![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16766 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-13.6.7-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 0x00000001fdee2100 (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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 55)
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"version" : 2,
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"deployVersion" : 210,
"modelCode" : "Mac14,9",
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"captureTime" : "2025-01-31 17:24:48.5431 +0000",
"incident" : "58A6F2E2-3D42-4DA9-9F59-BE235DE6D37B",
"pid" : 53348,
"translated" : false,
"cpuType" : "ARM-64",
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"bug_type" : "309",
"procLaunch" : "2025-01-31 11:12:18.9265 +0000",
"procStartAbsTime" : 2927940174049,
"procExitAbsTime" : 3464323429112,
"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":"A092BB52-F415-5C5B-924C-ED9DA992FBBE","thirdParty":true},
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B97F65CB-AB70-2664-1BC6-992D64AA7B45",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 33575,
"sleepWakeUUID" : "B4F333E0-E44B-4D98-ADFA-21365CB51A09",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4368039936\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1045b0000-1045b4000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":53348},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4368039936\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1045b0000-1045b4000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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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: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/hmed/Downloads/cryosparc_P17_J25_006_volume_map_sharp.mrc
Opened cryosparc_P17_J25_006_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 1.66, shown at level 0.0681, step 2, values float32
> open /Users/hmed/Downloads/cryosparc_P17_J25_006_volume_map_sharp.mrc
Opened cryosparc_P17_J25_006_volume_map_sharp.mrc as #2, grid size
280,280,280, pixel 1.66, shown at level 0.0681, step 2, values float32
> volume #1 level 0.2092
> volume #1 step 1
> volume #1 level 0.2447
> close #2
> open /Users/hmed/Downloads/cryosparc_P17_J24_006_volume_map_sharp.mrc
Opened cryosparc_P17_J24_006_volume_map_sharp.mrc as #2, grid size
280,280,280, pixel 1.66, shown at level 0.0569, step 2, values float32
> volume #2 step 1
> volume #2 level 0.3016
> volume #2 level 0.2571
> volume #2 level 0.226
> open /Users/hmed/Downloads/cryosparc_P17_J31_008_volume_map_sharp.mrc
Opened cryosparc_P17_J31_008_volume_map_sharp.mrc as #3, grid size
280,280,280, pixel 1.66, shown at level 0.0673, step 2, values float32
> volume #3 step 1
> volume #3 level 0.2163
> volume #3 level 0.2402
> volume #3 level 0.276
> volume style mesh meshLighting false squareMesh false
> color #005FFF transparency 20 target s
> lighting model all directional false
> style ball
Changed 0 atom styles
> size ballScale 0 stickRadius 0.08
Ball scale must be greater than 0.
> color byelement target a
> color C #E0E000 target a
> set bgColor black
> camera ortho
> open /Users/hmed/Downloads/7z3z.pdb
7z3z.pdb title:
Locked wuhan sars-COV2 prefusion spike ectodomain with lipid bound [more
info...]
Chain information for 7z3z.pdb #4
---
Chain | Description | UniProt
A B C | spike glycoprotein | SPIKE_SARS2 1-1208
Non-standard residues in 7z3z.pdb #4
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
STE — stearic acid
> volume flip #3
