d6ff models
> show #!17 models
> show #!18 models
> color #18 #d6d6d6ff models
> show #!19 models
> color #19 #85c2abff models
> hide #!19 models
> hide #!18 models
> hide #!17 models
> show #!18 models
> show #!19 models
> hide #!18 models
> hide #!19 models
> show #!20 models
> color #20 #85c2abff models
> show #!21 models
> color #21 #d6d6d6ff models
> show #!22 models
> color #22 #d6d6d6ff models
> hide #!22 models
> hide #!21 models
> view #21 clip false
No displayed objects specified.
> view #20 clip false
> show #!21 models
> hide #!20 models
> hide #!21 models
> show #!22 models
> close #14
> close #16
> close #15,17-20
> close #21-22
> open /Users/Celine/Downloads/cryosparc_P37_J483_class_05_00185_volume.mrc
Opened cryosparc_P37_J483_class_05_00185_volume.mrc as #14, grid size
128,128,128, pixel 1.67, shown at level 0.177, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J483_class_04_00185_volume.mrc
Opened cryosparc_P37_J483_class_04_00185_volume.mrc as #15, grid size
128,128,128, pixel 1.67, shown at level 0.189, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J483_class_03_00185_volume.mrc
Opened cryosparc_P37_J483_class_03_00185_volume.mrc as #16, grid size
128,128,128, pixel 1.67, shown at level 0.155, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J483_class_02_00185_volume.mrc
Opened cryosparc_P37_J483_class_02_00185_volume.mrc as #17, grid size
128,128,128, pixel 1.67, shown at level 0.159, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J483_class_01_00185_volume.mrc
Opened cryosparc_P37_J483_class_01_00185_volume.mrc as #18, grid size
128,128,128, pixel 1.67, shown at level 0.186, step 1, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J483_class_00_00185_volume.mrc
Opened cryosparc_P37_J483_class_00_00185_volume.mrc as #19, grid size
128,128,128, pixel 1.67, shown at level 0.159, step 1, values float32
> color #14 #85c2abff models
> color #15 #d6d6d6ff models
> color #16 #d6d6d6ff models
> color #17 #d6d6d6ff models
> color #18 #d6d6d6ff models
> color #19 #d6d6d6ff models
> hide #!19 models
> hide #!18 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> volume #14-22 step 1 level 0.2
> hide #!14 models
> show #!15 models
> show #!16 models
> hide #!15 models
> show #!17 models
> hide #!16 models
> show #!18 models
> hide #!17 models
> show #!19 models
> hide #!18 models
> close #14-19
> show #!2 models
> view #2 clip false
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> open /Users/Celine/Downloads/cryosparc_P37_J549_009_volume_map_sharp.mrc
Opened cryosparc_P37_J549_009_volume_map_sharp.mrc as #14, grid size
256,256,256, pixel 0.836, shown at level 0.0719, step 1, values float32
> volume #14 level 0.2
> select add #14
4 models selected
> view matrix models #14,1,0,0,17.352,0,1,0,19.692,0,0,1,16.298
> fitmap #14 inMap #2
Fit map cryosparc_P37_J549_009_volume_map_sharp.mrc in map
cryosparc_P37_J535_010_volume_map_sharp.mrc using 21724 points
correlation = 0.9156, correlation about mean = 0.5065, overlap = 2526
steps = 60, shift = 2.61, angle = 0.294 degrees
Position of cryosparc_P37_J549_009_volume_map_sharp.mrc (#14) relative to
cryosparc_P37_J535_010_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999858 0.00166121 -0.00028268 -0.16226524
-0.00166091 0.99999808 0.00103931 0.27630357
0.00028441 -0.00103884 0.99999942 0.23650584
Axis -0.52486713 -0.14322575 -0.83904760
Axis point 153.00715783 146.10219485 0.00000000
Rotation angle (degrees) 0.11342843
Shift along axis -0.15284576
> ui mousemode right select
> select subtract #14
Nothing selected
> hide #!2 models
> volume #14 level 0.1443
> show #!5 models
> view clip false
> hide #!5 models
> show #!5 models
> hide #!5 models
> save /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/LookingForDrug.cxs
> open "/Users/Celine/Seafile/TASK-1/ExpDataFiles/StructuralAnalysis/4.TASK
> structures/TASK-3/8k1j_emd_36793.map"
Opened 8k1j_emd_36793.map as #15, grid size 200,200,200, pixel 1.1, shown at
level 0.174, step 1, values float32
> open "/Users/Celine/Seafile/TASK-1/ExpDataFiles/StructuralAnalysis/4.TASK
