![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 12 months ago
Closed 12 months ago
#16261 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-14.5-arm64-arm-64bit
ChimeraX Version: 1.8rc202406042103 (2024-06-04 21:03:50 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000201840c00 (most recent call first):
File "/Applications/ChimeraX-1.8-rc2024.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 307 in event_loop
File "/Applications/ChimeraX-1.8-rc2024.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8-rc2024.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.segment._segment, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 56)
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{
"uptime" : 330000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 1497,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-11-07 11:03:47.5839 +0000",
"codeSigningMonitor" : 1,
"incident" : "8D2DB2D2-C688-4E52-8A0A-5A4B4959B0C9",
"pid" : 68222,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-11-06 16:36:55.2851 +0000",
"procStartAbsTime" : 7194802858810,
"procExitAbsTime" : 7977291312038,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8-rc2024.06.04.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"80B649B3-0BCC-54FF-AC78-C270F44AE6EC","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B228D314-B433-AC07-FAD2-662AB21FECFB",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 2,
"sleepWakeUUID" : "169C9BF9-6D5D-48E6-A915-B8E9B5EA9B2B",
"sip" : "enabled",
"vmRegionInfo" : "0x618992abb868 is not in any region. Bytes after previous region: 1688235391081 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600060000000-600080000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000e18992abb868","rawCodes":[1,247980987496552],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000e18992abb868 -> 0x0000618992abb868 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":68222},
"vmregioninfo" : "0x618992abb868 is not in any region. Bytes after previous region: 1688235391081 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600060000000-600080000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202406042103 (2024-06-04)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/yuanyuan/Desktop/data processing/J76_003_volume_map.mrc"
Opened J76_003_volume_map.mrc as #1, grid size 80,80,80, pixel 3.31, shown at
level 0.367, step 1, values float32
> open "/Users/yuanyuan/Desktop/data processing/DanB_hexemer.cif"
Summary of feedback from opening /Users/yuanyuan/Desktop/data
processing/DanB_hexemer.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for DanB_hexemer.cif #2
---
Chain | Description
A C | No description available
B D F | No description available
E | No description available
> hide atoms
> show cartoons
> volume #1 level 0.287
> view orient
> volume #1 level 0.1262
>
Incomplete command: segger
>
Unknown command: segger #1
> volume, segger
Unknown command: volume, segger
> volume segger
Expected a density maps specifier or a keyword
> ui windowfill toggle
> select add #2
41973 atoms, 42281 bonds, 2690 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,2.4935,0,1,0,-18.637,0,0,1,-40.983
> view matrix models #2,1,0,0,0.70673,0,1,0,-15.779,0,0,1,-51.514
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.51941,0.089189,0.84986,-85.054,0.54149,0.73502,-0.40808,10.624,-0.66106,0.67215,0.33349,65.111
> ui tool show "Segment Map"
Segmenting J76_003_volume_map.mrc, density threshold 0.126239
Showing 8 region surfaces
88 watershed regions, grouped to 8 regions
Showing J76_003_volume_map.seg - 8 regions, 8 surfaces
> ui mousemode right "translate selected models"
> ui mousemode right select
> select subtract #2
Nothing selected
Drag select of 135, 3767 of 12248 triangles, 131, 401 of 10272 triangles, 136,
2924 of 9396 triangles, 133, 1660 of 8216 triangles, 115, 87 of 5520
triangles, 1 J76_003_volume_map.mrc , 509 residues
Grouped 5 regions
Ungrouped to 5 regions
> open "/Users/yuanyuan/Desktop/data processing/DnaB_monomer.cif"
Summary of feedback from opening /Users/yuanyuan/Desktop/data
processing/DnaB_monomer.cif
---
warnings | Unknown polymer entity '1' on line 26
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for DnaB_monomer.cif #4
---
Chain | Description
A | No description available
Drag select of 132, 23 of 5568 triangles, 131, 265 of 10272 triangles, 136, 20
of 9396 triangles, 1 J76_003_volume_map.mrc , 22 residues
> select add #4
4488 atoms, 4552 bonds, 576 residues, 6 models selected
> select subtract #1
4488 atoms, 4552 bonds, 576 residues, 4 models selected
> select add #3
4488 atoms, 4552 bonds, 576 residues, 10 models selected
> select subtract #3
4488 atoms, 4552 bonds, 576 residues, 1 model selected
Drag select of 131, 215 of 10272 triangles, 136, 146 of 9396 triangles, 1
J76_003_volume_map.mrc , 12 residues
> ui mousemode right "translate selected models"
> select subtract #1
87 atoms, 12 residues, 3 models selected
> select add #3
87 atoms, 12 residues, 10 models selected
> select subtract #3
87 atoms, 12 residues, 1 model selected
> select add #4
4488 atoms, 4552 bonds, 576 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #4
4488 atoms, 4552 bonds, 576 residues, 1 model selected
> view matrix models #4,1,0,0,235.19,0,1,0,-3.734,0,0,1,-5.9654
> view matrix models #4,1,0,0,294.79,0,1,0,2.5461,0,0,1,-14.617
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.5122,-0.10551,0.85236,234.92,0.81617,0.2492,0.52131,36.123,-0.26741,0.96269,-0.041525,-26.736
> view matrix models
> #4,-0.82636,0.37165,0.42309,221.7,0.48665,0.093225,0.86861,23.282,0.28338,0.92368,-0.2579,-4.8056
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.82636,0.37165,0.42309,182.49,0.48665,0.093225,0.86861,41.128,0.28338,0.92368,-0.2579,-7.7111
> select subtract #4
Nothing selected
> select add #1
2 models selected
> transparency #1.1 60
> select add #3.2
3 models selected
> select subtract #3.2
2 models selected
> select add #3.5
3 models selected
> transparency #1.1#3.5 70
> select subtract #3.5
2 models selected
> select add #4
4488 atoms, 4552 bonds, 576 residues, 3 models selected
> view matrix models
> #1,1,0,0,-1.3318,0,1,0,-0.82222,0,0,1,1.4703,#4,-0.82636,0.37165,0.42309,181.16,0.48665,0.093225,0.86861,40.306,0.28338,0.92368,-0.2579,-6.2408
> undo
> select subtract #1
4488 atoms, 4552 bonds, 576 residues, 1 model selected
> view matrix models
> #4,-0.82636,0.37165,0.42309,155.28,0.48665,0.093225,0.86861,84.233,0.28338,0.92368,-0.2579,-34.295
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.80966,0.29761,0.50585,156.05,0.56592,0.1675,0.80727,86.798,0.15552,0.93988,-0.30404,-38.785
> view matrix models
> #4,0.32898,0.13684,0.93437,196.09,0.078939,0.982,-0.17161,67.744,-0.94103,0.13021,0.31225,-74.837
> hide #!1 models
> hide #2 models
> hide #!3 models
> show #!3 models
> view matrix models
> #4,0.14777,0.048392,0.98784,190.01,0.29392,0.95153,-0.090581,75.303,-0.94434,0.30373,0.12639,-75.402
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.14777,0.048392,0.98784,123.73,0.29392,0.95153,-0.090581,123.31,-0.94434,0.30373,0.12639,-36.988
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.44408,0.76289,-0.46988,105.2,0.89308,0.33464,-0.30072,152.75,-0.072177,-0.55319,-0.82992,9.9936
> view matrix models
> #4,0.31427,-0.0044308,-0.94932,143.82,0.91289,0.27582,0.30092,149.87,0.2605,-0.9612,0.090725,19.764
> view matrix models
> #4,-0.39332,0.71623,-0.57646,108.26,0.91939,0.30375,-0.2499,153.66,-0.003887,-0.62829,-0.77797,12.868
> view matrix models
> #4,-0.10413,0.43224,-0.89573,123.85,0.97273,0.23196,-0.001152,154.59,0.20727,-0.87142,-0.4446,20.661
> view matrix models
> #4,-0.45772,0.77508,-0.4356,104.34,0.88411,0.34498,-0.31518,152.42,-0.094016,-0.52938,-0.84316,9.0529
> view matrix models
> #4,0.52375,-0.33415,0.7836,142.66,0.29252,0.93447,0.20297,121.38,-0.80007,0.12291,0.58717,-33.141
> view matrix models
> #4,0.13159,0.065327,0.98915,122.96,0.29649,0.94956,-0.10216,123.5,-0.94593,0.30672,0.10558,-36.931
> view matrix models
> #4,0.25853,-0.84588,0.46652,140.36,0.094171,0.50271,0.85931,113.92,-0.9614,-0.17823,0.20962,-33.354
> view matrix models
> #4,0.26778,-0.79574,0.54322,139.66,-0.93712,-0.084139,0.3387,85.936,-0.22381,-0.59977,-0.76824,4.5163
> view matrix models
> #4,0.38695,-0.66737,0.6363,142.06,-0.91259,-0.17832,0.36794,87.569,-0.13209,-0.72306,-0.67804,8.4597