Opened cryosparc_P17_J31_008_volume_map_sharp.mrc z flip as #5, grid size
280,280,280, pixel 1.66, shown at step 1, values float32
> select add #4
52020 atoms, 52716 bonds, 15 pseudobonds, 3336 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,4.4905,0,1,0,10.782,0,0,1,-15.807
> view matrix models #4,1,0,0,6.8287,0,1,0,10.241,0,0,1,-12.141
> ui tool show "Fit in Map"
> fitmap #4 inMap #5
Fit molecule 7z3z.pdb (#4) to map cryosparc_P17_J31_008_volume_map_sharp.mrc z
flip (#5) using 52020 atoms
average map value = 0.1455, steps = 80
shifted from previous position = 2.74
rotated from previous position = 7.59 degrees
atoms outside contour = 41592, contour level = 0.27597
Position of 7z3z.pdb (#4) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc z flip (#5) coordinates:
Matrix rotation and translation
0.99123746 -0.13202663 -0.00415479 40.65284166
0.13202796 0.99124599 0.00004785 -19.72268286
0.00411210 -0.00059597 0.99999137 -12.34568028
Axis -0.00243701 -0.03129206 0.99950731
Axis point 171.82981474 296.29149864 0.00000000
Rotation angle (degrees) 7.59051950
Shift along axis -11.82150570
> select subtract #4
Nothing selected
> select add #4
52020 atoms, 52716 bonds, 15 pseudobonds, 3336 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.9515,-0.30729,-0.015128,92.697,0.30536,0.94923,-0.075585,-34.509,0.037587,0.067299,0.99702,-35.202
> view matrix models
> #4,0.93538,-0.35331,-0.015242,107.1,0.35034,0.93167,-0.096224,-36.595,0.048197,0.084666,0.99524,-41.31
> view matrix models
> #4,0.93421,-0.35252,0.054634,92.065,0.35634,0.92931,-0.096981,-37.303,-0.016584,0.11007,0.99379,-31.578
> view matrix models
> #4,0.92343,-0.38135,0.043004,103.75,0.38375,0.91853,-0.095036,-41.701,-0.0032591,0.10426,0.99454,-33.545
> fitmap #4 inMap #5
Fit molecule 7z3z.pdb (#4) to map cryosparc_P17_J31_008_volume_map_sharp.mrc z
flip (#5) using 52020 atoms
average map value = 0.1456, steps = 132
shifted from previous position = 4.7
rotated from previous position = 16.2 degrees
atoms outside contour = 41576, contour level = 0.27597
Position of 7z3z.pdb (#4) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc z flip (#5) coordinates:
Matrix rotation and translation
0.99124119 -0.13198337 -0.00461389 40.73396552
0.13198555 0.99125163 0.00016898 -19.73470931
0.00455122 -0.00077647 0.99998934 -12.40534785
Axis -0.00357948 -0.03469929 0.99939139
Axis point 172.31699301 296.87243324 0.00000000
Rotation angle (degrees) 7.58892780
Shift along axis -11.85882381
> view matrix models
> #4,0.39455,-0.91886,0.0053496,360.08,0.91797,0.3939,-0.046588,-57.357,0.040701,0.023292,0.9989,-26.219
> view matrix models
> #4,0.39058,-0.92045,-0.015168,365.83,0.92,0.3897,0.041569,-75.959,-0.032351,-0.03019,0.99902,3.2607
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.39058,-0.92045,-0.015168,362.78,0.92,0.3897,0.041569,-64.095,-0.032351,-0.03019,0.99902,-2.6205
> select add #5
52020 atoms, 52716 bonds, 15 pseudobonds, 3336 residues, 5 models selected
> select subtract #4
2 models selected
> select subtract #5
Nothing selected
> show #!3 models
> hide #!5 models
> select add #4
52020 atoms, 52716 bonds, 15 pseudobonds, 3336 residues, 3 models selected
> view matrix models
> #4,0.39058,-0.92045,-0.015168,363.22,0.92,0.3897,0.041569,-63.973,-0.032351,-0.03019,0.99902,19.252
> view matrix models
> #4,0.39058,-0.92045,-0.015168,358.08,0.92,0.3897,0.041569,-67.604,-0.032351,-0.03019,0.99902,50.933
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.97089,-0.21244,-0.11061,79.23,-0.20714,-0.97662,0.057524,508.65,-0.12024,-0.032938,-0.9922,503.43
> view matrix models