> structures/TASK-3/8k1q_emd_36799.map"
Opened 8k1q_emd_36799.map as #16, grid size 200,200,200, pixel 1.1, shown at
level 0.137, step 1, values float32
> open "/Users/Celine/Seafile/TASK-1/ExpDataFiles/StructuralAnalysis/4.TASK
> structures/TASK-3/8k1v_emd_36805.map"
Opened 8k1v_emd_36805.map as #17, grid size 200,200,200, pixel 1.1, shown at
level 0.149, step 1, values float32
> open "/Users/Celine/Seafile/TASK-1/ExpDataFiles/StructuralAnalysis/4.TASK
> structures/TASK-3/8k1z_emd_36806.map"
Opened 8k1z_emd_36806.map as #18, grid size 200,200,200, pixel 1.1, shown at
level 0.152, step 1, values float32
> hide #!14 models
> volume #14-22 step 1 level 0.2
> volume #15-22 step 1 level 0.2
> volume #15-22 step 1 level 0.1
> volume #15-22 step 1 level 0.5
> hide #!18 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> show #!16 models
> show #!17 models
> hide #!16 models
> show #!18 models
> hide #!17 models
> close #15-18
> show #!14 models
> close #14
> show #!2 models
> save
> /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/0611_LookingForDrug.cxs
> includeMaps true
> open /Users/Celine/Downloads/cryosparc_P37_J547_010_volume_map_sharp.mrc
Opened cryosparc_P37_J547_010_volume_map_sharp.mrc as #14, grid size
300,300,300, pixel 0.836, shown at level 0.0659, step 2, values float32
> hide #!2 models
> volume #14 level 0.2
> open /Users/Celine/Downloads/cryosparc_P37_J553_010_volume_map_sharp.mrc
Opened cryosparc_P37_J553_010_volume_map_sharp.mrc as #15, grid size
300,300,300, pixel 0.836, shown at level 0.0657, step 2, values float32
> hide #!15 models
> show #!15 models
> volume #15 level 0.2
> hide #!14 models
> show #!14 models
> hide #!15 models
> show #!15 models
> hide #!14 models
> color #15 #009193ff models
> show #!10 models
> hide #!15 models
> hide #!10 models
> color #14 #009193ff models
> show #!14 models
> show #!10 models
> hide #!10 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!2 models
> show #!10 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
> hide #!10 models
> hide #!2 models
> show #!2 models
> show #!9 models
> hide #!9 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> volume #2 level 0.1059
> show #!10 models
> hide #!2 models
> volume #10 level 0.1209
> show #!5 models
> hide #!5 models
> show #!14 models
> hide #!10 models
> show #!10 models
> volume #10 level 0.2
> view #10 clip false
> view clip false
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!14 models
> show #!14 models
> show #!10 models
> hide #!14 models
> show #!14 models
> hide #!10 models
> volume #14 level 0.128
> show #!10 models
> hide #!14 models
> hide #!10 models
> show #!14 models
> volume #14 level 0.1673
> volume #14 level 0.2
> show #!10 models
> hide #!14 models
> show #!1 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!10 models
> hide #!14 models
> show #!10 models
> show #!14 models
> hide #!10 models
> hide #!14 models
> show #!15 models
> show #!1 atoms
> hide #!1 models
> show #!10 models
> hide #!15 models
> show #!1 models
> color #10 #009193a2 models
> select #10
2 models selected
> select clear
> select #1/A:239@CD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> view clip false
> hide #!1 models
> select add #1
4330 atoms, 4420 bonds, 4 pseudobonds, 546 residues, 2 models selected
> show #!5 models
> select #10
3 models selected
> select clear
> select #10
3 models selected
> select subtract #10
Nothing selected
> hide #!10 models
> select #5/A:122@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:239@CG
1 atom, 1 residue, 1 model selected
> show #!10 models
> select add #5
4267 atoms, 4368 bonds, 2 pseudobonds, 529 residues, 2 models selected
> select subtract #5
Nothing selected
> select #5/B:122@CD2
1 atom, 1 residue, 1 model selected
> select clear
> select #5/B:118@CG2
1 atom, 1 residue, 1 model selected
> select #5/A:118@CD1
1 atom, 1 residue, 1 model selected
> select #5/B:122@CD2
1 atom, 1 residue, 1 model selected
Drag select of 10 cryosparc_P37_J494_010_volume_map_sharp (1).mrc masked
> select clear
> select #5/A:115@CD1