> view matrix models
> #4,0.57364,0.15892,-0.80354,150.6,0.55789,-0.79409,0.24121,148.1,-0.59975,-0.58666,-0.54418,-10.849
> view matrix models
> #4,0.64251,0.6623,-0.38541,145.14,0.70141,-0.71084,-0.052244,154.53,-0.30857,-0.23676,-0.92126,-1.1401
> view matrix models
> #4,0.55485,0.097366,-0.82623,150.69,0.54731,-0.79068,0.27436,147.45,-0.62657,-0.60443,-0.492,-12.01
> view matrix models
> #4,0.64606,0.55905,-0.51968,147.24,0.66009,-0.75108,0.012617,152.98,-0.38327,-0.35119,-0.85427,-3.1761
> view matrix models
> #4,0.63449,0.43245,-0.64064,148.93,0.62012,-0.77956,0.087946,151.29,-0.46138,-0.45307,-0.76279,-5.6324
> view matrix models
> #4,0.64645,0.59803,-0.47377,146.54,0.67451,-0.73817,-0.011405,153.55,-0.35655,-0.31219,-0.88057,-2.412
> view matrix models
> #4,0.63036,0.40524,-0.66214,149.2,0.61263,-0.78353,0.1037,150.95,-0.47678,-0.47102,-0.74217,-6.1562
> ui mousemode right "move picked models"
> view matrix models
> #4,0.63036,0.40524,-0.66214,152.21,0.61263,-0.78353,0.1037,165.63,-0.47678,-0.47102,-0.74217,22.05
> ui mousemode right "translate selected atoms"
> select add #3
4488 atoms, 4552 bonds, 576 residues, 10 models selected
> select subtract #4
9 models selected
> transparency #3 60
> select subtract #3
Nothing selected
> select add #4
4488 atoms, 4552 bonds, 576 residues, 1 model selected
> volume #1 level 0.1061
> view orient
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.15265,-0.078334,-0.98517,27.063,0.54922,-0.83547,-0.018667,138.96,-0.82162,-0.54393,0.17055,148.17
> view matrix models
> #4,0.30844,0.63778,-0.70576,145.78,0.59446,-0.70845,-0.38041,91.435,-0.74262,-0.30221,-0.59765,44.412
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.30844,0.63778,-0.70576,133.64,0.59446,-0.70845,-0.38041,130.55,-0.74262,-0.30221,-0.59765,-116.87
> view matrix models
> #4,0.30844,0.63778,-0.70576,170.83,0.59446,-0.70845,-0.38041,88.227,-0.74262,-0.30221,-0.59765,-119.51
> select add #3.5
4488 atoms, 4552 bonds, 576 residues, 2 models selected
> transparency (#4 & sel) 100
> select subtract #3.5
4488 atoms, 4552 bonds, 576 residues, 1 model selected
> view matrix models
> #4,0.30844,0.63778,-0.70576,-20.243,0.59446,-0.70845,-0.38041,58.794,-0.74262,-0.30221,-0.59765,-0.040379
> view matrix models
> #4,0.30844,0.63778,-0.70576,-20.48,0.59446,-0.70845,-0.38041,150.81,-0.74262,-0.30221,-0.59765,39.26
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.18684,0.98145,-0.042989,105.5,0.78603,-0.1756,-0.59272,163.47,-0.58927,0.076954,-0.80426,40.084
> view matrix models
> #4,0.26153,0.96503,-0.017848,112.09,0.77123,-0.22006,-0.59731,158.85,-0.58035,0.14245,-0.80181,45.557
> view matrix models
> #4,-0.91636,0.19162,-0.35153,-54.7,0.32238,0.87381,-0.36404,252.12,0.23741,-0.44692,-0.8625,34.144
> view matrix models
> #4,-0.15478,0.57917,-0.80038,-62.747,0.69978,0.63615,0.32499,365.73,0.69739,-0.50979,-0.50376,110.54
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.15478,0.57917,-0.80038,-69.647,0.69978,0.63615,0.32499,279.17,0.69739,-0.50979,-0.50376,67.655
> select add #3.5
4488 atoms, 4552 bonds, 576 residues, 2 models selected
> ui tool show "Fit to Segments"
> ui tool show "Fit in Map"
> fitmap #4 inMap #1
Fit molecule DnaB_monomer.cif (#4) to map J76_003_volume_map.mrc (#1) using
4488 atoms
average map value = 0.002465, steps = 2000
shifted from previous position = 12.9
rotated from previous position = 6.03 degrees
atoms outside contour = 4406, contour level = 0.10614
Position of DnaB_monomer.cif (#4) relative to J76_003_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.15415945 0.52269517 -0.83846565 -75.17850495
0.63372641 0.70337148 0.32196186 288.32959054
0.75804072 -0.48172435 -0.43967708 91.68831762
Axis -0.44877862 -0.89148963 0.06199988
Axis point -146.71133239 0.00000000 -4.19014281
Rotation angle (degrees) 116.43821633
Shift along axis -217.61967093
> fitmap #4 inMap #1
Fit molecule DnaB_monomer.cif (#4) to map J76_003_volume_map.mrc (#1) using
4488 atoms
average map value = 0.002489, steps = 2000
shifted from previous position = 1.91
rotated from previous position = 1.63 degrees
atoms outside contour = 4406, contour level = 0.10614
Position of DnaB_monomer.cif (#4) relative to J76_003_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.15723538 0.52159479 -0.83857971 -75.95120913
0.61166987 0.71809463 0.33196400 288.41805287
0.77533028 -0.46073745 -0.43195369 96.05269272
Axis -0.44030853 -0.89645142 0.05003249
Axis point -146.25521485 0.00000000 -4.41424376
Rotation angle (degrees) 115.82011918
Shift along axis -220.30505215
> fitmap #4 inMap #1
Fit molecule DnaB_monomer.cif (#4) to map J76_003_volume_map.mrc (#1) using
4488 atoms
average map value = 0.002409, steps = 2000
shifted from previous position = 1.99
rotated from previous position = 1.78 degrees
atoms outside contour = 4410, contour level = 0.10614
Position of DnaB_monomer.cif (#4) relative to J76_003_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.14663413 0.51192377 -0.84642336 -78.52090325
0.59046355 0.73180683 0.34031102 288.66698179
0.79363169 -0.44988092 -0.40958018 102.34948235
Axis -0.43365116 -0.90004938 0.04310202
Axis point -148.90299913 0.00000000 -4.45800859
Rotation angle (degrees) 114.34334553
Shift along axis -221.35238870
> fitmap #4 inMap #1
Fit molecule DnaB_monomer.cif (#4) to map J76_003_volume_map.mrc (#1) using
4488 atoms
average map value = 0.002391, steps = 2000
shifted from previous position = 4.08
rotated from previous position = 2.5 degrees
atoms outside contour = 4406, contour level = 0.10614
Position of DnaB_monomer.cif (#4) relative to J76_003_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.15022520 0.51680871 -0.84281740 -75.80712190
0.62437276 0.71056805 0.32442524 289.09976744
0.76654490 -0.47749537 -0.42942650 94.12208977
Axis -0.44518910 -0.89344325 0.05971457
Axis point -147.59414278 -0.00000000 -4.15720487
Rotation angle (degrees) 115.75614271
Shift along axis -218.92527126
> fitmap #4 inMap #1
Fit molecule DnaB_monomer.cif (#4) to map J76_003_volume_map.mrc (#1) using
4488 atoms
average map value = 0.002472, steps = 2000
shifted from previous position = 1.44
rotated from previous position = 1.24 degrees
atoms outside contour = 4406, contour level = 0.10614
Position of DnaB_monomer.cif (#4) relative to J76_003_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.14663162 0.50306347 -0.85171963 -78.28516103
0.61216583 0.72248940 0.32134419 287.73754875
0.77701492 -0.47427443 -0.41389805 98.02379105
Axis -0.43812710 -0.89690303 0.06007992
Axis point -149.05603113 0.00000000 -3.32731340
Rotation angle (degrees) 114.77273968
Shift along axis -217.88456722
> view matrix models
> #3.5,1,0,0,-87.603,0,1,0,46,0,0,1,-25.391,#4,-0.14663,0.50306,-0.85172,-165.89,0.61217,0.72249,0.32134,333.74,0.77701,-0.47427,-0.4139,72.632
> undo
> select subtract #3.5
4488 atoms, 4552 bonds, 576 residues, 1 model selected
> view matrix models
> #4,-0.14663,0.50306,-0.85172,18.798,0.61217,0.72249,0.32134,261.68,0.77701,-0.47427,-0.4139,114.3
> fitmap #4 inMap #1
Fit molecule DnaB_monomer.cif (#4) to map J76_003_volume_map.mrc (#1) using
4488 atoms
average map value = 0.2378, steps = 104
shifted from previous position = 14.9
rotated from previous position = 11.5 degrees
atoms outside contour = 1352, contour level = 0.10614
Position of DnaB_monomer.cif (#4) relative to J76_003_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.25249770 0.34144939 -0.90534924 -3.52147147
0.57356224 0.80637749 0.14415869 246.39271540
0.77927614 -0.48287439 -0.39945093 104.01681363
Axis -0.34595701 -0.92946924 0.12806512
Axis point -92.66666222 0.00000000 42.35282086
Rotation angle (degrees) 115.01057719
Shift along axis -214.47524686
> select subtract #4
Nothing selected
> hide #4 models
> volume #1 level 0.1162
> show #2 models
> fitmap #2 inMap #1
Fit molecule DanB_hexemer.cif (#2) to map J76_003_volume_map.mrc (#1) using
41973 atoms
average map value = 0.1969, steps = 244
shifted from previous position = 27.6
rotated from previous position = 47.1 degrees
atoms outside contour = 15251, contour level = 0.11619
Position of DanB_hexemer.cif (#2) relative to J76_003_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.96009896 -0.12368464 0.25082283 -43.32002405
0.27502147 0.58025862 -0.76659189 133.32496107
-0.05072646 0.80498574 0.59112163 -94.27003486
Axis 0.95295186 0.18284936 0.24176199