> #4,0.96893,-0.2151,-0.12213,82.799,-0.20787,-0.9757,0.069272,506.06,-0.13406,-0.041733,-0.99009,508.25
> view matrix models
> #4,0.97009,-0.214,-0.11457,80.635,-0.20744,-0.97598,0.066534,506.62,-0.12606,-0.040778,-0.99118,506.38
> view matrix models
> #4,0.96962,-0.21019,-0.12513,82.157,-0.20715,-0.97761,0.036985,513.33,-0.1301,-0.0099409,-0.99145,500.3
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.96962,-0.21019,-0.12513,74.913,-0.20715,-0.97761,0.036985,490.28,-0.1301,-0.0099409,-0.99145,507.04
> view matrix models
> #4,0.96962,-0.21019,-0.12513,81.69,-0.20715,-0.97761,0.036985,489.66,-0.1301,-0.0099409,-0.99145,507.75
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.98248,-0.17587,-0.061706,57.037,-0.17798,-0.98356,-0.030412,498.76,-0.055344,0.040861,-0.99763,479.8
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.98248,-0.17587,-0.061706,65.965,-0.17798,-0.98356,-0.030412,498.79,-0.055344,0.040861,-0.99763,484.56
> view matrix models
> #4,0.98248,-0.17587,-0.061706,68.348,-0.17798,-0.98356,-0.030412,500.11,-0.055344,0.040861,-0.99763,483.26
> fitmap #4 inMap #3
Fit molecule 7z3z.pdb (#4) to map cryosparc_P17_J31_008_volume_map_sharp.mrc
(#3) using 52020 atoms
average map value = 0.234, steps = 124
shifted from previous position = 8.27
rotated from previous position = 7.1 degrees
atoms outside contour = 34918, contour level = 0.27597
Position of 7z3z.pdb (#4) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.96074048 -0.27744860 -0.00009584 79.01524467
-0.27744858 -0.96074047 0.00018826 509.55919055
-0.00014431 -0.00015428 -0.99999998 472.88917159
Axis -0.99013663 0.14010514 0.00006114
Axis point 0.00000000 260.39060995 236.42472826
Rotation angle (degrees) 179.99008895
Shift along axis -6.81511248
> select subtract #4
Nothing selected
> show surfaces
> hide surfaces
> lighting soft
> volume #!3 style surface
> select ::name="STE"
165 atoms, 162 bonds, 3 residues, 1 model selected
> open /Users/hmed/Downloads/6zb4.pdb
6zb4.pdb title:
Sars cov-2 spike protein, closed conformation, C1 symmetry [more info...]
Chain information for 6zb4.pdb #6
---
Chain | Description | UniProt
A B C | spike glycoprotein | SPIKE_SARS2 1-1210
Non-standard residues in 6zb4.pdb #6
---
EIC — linoleic acid (9,12-linoleic acid)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> mmaker #6 to #4
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 7z3z.pdb, chain C (#4) with 6zb4.pdb, chain A (#6), sequence
alignment score = 5721.5
RMSD between 995 pruned atom pairs is 1.246 angstroms; (across all 1046 pairs:
1.453)
> close #5
> fitmap #6 inMap #3
Fit molecule 6zb4.pdb (#6) to map cryosparc_P17_J31_008_volume_map_sharp.mrc
(#3) using 24841 atoms
average map value = 0.2539, steps = 72
shifted from previous position = 1.12
rotated from previous position = 0.327 degrees
atoms outside contour = 15789, contour level = 0.27597
Position of 6zb4.pdb (#6) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.19188740 0.86315151 0.46706391 56.13621168
-0.91456276 -0.01537571 0.40415163 292.81506960
0.35602553 -0.50471087 0.78645582 168.34451145
Axis -0.45450917 0.05552871 -0.88900955
Axis point 151.57117030 160.54948454 0.00000000
Rotation angle (degrees) 91.06096338
Shift along axis -158.91465688
> select add #6
25006 atoms, 25578 bonds, 32 pseudobonds, 3166 residues, 4 models selected
> view matrix models
> #4,0.96074,-0.27745,-9.5839e-05,81.372,-0.27745,-0.96074,0.00018826,505.93,-0.00014431,-0.00015428,-1,478.7,#6,0.19189,0.86315,0.46706,58.493,-0.91456,-0.015376,0.40415,289.18,0.35603,-0.50471,0.78646,174.15
> view matrix models