1 atom, 1 residue, 1 model selected
> select clear
> select #5/B:302@CAB
1 atom, 1 residue, 1 model selected
> select #5/B:302@CAB
1 atom, 1 residue, 1 model selected
> select up
35 atoms, 38 bonds, 1 residue, 1 model selected
> select #5/A:239@CD1
1 atom, 1 residue, 1 model selected
> select #5/A:305@CAB
1 atom, 1 residue, 1 model selected
> select #5/A:168@CD1
1 atom, 1 residue, 1 model selected
> select #5/A:305@CAA
1 atom, 1 residue, 1 model selected
> color #10 #009193ff models
> open
> /Volumes/sd23D002/celine/TASK1_1-269/apo/Class3D/job050/run_it025_class001.mrc
Opened run_it025_class001.mrc as #16, grid size 256,256,256, pixel 0.836,
shown at level 0.00642, step 1, values float32
> open
> /Volumes/sd23D002/celine/TASK1_1-269/apo/Class3D/job050/run_it025_class002.mrc
Opened run_it025_class002.mrc as #17, grid size 256,256,256, pixel 0.836,
shown at level 0.00724, step 1, values float32
> open
> /Volumes/sd23D002/celine/TASK1_1-269/apo/Class3D/job050/run_it025_class003.mrc
Opened run_it025_class003.mrc as #18, grid size 256,256,256, pixel 0.836,
shown at level 0.0074, step 1, values float32
> open
> /Volumes/sd23D002/celine/TASK1_1-269/apo/Class3D/job050/run_it025_class004.mrc
Opened run_it025_class004.mrc as #19, grid size 256,256,256, pixel 0.836,
shown at level 0.00864, step 1, values float32
> select add #5
4267 atoms, 4368 bonds, 2 pseudobonds, 529 residues, 2 models selected
> hide #!5 models
> select subtract #5
Nothing selected
> hide #!10 models
> hide #!19 models
> hide #!18 models
> hide #!17 models
> volume #16 level 0.007393
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!18 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> hide #!18 models
> show #!16 models
> volume #16 level -0.0007005
> volume #16 level 0.0004944
> open
> /Volumes/sd23D002/celine/TASK1_1-269/apo/Import/J267mask_6-12/J267_mask_6-12.mrc
Opened J267_mask_6-12.mrc as #20, grid size 256,256,256, pixel 0.836, shown at
level 1, step 1, values float32
> open
> /Volumes/sd23D002/celine/TASK1_1-269/apo/Import/J267ref_256px/cryosparc_P37_J267_010_volume_map.mrc
Opened cryosparc_P37_J267_010_volume_map.mrc as #21, grid size 256,256,256,
pixel 0.836, shown at level 0.0618, step 1, values float32
> hide #!16 models
> hide #!20 models
> show #!20 models
> volume #20 level 1
> hide #!20 models
> show #!20 models
> hide #!21 models
> show #!21 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> close #20
> close #16
> close #17-19,21
> open /Volumes/sd23D002/celine/TASK1_1-269/J267_mask_6-12.mrc
Opened J267_mask_6-12.mrc as #16, grid size 256,256,256, pixel 0.836, shown at
level 1, step 1, values float32
> open
> /Volumes/sd23D002/celine/TASK1_1-269/apo/Import/J267mask_6-12/J267_mask_6-12.mrc
Opened J267_mask_6-12.mrc as #17, grid size 256,256,256, pixel 0.836, shown at
level 1, step 1, values float32
> close #16
> volume #17 level 1
> open
> /Volumes/sd23D002/celine/TASK1_1-269/apo/MaskCreate/J267_mask_6-12/mask.mrc
Opened mask.mrc as #16, grid size 256,256,256, pixel 0.836, shown at level 1,
step 1, values float32
> hide #!17 models
> hide #!16 models
> show #!16 models
> volume #16 level 1
> show #!17 models
> hide #!17 models
> hide #!16 models
> show #!17 models
> show #!16 models
> hide #!17 models
> hide #!16 models
> show #!5 models
> show #!2 models
> select #5/A:257
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2
3 models selected
> select subtract #2
Nothing selected
> select #2
3 models selected
> hide #!2 models
> hide #!5 models
> show #!16 models
> show #!17 models
> hide #!16 target m
> close #16
> open
> /Volumes/sd23D002/celine/TASK1_1-269/apo/MaskCreate/J267_mask_6-12/mask.mrc
Opened mask.mrc as #16, grid size 256,256,256, pixel 0.836, shown at level 1,
step 1, values float32
> hide #!17 models
> volume #16 level 1
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> open /Users/Celine/Downloads/cryosparc_P37_J557_011_volume_map_sharp.mrc
Opened cryosparc_P37_J557_011_volume_map_sharp.mrc as #18, grid size
300,300,300, pixel 0.836, shown at level 0.0669, step 2, values float32