Axis point 0.00000000 155.17742527 98.42091458
Rotation angle (degrees) 55.54633320
Shift along axis -39.69442535
> fitmap #2 inMap #1
Fit molecule DanB_hexemer.cif (#2) to map J76_003_volume_map.mrc (#1) using
41973 atoms
average map value = 0.1969, steps = 48
shifted from previous position = 0.076
rotated from previous position = 0.0597 degrees
atoms outside contour = 15235, contour level = 0.11619
Position of DanB_hexemer.cif (#2) relative to J76_003_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.95989530 -0.12385199 0.25151879 -43.45941616
0.27571770 0.57958723 -0.76684965 133.35938271
-0.05080122 0.80544356 0.59049124 -94.22794273
Axis 0.95278962 0.18320207 0.24213413
Axis point 0.00000000 155.05777264 98.40396839
Rotation angle (degrees) 55.59861931
Shift along axis -39.79176755
> fitmap #2 inMap #1
Fit molecule DanB_hexemer.cif (#2) to map J76_003_volume_map.mrc (#1) using
41973 atoms
average map value = 0.1969, steps = 48
shifted from previous position = 0.0874
rotated from previous position = 0.0681 degrees
atoms outside contour = 15254, contour level = 0.11619
Position of DanB_hexemer.cif (#2) relative to J76_003_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.96012793 -0.12367549 0.25071645 -43.29626225
0.27492548 0.58034880 -0.76655805 133.32152548
-0.05069855 0.80492213 0.59121064 -94.27826370
Axis 0.95297531 0.18278376 0.24171917
Axis point 0.00000000 155.19601202 98.42205105
Rotation angle (degrees) 55.53910123
Shift along axis -39.68012281
> volume #1 level 0.2594
> volume #1 style image
> volume #1 level -0.02731,0 level 0.3672,0.8 level 0.891,1
> volume #1 level -0.02731,0 level 0.06575,0.7853 level 0.891,1
> volume #1 style surface
> volume #1 level 0.189
> volume #1 level 0.1865
> volume #1 level 0.1087
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #2 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> show #2 models
> view orient
> color #1 #ff40ffff models
> undo
> color #1 #e8f8f2ff models
> show #!1 models
> hide #!1 models
> color #2 #e22bcaff
> color #2 #e2312cff
> hide #!3 models
> show #!1 models
> select add #1
3 models selected
> select add #1
3 models selected
> select add #1
3 models selected
> show #!3 models
> hide #!3 models
> hide #3.2 models
> hide #3.3 models
> hide #3.4 models
> hide #3.5 models
> hide #3.6 models
> hide #3.7 models
> hide #3.8 models
> hide #3.9 models
> select add #1
3 models selected
> select add #1
3 models selected
> transparency #1.1 70
> volume #1 level 0.2066
> color #2 #d87cbfff
> select add #1
3 models selected
> select add #1
3 models selected
> select add #1
3 models selected
> select add #2
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> hide #!1 models
> show #!1 models
> view matrix models
> #1,1,0,0,0.080255,0,1,0,0.47402,0,0,1,-0.14283,#2,0.96013,-0.12368,0.25072,-43.216,0.27493,0.58035,-0.76656,133.8,-0.050699,0.80492,0.59121,-94.421
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 4 models selected
> close #1
> hide #2 models
> show #2 models
> select subtract #2
Nothing selected
> open "/Users/yuanyuan/Desktop/data processing/DanB_hexemer.cif"
Summary of feedback from opening /Users/yuanyuan/Desktop/data
processing/DanB_hexemer.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for DanB_hexemer.cif #1
---
Chain | Description
A C | No description available
B D F | No description available
E | No description available
> hide #1-2 atoms
> show #1-2 cartoons
> hide #2 models
> open "/Users/yuanyuan/Desktop/data processing/AF3_bsdnac_hexamer copy.cif"
Chain information for AF3_bsdnac_hexamer copy.cif #5
---
Chain | Description
A B C D E F | .
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> close #2
> close #4
> select add #5
26928 atoms, 27312 bonds, 3456 residues, 1 model selected
> view matrix models #5,1,0,0,5.765,0,1,0,-22.054,0,0,1,66.915
> view orient
> view matrix models #5,1,0,0,168.43,0,1,0,156.64,0,0,1,66.915
> select subtract #5
Nothing selected
> select add #5
26928 atoms, 27312 bonds, 3456 residues, 1 model selected
> view matrix models #5,1,0,0,160.68,0,1,0,148.91,0,0,1,172.6
> select subtract #5
Nothing selected
> ui tool show "Fit in Map"
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 1 model selected
> select add #5
68901 atoms, 69593 bonds, 6146 residues, 2 models selected
> select subtract #5
41973 atoms, 42281 bonds, 2690 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
41973 atoms, 42281 bonds, 2690 residues, 1 model selected
> close #1
> open "/Users/yuanyuan/Desktop/data processing/J76_003_volume_map.mrc"
Opened J76_003_volume_map.mrc as #1, grid size 80,80,80, pixel 3.31, shown at
level 0.367, step 1, values float32
> open "/Users/yuanyuan/Desktop/data processing/6qel_DanB_hexemer.cif"
Summary of feedback from opening /Users/yuanyuan/Desktop/data
processing/6qel_DanB_hexemer.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 6qel_DanB_hexemer.cif #2
---
Chain | Description
A C | No description available
B D F | No description available
E | No description available
> view orient
> show #!3 models
> hide #!3 models
> hide #2 models
> hide #5 models
> volume #1 level 0.237
> view orient
> volume #1 level 0.1743
> transparency #1 60
> show #5 models
> hide #5 atoms
> show #5 cartoons
> ui tool show "Fit in Map"
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1842, steps = 156
shifted from previous position = 57.3
rotated from previous position = 16.5 degrees
atoms outside contour = 13634, contour level = 0.17428
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.95900659 0.27855891 -0.05207001 124.17735505
-0.27859999 0.96038445 0.00661458 126.81169963
0.05184978 0.00816328 0.99862153 134.57261921
Axis 0.00273250 -0.18335457 -0.98304305
Axis point 408.09656705 -387.25085696 0.00000000
Rotation angle (degrees) 16.46232418
Shift along axis -155.20286786
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1842, steps = 48
shifted from previous position = 0.0414
rotated from previous position = 0.0461 degrees
atoms outside contour = 13627, contour level = 0.17428
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.95916476 0.27812885 -0.05145193 124.14997755
-0.27817763 0.96050862 0.00635495 126.79146666
0.05118752 0.00821733 0.99865525 134.59770978
Axis 0.00329217 -0.18143831 -0.98339682
Axis point 409.81090817 -388.04102317 0.00000000
Rotation angle (degrees) 16.43034225
Shift along axis -154.95906604
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1842, steps = 60
shifted from previous position = 0.0677
rotated from previous position = 0.0371 degrees
atoms outside contour = 13635, contour level = 0.17428
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.95899858 0.27863235 -0.05182419 124.19711369
-0.27868341 0.96036180 0.00638437 126.82686487
0.05154886 0.00831994 0.99863582 134.56297390
Axis 0.00341477 -0.18237207 -0.98322366
Axis point 408.76657012 -387.48706490 0.00000000
Rotation angle (degrees) 16.46397967
Shift along axis -155.01107253
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1842, steps = 44
shifted from previous position = 0.0536
rotated from previous position = 0.0333 degrees
atoms outside contour = 13625, contour level = 0.17428
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.95915602 0.27813848 -0.05156277 124.16158406
-0.27818903 0.96050543 0.00633864 126.79473608
0.05128934 0.00826446 0.99864964 134.58828617
Axis 0.00340396 -0.18179512 -0.98333054
Axis point 409.61768603 -388.14726140 0.00000000
Rotation angle (degrees) 16.43211959
Shift along axis -154.97279517
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1842, steps = 60
shifted from previous position = 0.0533
rotated from previous position = 0.0232 degrees
atoms outside contour = 13634, contour level = 0.17428
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.95904324 0.27850092 -0.05170399 124.19858389
-0.27855312 0.96039990 0.00633952 126.82574674
0.05142207 0.00832244 0.99864233 134.56483976
Axis 0.00350016 -0.18203336 -0.98328613
Axis point 409.15237844 -387.73098622 0.00000000
Rotation angle (degrees) 16.45495300
Shift along axis -154.96754216
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1842, steps = 44
shifted from previous position = 0.0566
rotated from previous position = 0.0265 degrees
atoms outside contour = 13627, contour level = 0.17428
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.95916904 0.27810479 -0.05150214 124.15936683