> #4,0.96074,-0.27745,-9.5839e-05,79.686,-0.27745,-0.96074,0.00018826,506.7,-0.00014431,-0.00015428,-1,478.24,#6,0.19189,0.86315,0.46706,56.807,-0.91456,-0.015376,0.40415,289.96,0.35603,-0.50471,0.78646,173.7
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99014,-0.139,-0.017591,47.779,-0.13944,-0.98985,-0.027544,488.2,-0.013583,0.029726,-0.99947,474.81,#6,0.32527,0.84773,0.419,50.411,-0.86826,0.092208,0.48747,262.03,0.37461,-0.52236,0.76604,176.33
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99014,-0.139,-0.017591,46.579,-0.13944,-0.98985,-0.027544,492.19,-0.013583,0.029726,-0.99947,474.63,#6,0.32527,0.84773,0.419,49.211,-0.86826,0.092208,0.48747,266.03,0.37461,-0.52236,0.76604,176.14
> view matrix models
> #4,0.99014,-0.139,-0.017591,46.849,-0.13944,-0.98985,-0.027544,492.03,-0.013583,0.029726,-0.99947,475.34,#6,0.32527,0.84773,0.419,49.482,-0.86826,0.092208,0.48747,265.86,0.37461,-0.52236,0.76604,176.86
> fitmap #6 inMap #3
Fit molecule 6zb4.pdb (#6) to map cryosparc_P17_J31_008_volume_map_sharp.mrc
(#3) using 24841 atoms
average map value = 0.2538, steps = 104
shifted from previous position = 6.44
rotated from previous position = 8.32 degrees
atoms outside contour = 15797, contour level = 0.27597
Position of 6zb4.pdb (#6) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.19188362 0.86319372 0.46698746 56.14590728
-0.91461024 -0.01527652 0.40404794 292.82222086
0.35590559 -0.50464169 0.78655449 168.33599498
Axis -0.45442191 0.05555036 -0.88905280
Axis point 151.60223110 160.54012210 0.00000000
Rotation angle (degrees) 91.05540224
Shift along axis -158.90713935
> view matrix models
> #4,0.99014,-0.139,-0.017591,47.631,-0.13944,-0.98985,-0.027544,492.11,-0.013583,0.029726,-0.99947,478.51,#6,0.19188,0.86319,0.46699,56.928,-0.91461,-0.015277,0.40405,292.91,0.35591,-0.50464,0.78655,171.51
> view matrix models
> #4,0.99014,-0.139,-0.017591,46.443,-0.13944,-0.98985,-0.027544,494.15,-0.013583,0.029726,-0.99947,477.13,#6,0.19188,0.86319,0.46699,55.74,-0.91461,-0.015277,0.40405,294.94,0.35591,-0.50464,0.78655,170.12
> view matrix models
> #4,0.99014,-0.139,-0.017591,45.64,-0.13944,-0.98985,-0.027544,492.82,-0.013583,0.029726,-0.99947,479.89,#6,0.19188,0.86319,0.46699,54.937,-0.91461,-0.015277,0.40405,293.61,0.35591,-0.50464,0.78655,172.89
> view matrix models
> #4,0.99014,-0.139,-0.017591,48.387,-0.13944,-0.98985,-0.027544,493.63,-0.013583,0.029726,-0.99947,479.06,#6,0.19188,0.86319,0.46699,57.684,-0.91461,-0.015277,0.40405,294.43,0.35591,-0.50464,0.78655,172.05
> view matrix models
> #4,0.99014,-0.139,-0.017591,43.397,-0.13944,-0.98985,-0.027544,490.24,-0.013583,0.029726,-0.99947,478.09,#6,0.19188,0.86319,0.46699,52.694,-0.91461,-0.015277,0.40405,291.03,0.35591,-0.50464,0.78655,171.09
> view matrix models
> #4,0.99014,-0.139,-0.017591,46.092,-0.13944,-0.98985,-0.027544,489.04,-0.013583,0.029726,-0.99947,478.66,#6,0.19188,0.86319,0.46699,55.389,-0.91461,-0.015277,0.40405,289.84,0.35591,-0.50464,0.78655,171.66
> fitmap #6 inMap #3
Fit molecule 6zb4.pdb (#6) to map cryosparc_P17_J31_008_volume_map_sharp.mrc
(#3) using 24841 atoms
average map value = 0.2538, steps = 128
shifted from previous position = 4.53
rotated from previous position = 0.0036 degrees
atoms outside contour = 15795, contour level = 0.27597
Position of 6zb4.pdb (#6) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.19183504 0.86321886 0.46696093 56.15232829
-0.91462239 -0.01529713 0.40401965 292.83831204
0.35590054 -0.50459805 0.78658478 168.32616517
Axis -0.45438610 0.05553964 -0.88907178
Axis point 151.61333715 160.53908419 0.00000000
Rotation angle (degrees) 91.05651697