> close #17
> close #16
> volume #18 level 0.2
Drag select of 18 cryosparc_P37_J557_011_volume_map_sharp.mrc
> select clear
> open /Users/Celine/Downloads/cryosparc_P37_J575_010_volume_map_sharp.mrc
Opened cryosparc_P37_J575_010_volume_map_sharp.mrc as #16, grid size
300,300,300, pixel 0.836, shown at level 0.0723, step 2, values float32
> hide #!18 models
> hide #!16 models
> show #!16 models
> show #!7 models
> volume #16 level 0.2
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!16 models
> show #!16 models
> hide #!7 models
> show #!7 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!18 models
> hide #!18 models
> show #!16 models
> hide #!7 models
> open /Users/Celine/Downloads/cryosparc_P37_J577_010_volume_map_sharp.mrc
Opened cryosparc_P37_J577_010_volume_map_sharp.mrc as #17, grid size
300,300,300, pixel 0.836, shown at level 0.0728, step 2, values float32
> hide #!17 models
> hide #!16 models
> show #!18 models
> show #!16 models
> hide #!18 models
> show #!18 models
> hide #!16 models
> volume #17 level 0.2
> color #18 #009193ff models
> show #!16 models
> hide #!18 models
> show #!18 models
> hide #!16 models
> close #18
> show #!14 models
> show #!15 models
> hide #!14 models
> show #!14 models
> close #14
> close #15
> show #!17 models
> show #!16 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!16 models
> hide #!17 models
> show #!16 models
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> hide #!16 models
> show #!17 models
> show #!16 models
Drag select of 16 cryosparc_P37_J575_010_volume_map_sharp.mrc , 17
cryosparc_P37_J577_010_volume_map_sharp.mrc
> select clear
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!16 models
> hide #!17 models
> show #!16 models
> hide #!10 models
> show #!17 models
> hide #!16 models
> show #!10 models
> hide #!17 models
> show #!17 models
> hide #!10 models
> show #!10 models
> show #!16 models
> hide #!17 models
> hide #!16 models
> close #16
> close #17
> open /Users/Celine/Downloads/cryosparc_P37_J494_010_volume_mask_refine.mrc
Opened cryosparc_P37_J494_010_volume_mask_refine.mrc as #14, grid size
300,300,300, pixel 0.836, shown at level 1, step 2, values float32
> volume #14 level 1
> volume #14 step 1
> volume #14 level 0.2
> volume #14 step 2
> hide #!10 models
> open
> /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/masks/J267_mask_6-12.mrc
Opened J267_mask_6-12.mrc as #15, grid size 256,256,256, pixel 0.836, shown at
level 1, step 1, values float32
> open
> /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/masks/J267_mask_6-12.mrc
Opened J267_mask_6-12.mrc as #16, grid size 256,256,256, pixel 0.836, shown at
level 1, step 1, values float32
> close #15
> volume #16 level 1
> hide #!16 models
> show #!3 models
> hide #!14 models
> volume #3 level 0.03678
> volume #3 level 0.02
> open
> /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/masks/J294_mask_6-12.mrc
Opened J294_mask_6-12.mrc as #15, grid size 150,150,150, pixel 1.67, shown at
level 1, step 1, values float32
> hide #!3 models
> show #!3 models
> hide #!3 models
> close #16
> show #!14 models
> volume #15 level 1
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> color #14 #ffb2b2ce models
> show #!14 models
> color #14 #ffb2b200 models
> color #14 #ffb2b21a models
> show #!10 models
> color #15 #99bfe5da models
> color #15 #99bfe5f3 models
> hide #!14 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> color #15 #99bfe54e models
> hide #!15 models
> show #!14 models
> show #!15 models
> hide #!15 models
> volume #15 level 1
> hide #!15 models
> volume #14 level 1
> volume #14 level 0.9659
> volume #14 level 1
> volume #14 step 1
> volume #14 step 2
> volume #14 step 1
> open /Users/Celine/Downloads/cryosparc_P37_J494_010_volume_mask_fsc_auto.mrc
Opened cryosparc_P37_J494_010_volume_mask_fsc_auto.mrc as #16, grid size
300,300,300, pixel 0.836, shown at level 0.896, step 2, values float32
> hide #!10 models
> show #!10 models
> color #16 #cccc99ad models
> color #16 #cccc99ff models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!16 models