-0.27815607 0.96051514 0.00631370 126.79319442
0.05122445 0.00826973 0.99865293 134.59051672
Axis 0.00345789 -0.18160157 -0.98336611
Axis point 409.78008339 -388.21139453 0.00000000
Rotation angle (degrees) 16.42948411
Shift along axis -154.94826682
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1842, steps = 60
shifted from previous position = 0.0566
rotated from previous position = 0.0265 degrees
atoms outside contour = 13634, contour level = 0.17428
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.95904296 0.27850178 -0.05170456 124.19857327
-0.27855397 0.96039965 0.00633965 126.82577148
0.05142265 0.00832251 0.99864230 134.56483003
Axis 0.00350004 -0.18203479 -0.98328586
Axis point 409.15045757 -387.72956699 0.00000000
Rotation angle (degrees) 16.45500946
Shift along axis -154.96769801
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1842, steps = 44
shifted from previous position = 0.0563
rotated from previous position = 0.0263 degrees
atoms outside contour = 13627, contour level = 0.17428
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.95916801 0.27810734 -0.05150774 124.15956938
-0.27815858 0.96051440 0.00631549 126.79330791
0.05123031 0.00826970 0.99865263 134.59030429
Axis 0.00345465 -0.18161956 -0.98336280
Axis point 409.76589513 -388.20733943 0.00000000
Rotation angle (degrees) 16.42969446
Shift along axis -154.95031543
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1842, steps = 60
shifted from previous position = 0.0563
rotated from previous position = 0.0262 degrees
atoms outside contour = 13634, contour level = 0.17428
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.95904327 0.27850087 -0.05170376 124.19857786
-0.27855307 0.96039992 0.00633936 126.82576606
0.05142180 0.00832252 0.99864235 134.56484328
Axis 0.00350060 -0.18203255 -0.98328627
Axis point 409.15305812 -387.73121918 0.00000000
Rotation angle (degrees) 16.45494760
Shift along axis -154.96741204
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1842, steps = 44
shifted from previous position = 0.0563
rotated from previous position = 0.0261 degrees
atoms outside contour = 13627, contour level = 0.17428
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.95916786 0.27810767 -0.05150872 124.15958854
-0.27815892 0.96051431 0.00631538 126.79331593
0.05123122 0.00827010 0.99865258 134.59026540
Axis 0.00345553 -0.18162259 -0.98336224
Axis point 409.76379183 -388.20753367 0.00000000
Rotation angle (degrees) 16.42972453
Shift along axis -154.95047707
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1842, steps = 60
shifted from previous position = 0.0563
rotated from previous position = 0.0262 degrees
atoms outside contour = 13634, contour level = 0.17428
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.95904300 0.27850163 -0.05170458 124.19858741
-0.27855383 0.96039970 0.00633960 126.82578032
0.05142265 0.00832256 0.99864230 134.56481166
Axis 0.00350021 -0.18203493 -0.98328583
Axis point 409.15063431 -387.72994866 0.00000000
Rotation angle (degrees) 16.45500116
Shift along axis -154.96767429
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1842, steps = 44
shifted from previous position = 0.0567
rotated from previous position = 0.0265 degrees
atoms outside contour = 13627, contour level = 0.17428
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.95916904 0.27810490 -0.05150170 124.15931578
-0.27815617 0.96051511 0.00631388 126.79316062
0.05122408 0.00826944 0.99865295 134.59055141
Axis 0.00345707 -0.18160012 -0.98336638
Axis point 409.78055346 -388.21051902 0.00000000
Rotation angle (degrees) 16.42948580
Shift along axis -154.94824915
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1842, steps = 60
shifted from previous position = 0.0567
rotated from previous position = 0.0266 degrees
atoms outside contour = 13634, contour level = 0.17428
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.95904271 0.27850252 -0.05170522 124.19856402
-0.27855471 0.96039944 0.00633984 126.82577236
0.05142332 0.00832255 0.99864227 134.56481975
Axis 0.00349977 -0.18203660 -0.98328553
Axis point 409.14835364 -387.72829227 0.00000000
Rotation angle (degrees) 16.45506022
Shift along axis -154.96790586
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1842, steps = 44
shifted from previous position = 0.0563
rotated from previous position = 0.0263 degrees
atoms outside contour = 13627, contour level = 0.17428
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.95916806 0.27810718 -0.05150760 124.15957124
-0.27815841 0.96051445 0.00631553 126.79328681
0.05123019 0.00826961 0.99865263 134.59031164
Axis 0.00345441 -0.18161923 -0.98336286
Axis point 409.76619338 -388.20747127 0.00000000
Rotation angle (degrees) 16.42968359
Shift along axis -154.95031565
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1842, steps = 60
shifted from previous position = 0.0564
rotated from previous position = 0.0263 degrees
atoms outside contour = 13634, contour level = 0.17428
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.95904291 0.27850188 -0.05170492 124.19863083
-0.27855406 0.96039963 0.00633998 126.82580378
0.05142308 0.00832231 0.99864228 134.56480395
Axis 0.00349910 -0.18203608 -0.98328563
Axis point 409.14955690 -387.72917063 0.00000000
Rotation angle (degrees) 16.45501944
Shift along axis -154.96792611
> select add #5
26928 atoms, 27312 bonds, 3456 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.8033,-0.37516,0.46256,135.36,0.53535,0.11454,-0.83683,122.45,0.26096,0.91986,0.29285,119.14
> view orient
> view matrix models
> #5,-0.035166,0.93147,0.36211,125.24,0.38197,0.34735,-0.85641,120.63,-0.92351,0.1082,-0.36801,119
> view matrix models
> #5,0.045443,0.87929,0.47412,126.85,0.5381,0.37833,-0.75321,121.42,-0.84166,0.28935,-0.45595,116.5
> view matrix models
> #5,-0.53839,0.55594,-0.63329,117.07,0.26496,0.82507,0.49905,132.97,0.79996,0.10088,-0.59152,114.4
> view matrix models
> #5,0.062774,0.63251,-0.77201,114.16,-0.19313,0.76661,0.61238,135.28,0.97916,0.11066,0.17028,123.01
> view matrix models
> #5,0.436,0.66869,-0.60229,115.42,-0.41071,0.74334,0.52798,134.73,0.80076,0.017166,0.59874,128.94
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.436,0.66869,-0.60229,-1.0843,-0.41071,0.74334,0.52798,162.82,0.80076,0.017166,0.59874,128.94
> view matrix models
> #5,0.436,0.66869,-0.60229,-6.4595,-0.41071,0.74334,0.52798,153.44,0.80076,0.017166,0.59874,128.94
> view matrix models
> #5,0.436,0.66869,-0.60229,-23.209,-0.41071,0.74334,0.52798,131.8,0.80076,0.017166,0.59874,127.52
> view matrix models
> #5,0.436,0.66869,-0.60229,-24.257,-0.41071,0.74334,0.52798,126.55,0.80076,0.017166,0.59874,127.23
> view matrix models
> #5,0.436,0.66869,-0.60229,-21.338,-0.41071,0.74334,0.52798,131.27,0.80076,0.017166,0.59874,127.52
> view matrix models
> #5,0.436,0.66869,-0.60229,-14.175,-0.41071,0.74334,0.52798,136.46,0.80076,0.017166,0.59874,127.91
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.26246,0.69276,-0.67172,-14.963,-0.22154,0.72079,0.6568,137.91,0.93917,-0.023573,0.34265,125.07
> view matrix models
> #5,0.12417,0.73499,-0.66661,-15.061,0.52188,0.52301,0.67387,138.74,0.84393,-0.43157,-0.31863,120.56
> view matrix models
> #5,0.18247,0.78307,-0.59456,-14.655,0.50451,0.44446,0.74022,140.13,0.8439,-0.43503,-0.31397,120.64
> view matrix models
> #5,0.15543,0.7977,-0.58267,-14.595,0.50368,0.44341,0.74141,140.15,0.84979,-0.40872,-0.33287,120.21
> ui mousemode right "move picked models"
> view matrix models
> #5,0.15543,0.7977,-0.58267,125.15,0.50368,0.44341,0.74141,126.52,0.84979,-0.40872,-0.33287,121.64
> select subtract #5
Nothing selected
> ui mousemode right "rotate selected models"
> select add #5
26928 atoms, 27312 bonds, 3456 residues, 1 model selected
> view matrix models
> #5,0.071827,0.76748,-0.63704,124.85,0.51813,0.51704,0.68133,125.24,0.85228,-0.37901,-0.36052,121.09
> view matrix models
> #5,0.0027857,0.76317,-0.64619,124.85,0.52192,0.55009,0.65192,124.64,0.85299,-0.33908,-0.39678,120.36
> view matrix models
> #5,0.0073106,0.73919,-0.67346,124.71,0.52106,0.572,0.63349,124.26,0.85349,-0.35554,-0.38098,120.67
> ui mousemode right "rotate slab"
> ui mousemode right zone
> ui mousemode right "contour level"
> volume #1 level 0.1701
> ui mousemode right "contour level"
> ui mousemode right "move planes"
> volume #1 region 0,0,0,79,79,79