Shift along axis -158.90474578
> hide #!4 models
> view matrix models
> #4,0.99014,-0.139,-0.017591,44.665,-0.13944,-0.98985,-0.027544,489.34,-0.013583,0.029726,-0.99947,483.57,#6,0.19184,0.86322,0.46696,54.726,-0.91462,-0.015297,0.40402,293.13,0.3559,-0.5046,0.78658,173.24
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99976,0.021942,0.0017779,4.1987,0.021991,-0.99915,-0.034882,456.4,0.0010111,0.034912,-0.99939,479.16,#6,0.33149,0.86172,0.38412,50.314,-0.86997,0.12166,0.47786,262.88,0.36505,-0.49258,0.79,170.41
> view matrix models
> #4,0.99961,0.024244,0.013909,0.76773,0.024549,-0.99945,-0.022182,452.75,0.013364,0.022514,-0.99966,479,#6,0.32944,0.86726,0.37327,51.126,-0.87368,0.13012,0.46877,263.29,0.35798,-0.48055,0.80058,168.4
> volume #3 level 0.1865
> view matrix models
> #4,0.99991,0.0092239,0.0093285,4.9513,0.0094578,-0.99963,-0.02535,457,0.0090912,0.025436,-0.99964,479.35,#6,0.31771,0.86708,0.38371,51.12,-0.8775,0.11556,0.46544,265.87,0.35923,-0.48458,0.79758,169.12
> view matrix models
> #4,0.99991,0.0060904,0.011987,4.9502,0.0062612,-0.99988,-0.014257,455.05,0.011898,0.014331,-0.99983,481.08,#6,0.31403,0.86875,0.38295,51.382,-0.88243,0.11826,0.45535,267.24,0.3503,-0.48092,0.80374,168.86
> fitmap #6 inMap #3
Fit molecule 6zb4.pdb (#6) to map cryosparc_P17_J31_008_volume_map_sharp.mrc
(#3) using 24841 atoms
average map value = 0.2539, steps = 232
shifted from previous position = 4.63
rotated from previous position = 8.54 degrees
atoms outside contour = 12330, contour level = 0.18652
Position of 6zb4.pdb (#6) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.19187432 0.86323275 0.46691912 56.15002187
-0.91461801 -0.01524314 0.40403161 292.83232845
0.35589063 -0.50457593 0.78660345 168.33132832
Axis -0.45438055 0.05552363 -0.88907561
Axis point 151.61574647 160.53819194 0.00000000
Rotation angle (degrees) 91.05330958
Shift along axis -158.91364292
> hide #!6 models
> select subtract #6
165 atoms, 162 bonds, 3 residues, 1 model selected
> show #!4 models
> view matrix models
> #4,0.9997,0.023334,-0.007425,5.237,0.023133,-0.99939,-0.026131,453.53,-0.0080302,0.025951,-0.99963,483.05
> fitmap #4 inMap #3
Fit molecule 7z3z.pdb (#4) to map cryosparc_P17_J31_008_volume_map_sharp.mrc
(#3) using 52020 atoms
average map value = 0.2341, steps = 140
shifted from previous position = 14.7
rotated from previous position = 17.5 degrees
atoms outside contour = 26893, contour level = 0.18652
Position of 7z3z.pdb (#4) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.96074367 -0.27743727 -0.00039550 79.06393076
-0.27743720 -0.96074375 0.00022697 509.55123729
-0.00044295 -0.00010833 -0.99999990 472.96112260
Axis -0.99013744 0.14009927 0.00021223
Axis point 0.00000000 260.38940539 236.46720953
Rotation angle (degrees) 179.99029854
Shift along axis -6.79602357
> select add #4
52020 atoms, 52716 bonds, 15 pseudobonds, 3336 residues, 3 models selected
> select subtract #4
3 models selected
> open /Users/hmed/Documents/SARS-CoV-2/KNP1/JN1-6/KP3-RBD-fromJN110.pdb
Chain information for KP3-RBD-fromJN110.pdb #5
---
Chain | Description
A | No description available
> mmaker #5 to #7
No 'to' model specified
> mmaker #5 to #4
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 7z3z.pdb, chain A (#4) with KP3-RBD-fromJN110.pdb, chain A (#5),
sequence alignment score = 898.4
RMSD between 189 pruned atom pairs is 0.822 angstroms; (across all 200 pairs:
1.081)
> fitmap #6 inMap #3
Fit molecule 6zb4.pdb (#6) to map cryosparc_P17_J31_008_volume_map_sharp.mrc
(#3) using 24841 atoms
average map value = 0.2538, steps = 172
shifted from previous position = 0.00803