> color #14 #ffb2b233 models
> color #14 #ffb2b21a models
> hide #!14 models
> show #!16 models
> volume #16 level 1
> volume #16 step 1
> volume #16 step 2
> hide #!16 models
> open /Users/Celine/Downloads/cryosparc_P37_J494_010_volume_mask_fsc.mrc
Opened cryosparc_P37_J494_010_volume_mask_fsc.mrc as #17, grid size
300,300,300, pixel 0.836, shown at level 0.989, step 2, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J494_010_volume_mask_fsc_auto.mrc
Opened cryosparc_P37_J494_010_volume_mask_fsc_auto.mrc as #18, grid size
300,300,300, pixel 0.836, shown at level 0.896, step 2, values float32
> hide #!18 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!18 models
> show #!17 models
> hide #!18 models
> show #!18 models
> hide #!17 models
> show #!17 models
> hide #!18 models
> show #!18 models
> hide #!17 models
> show #!17 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!17 models
> show #!17 models
> hide #!18 models
> show #!18 models
> hide #!17 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!17 models
> show #!18 models
> show #!3 models
> hide #!17 models
> hide #!18 models
> color #3 #ffb2ff6d models
> color #3 #ffb2ff3f models
> color #3 #ffb2ff40 models
> open
> /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/masks/J294_mask_4-6.mrc
Opened J294_mask_4-6.mrc as #19, grid size 150,150,150, pixel 1.67, shown at
level 1, step 1, values float32
> volume #19 level 1
> hide #!19 models
> show #!18 models
> hide #!3 models
> color #18 #009193ff models
> color #18 #0091933d models
> color #18 #ff7e79ff models
> color #18 #ff7e79ad models
> color #18 #ff7e79b4 models
> color #18 #ff7e79b3 models
> open /Users/Celine/Downloads/cryosparc_P37_J598_fsc_mask_auto.mrc
Opened cryosparc_P37_J598_fsc_mask_auto.mrc as #20, grid size 300,300,300,
pixel 0.836, shown at level 0.918, step 2, values float32
> hide #!18 models
> show #!18 models
> hide #!18 models
> close #20
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> open /Users/Celine/Downloads/cryosparc_P37_J592_010_volume_map_sharp.mrc
Opened cryosparc_P37_J592_010_volume_map_sharp.mrc as #20, grid size
300,300,300, pixel 0.836, shown at level 0.0896, step 2, values float32
> volume #20 level 0.2
> hide #!20 models
> show #!20 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
Drag select of 20 cryosparc_P37_J592_010_volume_map_sharp.mrc
> select clear
> open /Users/Celine/Downloads/cryosparc_P37_J553_010_volume_map_sharp.mrc
Opened cryosparc_P37_J553_010_volume_map_sharp.mrc as #21, grid size
300,300,300, pixel 0.836, shown at level 0.0657, step 2, values float32
> open /Users/Celine/Downloads/cryosparc_P37_J557_011_volume_map_sharp.mrc
Opened cryosparc_P37_J557_011_volume_map_sharp.mrc as #22, grid size
300,300,300, pixel 0.836, shown at level 0.0669, step 2, values float32
> volume #22 level 0.2
> hide #!20 models
> hide #!21 models
> hide #!22 models
> show #!10 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!21 models
> volume #21 level 0.2
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> close #21
> show #!22 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> close #22
> show #!20 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> open "/Users/Celine/Seafile/TASK-1/ExpDataFiles/StructuralAnalysis/4.TASK
> structures/TASK-3/hsTASK3_MSP1D1_apo-pH7-5KCl_res35_emd36805.map"
Opened hsTASK3_MSP1D1_apo-pH7-5KCl_res35_emd36805.map as #21, grid size
200,200,200, pixel 1.1, shown at level 0.149, step 1, values float32
> close #21
> color #20 #85cab2ff models
> save /Users/Celine/Desktop/image31.png supersample 3
> lighting simple
> open /Users/Celine/Downloads/cryosparc_P37_J608_010_volume_map_sharp.mrc
Opened cryosparc_P37_J608_010_volume_map_sharp.mrc as #21, grid size
256,256,256, pixel 0.836, shown at level 0.0799, step 1, values float32
> show #!1 models
> hide #!1 models
> select add #21
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #21,1,0,0,13.341,0,1,0,20.339,0,0,1,19.665
> ui mousemode right select
> fitmap #21 inMap #20
You deleted or moved a volume file that is still open in ChimeraX.