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.15223,0.74871,-0.64518,125.16,0.50712,0.61948,0.59923,123.52,0.84833,-0.23597,-0.47399,118.68
> view matrix models
> #5,0.38698,0.81544,-0.43048,126.52,-0.90649,0.42193,-0.015652,119.52,0.16887,0.39628,0.90247,130.75
> view matrix models
> #5,0.35635,0.78586,-0.50541,125.91,-0.9119,0.41039,-0.0048304,119.74,0.20362,0.46261,0.86286,129.74
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.175, steps = 160
shifted from previous position = 24.4
rotated from previous position = 43.8 degrees
atoms outside contour = 13848, contour level = 0.17007
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.10071993 0.71499082 -0.69184075 126.56456206
-0.67336508 0.46292058 0.57644082 136.86586860
0.73241721 0.52392048 0.43482452 146.17130472
Axis -0.02639646 -0.71582491 -0.69778071
Axis point 58.04187157 0.00000000 82.83712170
Rotation angle (degrees) 95.82482894
Shift along axis -203.30837147
> view matrix models
> #5,-0.043483,0.80649,-0.58965,126.99,-0.67266,0.41275,0.61414,137.69,0.73868,0.42333,0.52454,147.98
> select subtract #5
Nothing selected
> view orient
> view
> view orient
> ui tool show "Side View"
> ui mousemode right zoom
> ui mousemode right translate
> hide #5 models
> ui mousemode right "rotate selected models"
> show #5 models
> select add #5
26928 atoms, 27312 bonds, 3456 residues, 1 model selected
> view matrix models
> #5,-0.013313,0.8007,-0.59892,126.89,-0.31406,0.56531,0.76275,137.84,0.94931,0.19825,0.24394,146.16
> view matrix models
> #5,0.96166,-0.17007,0.21512,142.63,0.044234,0.87039,0.49038,131.91,-0.27064,-0.46206,0.84454,159.65
> view matrix models
> #5,0.95795,-0.264,0.11241,142.15,-0.0051935,0.37575,0.9267,140.83,-0.28689,-0.88832,0.35858,157.23
> view matrix models
> #5,0.3355,0.75134,-0.56827,127.21,0.054917,0.58661,0.80801,137.77,0.94044,-0.3023,0.15555,148.95
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.3355,0.75134,-0.56827,123.99,0.054917,0.58661,0.80801,131.58,0.94044,-0.3023,0.15555,121.02
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.12958,-0.68062,0.72108,150.5,0.31842,0.66014,0.68032,129.22,-0.93905,0.31776,0.13118,118.25
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.12958,-0.68062,0.72108,151.94,0.31842,0.66014,0.68032,128.03,-0.93905,0.31776,0.13118,130.7
> view matrix models
> #5,-0.12958,-0.68062,0.72108,151.19,0.31842,0.66014,0.68032,123.43,-0.93905,0.31776,0.13118,127.8
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.088076,-0.63452,0.76787,151.34,0.31736,0.71282,0.62543,122.39,-0.9442,0.29878,0.13859,128.03
> view matrix models
> #5,-0.070055,-0.60272,0.79487,151.39,0.31603,0.74238,0.59076,121.76,-0.94616,0.29259,0.13847,128.08
> view matrix models
> #5,-0.13153,-0.53776,0.83277,151.41,0.31438,0.77408,0.54952,121.04,-0.94014,0.33409,0.06725,126.93
> view matrix models
> #5,-0.11782,-0.60893,0.78442,151.37,0.30522,0.72948,0.61213,122.12,-0.94497,0.31154,0.099905,127.49
> view matrix models
> #5,-0.12234,-0.63285,0.76455,151.33,0.31565,0.70553,0.6345,122.55,-0.94096,0.31895,0.11344,127.58
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.25431,-0.71724,0.64876,150.77,-0.72053,0.58798,0.36759,121.56,-0.64511,-0.37397,-0.66632,123.4
> ui mousemode right "move picked models"
> view matrix models #1,1,0,0,-1.2137,0,1,0,-3.6195,0,0,1,-6.844
> view matrix models
> #5,-0.25431,-0.71724,0.64876,156.78,-0.72053,0.58798,0.36759,98.902,-0.64511,-0.37397,-0.66632,222.94
> view matrix models #1,1,0,0,-5.8539,0,1,0,-2.0884,0,0,1,-57.881
> view matrix models
> #5,-0.25431,-0.71724,0.64876,156.82,-0.72053,0.58798,0.36759,102.25,-0.64511,-0.37397,-0.66632,217.89
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.25314,-0.76076,0.59763,156.55,-0.91178,0.39411,0.11548,101.01,-0.32339,-0.51567,-0.79341,217.11
> view matrix models
> #5,0.98672,-0.14651,-0.070176,142.61,-0.016242,-0.51879,0.85475,115.52,-0.16164,-0.84225,-0.51428,222.66
> view matrix models
> #5,0.54647,0.56554,-0.61769,131.32,0.82989,-0.26661,0.4901,108.34,0.11249,-0.78044,-0.61503,220.69
> view matrix models
> #5,0.21838,0.67687,-0.70296,129.86,0.96187,-0.02774,0.2721,103.83,0.16468,-0.73558,-0.65712,219.79
> view matrix models
> #5,0.15473,0.68759,-0.70942,129.78,0.98774,-0.092483,0.1258,102.58,0.020888,-0.72018,-0.69347,219.42
> view matrix models
> #5,0.21566,0.66811,-0.71212,129.83,0.97435,-0.099286,0.20193,103.54,0.064208,-0.73741,-0.67239,219.75
> view matrix models
> #5,0.21984,0.643,-0.73364,129.76,0.97355,-0.096609,0.20706,103.58,0.062263,-0.75975,-0.64723,220.21
> ui mousemode right "move picked models"
> view matrix models
> #5,0.21984,0.643,-0.73364,119.93,0.97355,-0.096609,0.20706,133.06,0.062263,-0.75975,-0.64723,69.668
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.14412,0.63384,-0.75992,119.79,0.98743,-0.041815,0.15239,131.99,0.064817,-0.77233,-0.6319,69.939
> view matrix models
> #5,0.12497,0.66504,-0.73628,119.85,0.98993,-0.033893,0.1374,131.75,0.066425,-0.74604,-0.66258,69.379
> select subtract #5
Nothing selected
> select add #1
2 models selected
> view matrix models
> #1,0.99577,0.091838,0.0011946,-16.891,-0.091845,0.99573,0.0096533,9.1732,-0.00030294,-0.0097222,0.99995,-56.625
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.97695,0.20197,-0.069106,-19.43,-0.20016,0.97923,0.032313,22.48,0.074197,-0.017736,0.99709,-64.947
> view matrix models
> #1,0.99316,0.0026681,0.11674,-19.798,-0.0028033,1,0.00099389,-1.8472,-0.11673,-0.0013143,0.99316,-41.708
> view matrix models
> #1,-0.50537,0.71151,0.48822,40.401,-0.51636,0.20395,-0.83173,267.42,-0.69136,-0.67243,0.26433,207.03
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,314.39,0.90068,0.15362,-0.40641,36.824,0.41263,-0.59538,0.68939,1.2589
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1807, steps = 120
shifted from previous position = 18.9
rotated from previous position = 26.4 degrees
atoms outside contour = 13725, contour level = 0.17007
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99500820 -0.05762755 -0.08147234 124.26027516
0.05672159 -0.34511918 0.93684332 134.15953617
-0.08210565 -0.93678803 -0.34012769 133.14997385
Axis -0.99814275 0.00033738 0.06091741
Axis point 0.00000000 116.10717634 23.46108391
Rotation angle (degrees) 110.18908033
Shift along axis -115.87307881
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1807, steps = 44
shifted from previous position = 0.0427
rotated from previous position = 0.0267 degrees
atoms outside contour = 13744, contour level = 0.17007
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99497299 -0.05763518 -0.08189591 124.22289225
0.05713161 -0.34496180 0.93687637 134.15030077
-0.08224800 -0.93684553 -0.33993488 133.16750740
Axis -0.99812942 0.00018756 0.06113613
Axis point 0.00000000 116.11658667 23.48265963
Rotation angle (degrees) 110.17946681
Shift along axis -115.82401618
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1807, steps = 44
shifted from previous position = 0.00354
rotated from previous position = 0.0179 degrees
atoms outside contour = 13738, contour level = 0.17007
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99498225 -0.05782469 -0.08164939 124.22418671
0.05683345 -0.34497639 0.93688913 134.15257835
-0.08234243 -0.93682848 -0.33995901 133.16514586
Axis -0.99813289 0.00036919 0.06107861
Axis point 0.00000000 116.12456618 23.47072431
Rotation angle (degrees) 110.18036583
Shift along axis -115.80917795
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1807, steps = 44
shifted from previous position = 0.0143
rotated from previous position = 0.0135 degrees
atoms outside contour = 13740, contour level = 0.17007
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99497220 -0.05772107 -0.08184501 124.21973158
0.05704536 -0.34506394 0.93684401 134.16027975
-0.08231740 -0.93680262 -0.34003631 133.17624781
Axis -0.99812927 0.00025165 0.06113839
Axis point 0.00000000 116.12276237 23.48642507
Rotation angle (degrees) 110.18570432
Shift along axis -115.81140668
Opened AF3_bsdnac_hexamer copy.cif map 5 as #4, grid size 130,112,118, pixel
1.67, shown at level 0.0955, step 1, values float32
> fitmap #5 inMap #1 resolution 5 metric correlation
Fit map AF3_bsdnac_hexamer copy.cif map 5 in map J76_003_volume_map.mrc using
105482 points
correlation = 0.6047, correlation about mean = 0.01652, overlap = 6613
steps = 72, shift = 2.6, angle = 5.18 degrees