rotated from previous position = 0.0097 degrees
atoms outside contour = 12329, contour level = 0.18652
Position of 6zb4.pdb (#6) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.19181480 0.86321117 0.46698346 56.14874063
-0.91468443 -0.01524063 0.40388131 292.85093490
0.35575198 -0.50461292 0.78664244 168.34304734
Axis -0.45432396 0.05562515 -0.88909819
Axis point 151.63138869 160.54768294 0.00000000
Rotation angle (degrees) 91.05382566
Shift along axis -158.89333798
> fitmap #5 inMap #3
Fit molecule KP3-RBD-fromJN110.pdb (#5) to map
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) using 1607 atoms
average map value = 0.2117, steps = 72
shifted from previous position = 4.99
rotated from previous position = 10 degrees
atoms outside contour = 694, contour level = 0.18652
Position of KP3-RBD-fromJN110.pdb (#5) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.99980714 -0.01961160 0.00102933 439.36931624
0.01963794 -0.99797029 0.06057769 421.28147545
-0.00016078 0.06058622 0.99816295 17.51638164
Axis 0.00021726 0.03030782 0.99954059
Axis point 217.61828727 212.53296218 0.00000000
Rotation angle (degrees) 178.87499435
Shift along axis 30.37191467
> hide #5 models
> hide #!4 models
> show #5 models
> show #!4 models
> open /Users/hmed/Documents/SARS-CoV-2/KNP1/JN1-6/KP3-RBD-fromJN110.pdb
Chain information for KP3-RBD-fromJN110.pdb #7
---
Chain | Description
A | No description available
> mmaker #5 to #4/C
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 7z3z.pdb, chain C (#4) with KP3-RBD-fromJN110.pdb, chain A (#5),
sequence alignment score = 884
RMSD between 189 pruned atom pairs is 0.823 angstroms; (across all 200 pairs:
1.081)
> fitmap #7 inMap #3
Fit molecule KP3-RBD-fromJN110.pdb (#7) to map
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) using 1607 atoms
average map value = -0.01687, steps = 192
shifted from previous position = 4.02
rotated from previous position = 17 degrees
atoms outside contour = 1607, contour level = 0.18652
Position of KP3-RBD-fromJN110.pdb (#7) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.97082224 0.16537043 -0.17365715 5.36131596
-0.13337835 0.97419837 0.18206524 -4.13574777
0.19928472 -0.15359087 0.96783028 -2.51806889
Axis -0.57479954 -0.63865013 -0.51159701
Axis point 15.47593322 0.00000000 31.07909351
Rotation angle (degrees) 16.97633333
Shift along axis 0.84785039
> mmaker #7 to #4/A
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 7z3z.pdb, chain A (#4) with KP3-RBD-fromJN110.pdb, chain A (#7),
sequence alignment score = 898.4
RMSD between 189 pruned atom pairs is 0.822 angstroms; (across all 200 pairs:
1.081)
> fitmap #7 inMap #3
Fit molecule KP3-RBD-fromJN110.pdb (#7) to map
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) using 1607 atoms
average map value = 0.2117, steps = 72
shifted from previous position = 4.99
rotated from previous position = 10 degrees
atoms outside contour = 694, contour level = 0.18652
Position of KP3-RBD-fromJN110.pdb (#7) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.99980714 -0.01961160 0.00102933 439.36931624
0.01963794 -0.99797029 0.06057769 421.28147545
-0.00016078 0.06058622 0.99816295 17.51638165
Axis 0.00021726 0.03030782 0.99954059
Axis point 217.61828727 212.53296218 0.00000000
Rotation angle (degrees) 178.87499435
Shift along axis 30.37191473
> fitmap #5 inMap #3
Fit molecule KP3-RBD-fromJN110.pdb (#5) to map
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) using 1607 atoms
average map value = 0.2118, steps = 76
shifted from previous position = 4.96
rotated from previous position = 9.82 degrees