/Users/Celine/Downloads/cryosparc_P37_J592_010_volume_map_sharp.mrc
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.
> fitmap #21 inMap #10
Fit map cryosparc_P37_J608_010_volume_map_sharp.mrc in map
cryosparc_P37_J494_010_volume_map_sharp (1).mrc masked using 167424 points
correlation = 0.8384, correlation about mean = 0.8559, overlap = 5966
steps = 136, shift = 5.54, angle = 0.116 degrees
Position of cryosparc_P37_J608_010_volume_map_sharp.mrc (#21) relative to
cryosparc_P37_J494_010_volume_map_sharp (1).mrc masked (#10) coordinates:
Matrix rotation and translation
0.99999799 0.00149104 -0.00134378 18.35293625
-0.00149134 0.99999886 -0.00022603 18.55677930
0.00134344 0.00022804 0.99999907 18.25529450
Axis 0.11239269 -0.66514644 -0.73820600
Axis point 1858.27815835 -14097.07238893 -0.00000000
Rotation angle (degrees) 0.11573850
Shift along axis -23.75640766
> select subtract #21
Nothing selected
> hide #!20 models
> show #!20 models
> volume #21 level 0.2
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!20 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!21 models
> show #!21 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!21 models
> hide #!10 models
> close #20
> save /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/0624.cxs
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J127_class_00_final_volume.mrc
Opened cryosparc_P37_J127_class_00_final_volume.mrc as #20, grid size
128,128,128, pixel 1.67, shown at level 0.135, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J127_class_01_final_volume.mrc
Opened cryosparc_P37_J127_class_01_final_volume.mrc as #22, grid size
128,128,128, pixel 1.67, shown at level 0.107, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J127_class_02_final_volume.mrc
Opened cryosparc_P37_J127_class_02_final_volume.mrc as #23, grid size
128,128,128, pixel 1.67, shown at level 0.137, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J127_class_03_final_volume.mrc
Opened cryosparc_P37_J127_class_03_final_volume.mrc as #24, grid size
128,128,128, pixel 1.67, shown at level 0.132, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J127_class_04_final_volume.mrc
Opened cryosparc_P37_J127_class_04_final_volume.mrc as #25, grid size
128,128,128, pixel 1.67, shown at level 0.113, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J504_class_00_final_volume.mrc
Opened cryosparc_P37_J504_class_00_final_volume.mrc as #26, grid size
128,128,128, pixel 1.67, shown at level 0.104, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J504_class_01_final_volume.mrc
Opened cryosparc_P37_J504_class_01_final_volume.mrc as #27, grid size
128,128,128, pixel 1.67, shown at level 0.125, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J504_class_02_final_volume.mrc
Opened cryosparc_P37_J504_class_02_final_volume.mrc as #28, grid size
128,128,128, pixel 1.67, shown at level 0.128, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J504_class_03_final_volume.mrc
Opened cryosparc_P37_J504_class_03_final_volume.mrc as #29, grid size
128,128,128, pixel 1.67, shown at level 0.0978, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J504_class_04_final_volume.mrc
Opened cryosparc_P37_J504_class_04_final_volume.mrc as #30, grid size
128,128,128, pixel 1.67, shown at level 0.109, step 1, values float32
> color #20 #d6d6d6ff models
> color #21 #d6d6d6ff models
> color #22 #d6d6d6ff models
> color #23 #d6d6d6ff models
> color #24 #d6d6d6ff models
> color #25 #d6d6d6ff models
> color #26 #d6d6d6ff models
> color #27 #d6d6d6ff models
> color #28 #d6d6d6ff models
> color #29 #d6d6d6ff models
> color #30 #d6d6d6ff models
> ui tool show "Side View"
Drag select of 20 cryosparc_P37_J127_class_00_final_volume.mrc , 22
cryosparc_P37_J127_class_01_final_volume.mrc , 23
cryosparc_P37_J127_class_02_final_volume.mrc , 24
cryosparc_P37_J127_class_03_final_volume.mrc , 25
cryosparc_P37_J127_class_04_final_volume.mrc , 26
cryosparc_P37_J504_class_00_final_volume.mrc , 27
cryosparc_P37_J504_class_01_final_volume.mrc , 28