Position of AF3_bsdnac_hexamer copy.cif map 5 (#4) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99696042 -0.07786153 0.00274030 126.19707336
-0.03082583 -0.36191162 0.93170261 132.69705066
-0.07155205 -0.92895509 -0.36321171 133.08838440
Axis -0.99888523 0.03988349 0.02525089
Axis point 0.00000000 115.36684602 21.18695517
Rotation angle (degrees) 111.35106490
Shift along axis -117.40337034
Average map value = 0.1794 for 26928 atoms, 13744 outside contour
> volume #4 level 0.3541
> close #4
Average map value = 0.1794 for 26928 atoms, 13744 outside contour
Opened AF3_bsdnac_hexamer copy.cif map 5 as #4, grid size 130,112,118, pixel
1.67, shown at level 0.0955, step 1, values float32
Correlation = 0.4679, Correlation about mean = 0.2235, Overlap = 6885
> select up
68901 atoms, 69593 bonds, 6146 residues, 7 models selected
> select up
68901 atoms, 69593 bonds, 6146 residues, 7 models selected
> select up
68901 atoms, 69593 bonds, 6146 residues, 7 models selected
> select down
2 models selected
> select down
2 models selected
> select down
2 models selected
> select down
2 models selected
> select up
68901 atoms, 69593 bonds, 6146 residues, 7 models selected
> select up
68901 atoms, 69593 bonds, 6146 residues, 7 models selected
> select down
2 models selected
> select down
2 models selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select ~sel
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select ~sel
Nothing selected
> select ~sel
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select ~sel
Nothing selected
> select ~sel
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select up
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select up
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select down
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select up
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select up
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select down
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select up
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select up
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select down
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select up
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select down
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select up
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select down
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select down
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select down
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select down
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select down
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select down
68901 atoms, 69593 bonds, 6146 residues, 15 models selected
> select subtract #3
68901 atoms, 69593 bonds, 6146 residues, 6 models selected
> select subtract #4
68901 atoms, 69593 bonds, 6146 residues, 4 models selected
> select subtract #2
26928 atoms, 27312 bonds, 3456 residues, 3 models selected
> select subtract #1
26928 atoms, 27312 bonds, 3456 residues, 1 model selected
> select add #1
26928 atoms, 27312 bonds, 3456 residues, 3 models selected
> hide #!1 models
> show #!1 models
> select subtract #1
26928 atoms, 27312 bonds, 3456 residues, 1 model selected
> view matrix models
> #5,-0.65334,0.65414,-0.38112,116.56,0.63505,0.74759,0.19449,112.2,0.41215,-0.11496,-0.90384,62.269
> view matrix models
> #5,-0.65599,-0.48096,-0.58168,122.86,-0.61914,0.78367,0.050256,111.73,0.43168,0.39311,-0.81186,59.454
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.65599,-0.48096,-0.58168,163.89,-0.61914,0.78367,0.050256,174.1,0.43168,0.39311,-0.81186,-45.397
> view matrix models
> #5,-0.65599,-0.48096,-0.58168,140.41,-0.61914,0.78367,0.050256,148.27,0.43168,0.39311,-0.81186,-2.5872
> view matrix models
> #5,-0.65599,-0.48096,-0.58168,177.91,-0.61914,0.78367,0.050256,199.75,0.43168,0.39311,-0.81186,-76.069
> ui mousemode right "move picked models"
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,289.58,0.90068,0.15362,-0.40641,-7.4736,0.41263,-0.59538,0.68939,65.598
> view matrix models
> #5,-0.65599,-0.48096,-0.58168,154.99,-0.61914,0.78367,0.050256,156.77,0.43168,0.39311,-0.81186,-13.485
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.47192,-0.50547,-0.72235,153.31,-0.67721,0.73244,-0.070098,155.83,0.56451,0.45611,-0.68796,-12.675
> view matrix models
> #5,-0.60958,-0.64614,-0.45926,157.62,-0.5107,0.76319,-0.39589,151.59,0.6063,-0.0067805,-0.79521,-10.454
> view matrix models
> #5,-0.3019,-0.7693,-0.56305,156.98,-0.56408,0.62028,-0.54504,151,0.76855,0.15306,-0.62121,-9.831
> view matrix models
> #5,-0.14984,-0.51725,-0.84261,151.62,0.9585,0.13308,-0.25213,156.32,0.24255,-0.84542,0.47585,11.201
> view matrix models
> #5,0.16169,-0.42146,-0.89232,149.94,0.69044,-0.59774,0.40744,169.9,-0.70509,-0.68197,0.19434,7.7927
> view matrix models
> #5,-0.9756,0.17304,0.13512,158.76,-0.1686,-0.98471,0.043745,169.62,0.14062,0.019897,0.98986,10.74
> view matrix models
> #5,0.11106,-0.88979,0.44264,169.15,0.51954,-0.32771,-0.78911,154.08,0.8472,0.31761,0.42588,1.0518
> view matrix models
> #5,0.74635,-0.66556,-0.0013146,161.51,0.16815,0.19047,-0.96718,148.47,0.64397,0.72163,0.25407,-3.7878
> view matrix models
> #5,0.69169,-0.70661,0.14926,163.64,0.33957,0.1358,-0.93073,149.11,0.63739,0.69445,0.33387,-2.6413
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.69169,-0.70661,0.14926,99.519,0.33957,0.1358,-0.93073,56.777,0.63739,0.69445,0.33387,105.11
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.47571,-0.86298,-0.1702,97.234,-0.012062,0.18708,-0.98227,56.202,0.87952,0.46933,0.078589,103.55
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.53406,-0.7995,-0.27493,95.459,-0.031881,0.30591,-0.95153,55.68,0.84485,0.51694,0.13789,103.93
> ui mousemode right "move picked models"
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,282.51,0.90068,0.15362,-0.40641,-6.28,0.41263,-0.59538,0.68939,60.118
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.92042,-0.302,0.24824,97.325,0.31812,0.20952,-0.92461,56.313,0.22723,0.93,0.28892,103.28
> fitmap #5 inMap #1 resolution 5 envelope false
Fit map AF3_bsdnac_hexamer copy.cif map 5 in map J76_003_volume_map.mrc using
1718080 points
correlation = 0.4035, correlation about mean = 0.3829, overlap = 6678
steps = 228, shift = 31, angle = 29.4 degrees
Position of AF3_bsdnac_hexamer copy.cif map 5 (#4) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.15309159 0.72950843 -0.66661864 129.93716689
-0.64895810 -0.58294513 -0.48890526 131.95238742
-0.74526261 0.35776029 0.56266440 127.65804660
Axis 0.52275284 0.04855678 -0.85110029
Axis point 144.23660089 25.27897381 0.00000000
Rotation angle (degrees) 125.92219892
Shift along axis -34.31759478
Average map value = 0.1743 for 26928 atoms, 14285 outside contour
> fitmap #5 inMap #1 resolution 5 envelope false
Fit map AF3_bsdnac_hexamer copy.cif map 5 in map J76_003_volume_map.mrc using
1718080 points
correlation = 0.4035, correlation about mean = 0.3829, overlap = 6678
steps = 40, shift = 0.0329, angle = 0.0965 degrees
Position of AF3_bsdnac_hexamer copy.cif map 5 (#4) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.15285853 0.72845952 -0.66781809 129.94309867
-0.64916648 -0.58353071 -0.48792908 131.94253088
-0.74512895 0.35894100 0.56208915 127.65360013
Axis 0.52309634 0.04775352 -0.85093468
Axis point 144.24031650 25.22650937 0.00000000
Rotation angle (degrees) 125.95502627
Shift along axis -34.35139499
Average map value = 0.1743 for 26928 atoms, 14290 outside contour
> fitmap #5 inMap #1 resolution 5 envelope false
Fit map AF3_bsdnac_hexamer copy.cif map 5 in map J76_003_volume_map.mrc using
1718080 points
correlation = 0.4035, correlation about mean = 0.3829, overlap = 6678
steps = 40, shift = 0.0684, angle = 0.0223 degrees
Position of AF3_bsdnac_hexamer copy.cif map 5 (#4) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.15284999 0.72822321 -0.66807772 129.96308242
-0.64925144 -0.58365934 -0.48766212 131.89187452
-0.74505668 0.35921127 0.56201229 127.68446641
Axis 0.52314455 0.04755271 -0.85091628
Axis point 144.24237855 25.18061867 0.00000000
Rotation angle (degrees) 125.96199709
Shift along axis -34.38749669
Average map value = 0.1743 for 26928 atoms, 14286 outside contour
> view matrix models
> #5,0.91383,-0.28154,-0.29266,82.548,-0.1776,0.37102,-0.91148,79.732,0.3652,0.88492,0.28904,121.35
> view matrix models
> #5,0.92986,-0.28041,-0.23818,83.156,-0.19787,0.16463,-0.9663,80.686,0.31017,0.94566,0.097603,118.71
> ui mousemode right translate
> ui mousemode right "move picked models"
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,234.1,0.90068,0.15362,-0.40641,8.7604,0.41263,-0.59538,0.68939,-50.075
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,232.98,0.90068,0.15362,-0.40641,8.7783,0.41263,-0.59538,0.68939,-52.658
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,225.68,0.90068,0.15362,-0.40641,8.8964,0.41263,-0.59538,0.68939,-69.425
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,218.52,0.90068,0.15362,-0.40641,8.9287,0.41263,-0.59538,0.68939,-85.05
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.88283,-0.46195,0.084936,88.366,0.36254,0.55522,-0.74853,79.593,0.29862,0.69161,0.65764,127.2
> view matrix models
> #5,0.8836,-0.45886,0.093218,88.439,0.34761,0.50946,-0.78715,79.508,0.31371,0.72794,0.60967,126.35
> view matrix models
> #5,0.88882,-0.45028,0.085096,88.272,0.33604,0.51419,-0.7891,79.463,0.31156,0.72997,0.60834,126.32
> view matrix models
> #5,0.86353,-0.49102,0.11495,88.961,0.43133,0.60106,-0.67282,80.047,0.26128,0.63058,0.73082,128.56
> view matrix models
> #5,0.92465,-0.37957,0.030862,87.059,0.29671,0.66725,-0.68319,79.582,0.23872,0.64087,0.72959,128.5
> view matrix models
> #5,0.96096,-0.27411,-0.037583,85.414,0.16767,0.68502,-0.70897,79.298,0.22008,0.67499,0.70424,127.96
> view matrix models
> #5,0.94856,-0.31655,0.0049906,86.249,0.21729,0.63951,-0.73743,79.253,0.23024,0.70059,0.6754,127.42
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right pivot
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.95227,-0.30407,0.02703,86.407,0.21028,0.58919,-0.78015,79.146,0.2213,0.7486,0.62501,126.48
> view matrix models
> #5,0.95488,-0.29695,0.0036747,86.077,0.19881,0.63,-0.75072,79.193,0.22061,0.71758,0.66062,127.13
> view matrix models
> #5,0.8381,0.055515,0.54269,89.828,0.32429,0.74924,-0.57747,80.16,-0.43866,0.65996,0.60994,127.76
> view matrix models
> #5,0.82185,0.091515,0.56231,89.802,0.37624,0.65396,-0.65634,79.902,-0.42779,0.75097,0.50302,125.8
> view matrix models
> #5,0.23553,-0.82384,-0.51557,84.874,-0.13687,0.49709,-0.85684,79.362,0.96218,0.27238,0.0043164,121.97
> view matrix models
> #5,-0.24284,-0.83557,-0.49281,85.796,-0.14061,0.53297,-0.83437,79.356,0.95982,-0.13333,-0.24691,122.13
> view matrix models
> #5,-0.21529,-0.7923,-0.57088,84.523,-0.19622,0.60777,-0.76949,79.611,0.95663,-0.053652,-0.28631,121.07
> view matrix models
> #5,-0.65365,-0.0047569,-0.75678,76.879,-0.3115,-0.90965,0.27477,103.49,-0.68972,0.41534,0.59311,129.72
> view matrix models
> #5,-0.62686,0.12071,-0.76973,75.741,-0.3099,-0.94504,0.10418,101.76,-0.71485,0.30385,0.62982,131.03
> view matrix models
> #5,-0.6683,0.12648,-0.73306,76.175,-0.14616,-0.98856,-0.037312,100.25,-0.72939,0.082208,0.67914,133.31
> view matrix models
> #5,-0.6724,0.11537,-0.73114,76.287,-0.137,-0.99011,-0.030237,100.33,-0.7274,0.079837,0.68156,133.35
> view matrix models
> #5,-0.44524,0.032169,-0.89483,74.739,-0.028428,-0.99936,-0.021782,100.37,-0.89496,0.01574,0.44587,131.28
> view matrix models
> #5,-0.445,-0.091537,-0.89084,75.726,-0.12397,-0.97889,0.16251,102.48,-0.88691,0.18276,0.42426,129.75
> ui mousemode right "move picked models"
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,275.95,0.90068,0.15362,-0.40641,-7.9716,0.41263,-0.59538,0.68939,61.663
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,271.97,0.90068,0.15362,-0.40641,9.6924,0.41263,-0.59538,0.68939,65.441
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,274.14,0.90068,0.15362,-0.40641,17.414,0.41263,-0.59538,0.68939,65.439
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,273.29,0.90068,0.15362,-0.40641,21.013,0.41263,-0.59538,0.68939,66.167
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.445,-0.091537,-0.89084,121.78,-0.12397,-0.97889,0.16251,191.51,-0.88691,0.18276,0.42426,48.077
> view matrix models
> #5,-0.445,-0.091537,-0.89084,129.42,-0.12397,-0.97889,0.16251,209.5,-0.88691,0.18276,0.42426,28.194
> hide #5 models
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view orient
> show #5 models
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.445,-0.091537,-0.89084,77.556,-0.12397,-0.97889,0.16251,154.24,-0.88691,0.18276,0.42426,147.92
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.49682,-0.19262,-0.84621,78.908,-0.049539,-0.96717,0.24924,155.08,-0.86644,0.16575,0.47096,148.57
> view matrix models
> #5,-0.55391,-0.32386,-0.76701,80.899,0.038608,-0.93025,0.3649,156.04,-0.83168,0.17251,0.52778,149.14
> view matrix models
> #5,-0.55394,-0.32384,-0.767,80.899,0.039052,-0.93035,0.3646,156.04,-0.83164,0.17201,0.528,149.14
> view matrix models
> #5,-0.94398,0.19629,-0.2653,83.262,-0.25778,-0.94051,0.22135,154.79,-0.20606,0.27734,0.93841,152.39
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.94398,0.19629,-0.2653,78.38,-0.25778,-0.94051,0.22135,156.5,-0.20606,0.27734,0.93841,147.68
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.96264,0.14529,-0.22852,79.22,-0.20146,-0.94815,0.24583,156.78,-0.18095,0.28269,0.94199,147.65
> view matrix models
> #5,-0.95822,0.15919,-0.23765,79.002,-0.20752,-0.95869,0.19454,156.27,-0.19687,0.23572,0.95167,148.14
> view matrix models
> #5,0.60057,0.41205,0.68522,86.008,-0.46707,-0.51479,0.71892,159.32,0.64897,-0.75181,-0.11671,142.17
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.60057,0.41205,0.68522,72.941,-0.46707,-0.51479,0.71892,155.78,0.64897,-0.75181,-0.11671,148.32
> view matrix models
> #5,0.60057,0.41205,0.68522,80.142,-0.46707,-0.51479,0.71892,156.67,0.64897,-0.75181,-0.11671,147.39
> view matrix models
> #5,0.60057,0.41205,0.68522,73.607,-0.46707,-0.51479,0.71892,158.58,0.64897,-0.75181,-0.11671,141.95
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.89097,0.15156,0.42802,72.242,-0.31019,-0.48525,0.81751,159.32,0.3316,-0.86114,-0.38533,140.02
> view matrix models
> #5,0.6039,-0.51564,-0.6078,65.562,0.15171,-0.67426,0.72275,159.1,-0.78249,-0.52867,-0.32895,139.47
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.6039,-0.51564,-0.6078,76.213,0.15171,-0.67426,0.72275,154.97,-0.78249,-0.52867,-0.32895,150.69
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.3007,-0.44678,-0.84259,74.02,0.15848,-0.89461,0.4178,153.08,-0.94046,-0.007901,0.33982,154.73
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.3007,-0.44678,-0.84259,49.93,0.15848,-0.89461,0.4178,229.9,-0.94046,-0.007901,0.33982,165.83
> view matrix models
> #5,-0.3007,-0.44678,-0.84259,49.692,0.15848,-0.89461,0.4178,228.72,-0.94046,-0.007901,0.33982,171.36
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.3384,-0.4162,-0.84396,49.488,0.13862,-0.90913,0.39276,228.57,-0.93074,0.015922,0.36534,171.46
> view matrix models
> #5,-0.37966,-0.4266,-0.8209,49.885,0.1257,-0.9029,0.41107,228.75,-0.91655,0.052877,0.39642,171.53
> view matrix models
> #5,-0.40825,-0.43408,-0.80306,50.184,0.20754,-0.90081,0.38141,228.29,-0.88897,-0.010953,0.45784,172.7
> view matrix models
> #5,-0.42531,-0.43985,-0.79097,50.389,0.25772,-0.89664,0.36003,227.95,-0.86758,-0.050726,0.49471,173.4
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.42531,-0.43985,-0.79097,93.042,0.25772,-0.89664,0.36003,100.61,-0.86758,-0.050726,0.49471,112.99
> view matrix models
> #5,-0.42531,-0.43985,-0.79097,89.68,0.25772,-0.89664,0.36003,110.82,-0.86758,-0.050726,0.49471,118.36
> ui mousemode right "rotate selected models"
> fitmap #5 inMap #1 resolution 5 envelope false
Fit map AF3_bsdnac_hexamer copy.cif map 5 in map J76_003_volume_map.mrc using
1718080 points
correlation = 0.3967, correlation about mean = 0.3746, overlap = 6557
steps = 144, shift = 11.6, angle = 17 degrees
Position of AF3_bsdnac_hexamer copy.cif map 5 (#4) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.09694432 -0.79752540 0.59544524 129.89752590
0.97081590 0.20762664 0.12003193 135.01168002
-0.21935881 0.56643129 0.79437856 114.80094016
Axis 0.22347335 0.40790155 0.88525476
Axis point 15.29323638 93.51624555 0.00000000
Rotation angle (degrees) 87.16414722
Shift along axis 185.72818753
Average map value = 0.171 for 26928 atoms, 14402 outside contour
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.68605,-0.3773,-0.62208,80.569,0.29785,-0.92574,0.233,112.21,-0.6638,-0.025434,0.74748,118.51
> view matrix models