cryosparc_P37_J504_class_02_final_volume.mrc , 29
cryosparc_P37_J504_class_03_final_volume.mrc , 30
cryosparc_P37_J504_class_04_final_volume.mrc
> show #!21 models
> select clear
> volume #20-30 step 1 level 0.2
> hide #!21 models
> hide #!22 models
> hide #!23 models
> hide #!24 models
> hide #!25 models
> hide #!26 models
> hide #!27 models
> hide #!28 models
> hide #!30 models
> hide #!29 models
> volume #20-30 step 1 level 0.25
> volume #20-30 step 1 level 0.15
> volume #20-30 step 1 level 0.2
> volume #20 level 0.1889
> volume #20 level 0.2
> save /Users/Celine/Desktop/image31.png supersample 3
> show #!21 models
> hide #!20 models
> hide #!21 models
> show #!22 models
> save /Users/Celine/Desktop/image32.png supersample 3
> hide #!22 models
> show #!23 models
> save /Users/Celine/Desktop/image33.png supersample 3
> hide #!23 models
> show #!24 models
> save /Users/Celine/Desktop/image34.png supersample 3
> hide #!24 models
> show #!25 models
> save /Users/Celine/Desktop/image35.png supersample 3
> hide #!25 models
> show #!26 models
> save /Users/Celine/Desktop/image31.png supersample 3
> hide #!26 models
> show #!27 models
> save /Users/Celine/Desktop/image32.png supersample 3
> hide #!27 models
> show #!28 models
> save /Users/Celine/Desktop/image33.png supersample 3
> hide #!28 models
> show #!29 models
> save /Users/Celine/Desktop/image34.png supersample 3
> hide #!29 models
> show #!30 models
> save /Users/Celine/Desktop/image35.png supersample 3
> hide #!30 models
> show #!27 models
> hide #!27 models
> show #!28 models
> volume #28 level 0.1432
> volume #26-30 step 1 level 0.15
> hide #!28 models
> show #!26 models
> save /Users/Celine/Desktop/image31.png supersample 3
> hide #!26 models
> show #!27 models
> save /Users/Celine/Desktop/image32.png supersample 3
> hide #!27 models
> show #!28 models
> save /Users/Celine/Desktop/image33.png supersample 3
> hide #!28 models
> show #!29 models
> save /Users/Celine/Desktop/image34.png supersample 3
> hide #!29 models
> show #!30 models
> save /Users/Celine/Desktop/image35.png supersample 3
> hide #!30 models
> show #!28 models
> color #28 #009193ff models
> color #28 #00919380 models
> color #28 #009193ff models
> color #28 #339999ff models
> color #28 #33ccccff models
> color #28 #339999ff models
> color #28 #009193ff models
> save /Users/Celine/Desktop/image31.png supersample 3
> volume #28 level 0.2
> save /Users/Celine/Desktop/image31.png supersample 3
> hide #!28 models
> show #!20 models
> color #20 #009193ff models
> save /Users/Celine/Desktop/image31.png supersample 3
> close #22-30
> close #20
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J506_class_00_00142_volume_sharp.mrc
Opened cryosparc_P37_J506_class_00_00142_volume_sharp.mrc as #20, grid size
128,128,128, pixel 1.67, shown at level 0.172, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J506_class_01_00142_volume_sharp.mrc
Opened cryosparc_P37_J506_class_01_00142_volume_sharp.mrc as #22, grid size
128,128,128, pixel 1.67, shown at level 0.156, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J506_class_02_00142_volume_sharp.mrc
Opened cryosparc_P37_J506_class_02_00142_volume_sharp.mrc as #23, grid size
128,128,128, pixel 1.67, shown at level 0.177, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J506_class_03_00142_volume_sharp.mrc
Opened cryosparc_P37_J506_class_03_00142_volume_sharp.mrc as #24, grid size
128,128,128, pixel 1.67, shown at level 0.173, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J506_class_04_00142_volume_sharp.mrc
Opened cryosparc_P37_J506_class_04_00142_volume_sharp.mrc as #25, grid size
128,128,128, pixel 1.67, shown at level 0.159, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J131_class_00_00162_volume_sharp.mrc
Opened cryosparc_P37_J131_class_00_00162_volume_sharp.mrc as #26, grid size
128,128,128, pixel 1.67, shown at level 0.193, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J131_class_01_00162_volume_sharp.mrc
Opened cryosparc_P37_J131_class_01_00162_volume_sharp.mrc as #27, grid size
128,128,128, pixel 1.67, shown at level 0.175, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J131_class_02_00162_volume_sharp.mrc
Opened cryosparc_P37_J131_class_02_00162_volume_sharp.mrc as #28, grid size
128,128,128, pixel 1.67, shown at level 0.201, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J131_class_03_00162_volume_sharp.mrc
Opened cryosparc_P37_J131_class_03_00162_volume_sharp.mrc as #29, grid size
128,128,128, pixel 1.67, shown at level 0.198, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J131_class_04_00162_volume_sharp.mrc
Opened cryosparc_P37_J131_class_04_00162_volume_sharp.mrc as #30, grid size
128,128,128, pixel 1.67, shown at level 0.176, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J132_class_00_00165_volume_sharp.mrc
Opened cryosparc_P37_J132_class_00_00165_volume_sharp.mrc as #31, grid size
128,128,128, pixel 1.67, shown at level 0.2, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J132_class_02_00165_volume_sharp.mrc
Opened cryosparc_P37_J132_class_02_00165_volume_sharp.mrc as #32, grid size
128,128,128, pixel 1.67, shown at level 0.207, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J132_class_03_00165_volume_sharp.mrc
Opened cryosparc_P37_J132_class_03_00165_volume_sharp.mrc as #33, grid size
128,128,128, pixel 1.67, shown at level 0.206, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J132_class_04_00165_volume_sharp.mrc
Opened cryosparc_P37_J132_class_04_00165_volume_sharp.mrc as #34, grid size
128,128,128, pixel 1.67, shown at level 0.184, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J133_class_00_00150_volume_sharp.mrc
Opened cryosparc_P37_J133_class_00_00150_volume_sharp.mrc as #35, grid size
128,128,128, pixel 1.67, shown at level 0.214, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J133_class_01_00150_volume_sharp.mrc
Opened cryosparc_P37_J133_class_01_00150_volume_sharp.mrc as #36, grid size
128,128,128, pixel 1.67, shown at level 0.198, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J133_class_02_00150_volume_sharp.mrc
Opened cryosparc_P37_J133_class_02_00150_volume_sharp.mrc as #37, grid size
128,128,128, pixel 1.67, shown at level 0.217, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J133_class_03_00150_volume_sharp.mrc
Opened cryosparc_P37_J133_class_03_00150_volume_sharp.mrc as #38, grid size
128,128,128, pixel 1.67, shown at level 0.215, step 1, values float32
> open /Users/Celine/Seafile/TASK-1/Meetings_presentations/250704_HDCryoNet-
> meeting/maps/cryosparc_P37_J133_class_04_00150_volume_sharp.mrc
Opened cryosparc_P37_J133_class_04_00150_volume_sharp.mrc as #39, grid size
128,128,128, pixel 1.67, shown at level 0.198, step 1, values float32
> volume #20-39 step 1 level 0.2
===== Log before crash end =====
Log:
Startup Messages
---
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 - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: 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 Pro
Model Identifier: Mac15,6
Model Number: Z1AV000K0D/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 11881.81.4
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.4 (23H420)
Kernel Version: Darwin 23.6.0
Time since boot: 78 days, 3 hours
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
PHL BDM3270:
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-EMalign: 0.1.1
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-LigandRecognizer: 0.2
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
finufft: 2.3.1
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: 3.10.0
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: 2.2.2
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
plotly: 5.24.1
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: 0.7.2
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
tenacity: 9.0.0
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
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 |
|---|---|
| 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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