> #5,-0.73239,-0.34736,-0.58561,80.822,0.23445,-0.93614,0.26206,112.7,-0.63924,0.054635,0.76706,118.1
> view matrix models
> #5,-0.72387,-0.21461,-0.65571,78.984,0.14669,-0.97653,0.15767,111.9,-0.67416,0.017946,0.73836,118.09
> ui mousemode right translate
> view orient
> ui mousemode right "move picked models"
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,241.93,0.90068,0.15362,-0.40641,118.95,0.41263,-0.59538,0.68939,123.64
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,276.23,0.90068,0.15362,-0.40641,15.547,0.41263,-0.59538,0.68939,54.583
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.93443,0.048402,-0.35285,80.769,-0.12242,-0.97401,0.19058,112.58,-0.33446,0.22128,0.91606,118.22
> view matrix models
> #5,-0.96442,-0.033808,-0.26221,82.488,-0.010335,-0.98621,0.16517,112.24,-0.26417,0.16201,0.95077,118.99
> view matrix models
> #5,-0.91979,0.10326,-0.37857,80.034,-0.16909,-0.97489,0.14491,112.11,-0.3541,0.1973,0.91416,118.4
> view matrix models
> #5,-0.94487,0.27133,-0.18331,81.065,-0.30626,-0.93038,0.2015,112.59,-0.11588,0.24653,0.96218,118.3
> ui mousemode right translate
> select subtract #5
Nothing selected
> select add #5
26928 atoms, 27312 bonds, 3456 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.93444,0.19027,-0.30103,80.295,-0.25421,-0.94837,0.18967,112.53,-0.24939,0.25376,0.93456,118.08
> view matrix models
> #5,-0.95591,0.14861,-0.2533,81.194,-0.19299,-0.968,0.16039,112.26,-0.22136,0.20221,0.954,118.67
> view matrix models
> #5,-0.95851,0.24512,-0.1455,81.722,-0.27022,-0.94386,0.19003,112.52,-0.090754,0.22147,0.97094,118.57
> view matrix models
> #5,-0.92056,0.35045,-0.17247,80.561,-0.36082,-0.93209,0.031919,110.69,-0.14957,0.091614,0.9845,119.78
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.87665,0.47781,-0.056396,80.895,-0.48001,-0.87658,0.034751,110.44,-0.032831,0.057534,0.9978,120.06
> ui mousemode right translate
> select subtract #5
Nothing selected
> select add #1
2 models selected
> transparency #1.1 50
> select subtract #1
Nothing selected
> ui mousemode right "rotate selected models"
> select add #5
26928 atoms, 27312 bonds, 3456 residues, 1 model selected
> view matrix models
> #5,-0.50193,0.69046,0.52089,85.574,-0.78529,-0.61621,0.060108,109.12,0.36248,-0.37887,0.85151,121.2
> select subtract #5
Nothing selected
> fitmap #5 inMap #1
Fit molecule AF3_bsdnac_hexamer copy.cif (#5) to map J76_003_volume_map.mrc
(#1) using 26928 atoms
average map value = 0.1682, steps = 108
shifted from previous position = 12.8
rotated from previous position = 20.6 degrees
atoms outside contour = 14489, contour level = 0.17007
Position of AF3_bsdnac_hexamer copy.cif (#5) relative to
J76_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.42188730 -0.79532449 0.43528159 134.12942873
-0.28484017 -0.33952186 -0.89643236 135.92275012
0.86074223 -0.50217911 -0.08330040 116.10567221
Axis 0.51023607 -0.55062416 0.66066041
Axis point -4.33200326 131.29051681 0.00000000
Rotation angle (degrees) 157.27279955
Shift along axis 70.30174379
> ui mousemode right "tape measure"
> view orient
> ui mousemode right "move picked models"
> view matrix models
> #5,-0.2341,0.67709,0.69767,76.791,-0.77356,-0.5644,0.28819,182.93,0.5889,-0.47222,0.6559,-9.0192
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,284.21,0.90068,0.15362,-0.40641,-53.542,0.41263,-0.59538,0.68939,100.88
> view matrix models
> #5,-0.2341,0.67709,0.69767,72.508,-0.77356,-0.5644,0.28819,172.43,0.5889,-0.47222,0.6559,9.831
> view matrix models
> #5,-0.2341,0.67709,0.69767,6.5161,-0.77356,-0.5644,0.28819,178.89,0.5889,-0.47222,0.6559,-53.185
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,280.36,0.90068,0.15362,-0.40641,-13.311,0.41263,-0.59538,0.68939,22.951
> view matrix models
> #5,-0.2341,0.67709,0.69767,14.052,-0.77356,-0.5644,0.28819,29.904,0.5889,-0.47222,0.6559,230.2
> view matrix models
> #1,-0.13606,-0.78862,-0.59964,306.06,0.90068,0.15362,-0.40641,39.102,0.41263,-0.59538,0.68939,-54.849
> view matrix models
> #5,-0.2341,0.67709,0.69767,14.71,-0.77356,-0.5644,0.28819,30.469,0.5889,-0.47222,0.6559,229.14
> view matrix models
> #5,-0.2341,0.67709,0.69767,3.9484,-0.77356,-0.5644,0.28819,53.192,0.5889,-0.47222,0.6559,169.41
> ui mousemode right "rotate selected models"
> select add #5
26928 atoms, 27312 bonds, 3456 residues, 1 model selected
> view matrix models
> #5,-0.18375,0.76462,0.61773,2.2894,-0.75001,-0.51528,0.4147,54.267,0.63539,-0.3871,0.66815,168.85
> view matrix models
> #5,-0.15826,0.80628,0.56997,1.3844,-0.73252,-0.48294,0.47977,54.76,0.66209,-0.34159,0.66705,168.46
> view matrix models
> #5,-0.51994,-0.41427,0.74702,13.167,-0.54245,-0.51542,-0.66339,41.433,0.65986,-0.75015,0.043263,164.29
> view matrix models
> #5,-0.51016,-0.40647,0.75797,13.224,-0.64959,-0.3955,-0.64931,40.811,0.56371,-0.82363,-0.062269,163.73
> view matrix models
> #5,-0.43076,-0.46428,0.77388,13.756,-0.65981,-0.42302,-0.62105,41.363,0.61571,-0.77814,-0.12412,162.6
> view matrix models
> #5,-0.11049,0.75037,0.65172,2.7079,-0.54624,-0.59366,0.59092,56.68,0.83031,-0.29071,0.47548,165.64
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.11049,0.75037,0.65172,108.25,-0.54624,-0.59366,0.59092,139.6,0.83031,-0.29071,0.47548,4.6402
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.11049,0.75037,0.65172,110.14,-0.54624,-0.59366,0.59092,133.13,0.83031,-0.29071,0.47548,0.61424
> hide #5 models
> show #5 models
> select subtract #5
Nothing selected
> select add #5
26928 atoms, 27312 bonds, 3456 residues, 1 model selected
> view matrix models
> #5,-0.11049,0.75037,0.65172,112.87,-0.54624,-0.59366,0.59092,130.01,0.83031,-0.29071,0.47548,8.9734
> view matrix models
> #5,-0.11049,0.75037,0.65172,108.59,-0.54624,-0.59366,0.59092,130.16,0.83031,-0.29071,0.47548,7.8523
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.95714,0.15241,-0.24627,103.66,-0.24213,-0.88768,0.39166,129.71,-0.15892,0.4345,0.88654,8.307
> view matrix models
> #5,-0.96333,0.13726,-0.23056,103.97,-0.21979,-0.89656,0.38455,129.67,-0.15393,0.42112,0.89385,8.4883
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.96333,0.13726,-0.23056,109.66,-0.21979,-0.89656,0.38455,127.71,-0.15393,0.42112,0.89385,14.887
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.61613,0.25363,-0.74569,102.35,-0.77488,-0.025463,0.63159,124.63,0.1412,0.96697,0.21222,2.424
> view matrix models
> #5,-0.28686,-0.33367,-0.89799,104.65,-0.48614,0.85842,-0.16367,108.27,0.82546,0.38959,-0.40845,-1.2419
> view matrix models
> #5,-0.24252,-0.61885,-0.74713,108.53,-0.3925,0.76687,-0.50779,104.84,0.8872,0.1701,-0.42888,0.11637
> view matrix models
> #5,-0.24231,-0.59821,-0.76382,108.18,-0.39767,0.77935,-0.48422,105.03,0.88495,0.18642,-0.42674,0.019907
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.24231,-0.59821,-0.76382,109.01,-0.39767,0.77935,-0.48422,102.22,0.88495,0.18642,-0.42674,6.0965
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.99031,0.098075,0.09834,114.66,0.071559,0.96715,-0.24392,103.04,-0.11903,-0.23452,-0.9648,4.2055
> view matrix models
> #5,-0.98424,0.12184,0.12814,114.82,0.087466,0.9653,-0.24605,103.01,-0.15367,-0.23096,-0.96075,4.2667
> view matrix models
> #5,-0.98396,0.13216,0.11984,114.65,0.10084,0.96613,-0.23753,103.09,-0.14717,-0.22164,-0.96396,4.1505
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.98396,0.13216,0.11984,116.31,0.10084,0.96613,-0.23753,115.97,-0.14717,-0.22164,-0.96396,10.03
> select subtract #5
Nothing selected
> ui mousemode right zoom
> ui mousemode right translate
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202406042103 (2024-06-04)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/yuanyuan/J76_003_volume_map.mrc
Opened J76_003_volume_map.mrc as #1, grid size 80,80,80, pixel 3.31, shown at
level 0.367, step 1, values float32
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16R000R0B/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 13 days, 21 hours, 56 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2422HE:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8rc202406042103
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.46
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.12.1
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 12 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 , 12 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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