atoms outside contour = 689, contour level = 0.18652
Position of KP3-RBD-fromJN110.pdb (#5) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.48704474 0.87172152 -0.05374962 -35.49639840
-0.87337699 0.48610583 -0.03022836 315.97422193
-0.00022271 0.06166624 0.99809680 17.32245786
Axis 0.05256118 -0.03061592 -0.99814828
Axis point 250.94919051 186.64994077 0.00000000
Rotation angle (degrees) 60.94665743
Shift along axis -28.82995496
> open /Users/hmed/Documents/SARS-CoV-2/KNP1/JN1-6/JN1-4/delta-rbd-
> JN1-4-p21_refine_7.pdb
Chain information for delta-rbd-JN1-4-p21_refine_7.pdb #8
---
Chain | Description
A | No description available
B L | No description available
E R | No description available
H | No description available
> mmaker #8 to #4/B
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 7z3z.pdb, chain B (#4) with delta-rbd-JN1-4-p21_refine_7.pdb, chain
E (#8), sequence alignment score = 932.1
RMSD between 178 pruned atom pairs is 0.833 angstroms; (across all 194 pairs:
1.444)
> select #8/E /H /L
4807 atoms, 4930 bonds, 1 pseudobond, 632 residues, 2 models selected
> select ~sel & ##selected
5067 atoms, 4934 bonds, 1 pseudobond, 890 residues, 2 models selected
> delete sel
> mmaker #8 to #4/B
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 7z3z.pdb, chain B (#4) with delta-rbd-JN1-4-p21_refine_7.pdb, chain
E (#8), sequence alignment score = 932.1
RMSD between 178 pruned atom pairs is 0.833 angstroms; (across all 194 pairs:
1.444)
> mmaker #8/E to #4/B
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 7z3z.pdb, chain B (#4) with delta-rbd-JN1-4-p21_refine_7.pdb, chain
E (#8), sequence alignment score = 932.1
RMSD between 178 pruned atom pairs is 0.833 angstroms; (across all 194 pairs:
1.444)
> show #5,7#!4,8 cartoons
> hide #5,7#!4,8 atoms
> select #8/E
1551 atoms, 1596 bonds, 196 residues, 1 model selected
> fitmap sel inMap #3
Fit molecule delta-rbd-JN1-4-p21_refine_7.pdb (#8) to map
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) using 1551 atoms
average map value = 0.2009, steps = 60
shifted from previous position = 4.83
rotated from previous position = 8.91 degrees
atoms outside contour = 704, contour level = 0.18652
Position of delta-rbd-JN1-4-p21_refine_7.pdb (#8) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.12283632 -0.84503049 -0.52041783 207.19781342
-0.28895455 -0.47121654 0.83334281 199.66482956
-0.94942957 0.25274186 -0.18629290 218.49898152
Axis -0.63715072 0.47079693 0.61023701
Axis point 0.00000000 206.71091561 179.19248005
Rotation angle (degrees) 152.89497870
Shift along axis 95.32151652
> select add #8
4807 atoms, 4930 bonds, 1 pseudobond, 632 residues, 2 models selected
> select subtract #8
Nothing selected
> select #8/H:96-109
99 atoms, 99 bonds, 14 residues, 1 model selected
> select ~sel & ##selected
4708 atoms, 4831 bonds, 1 pseudobond, 618 residues, 2 models selected
> open /Users/hmed/Documents/SARS-CoV-2/KNP1/JN1-6/KP3-RBD-fromJN110.pdb
Chain information for KP3-RBD-fromJN110.pdb #9
---
Chain | Description
A | No description available
> mmaker #9 to #4/B
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 7z3z.pdb, chain B (#4) with KP3-RBD-fromJN110.pdb, chain A (#9),
sequence alignment score = 898.4
RMSD between 189 pruned atom pairs is 0.822 angstroms; (across all 200 pairs:
1.081)
> fitmap #9 inMap #3
Fit molecule KP3-RBD-fromJN110.pdb (#9) to map
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) using 1607 atoms
average map value = 0.2118, steps = 76
shifted from previous position = 5.01
rotated from previous position = 9.93 degrees
atoms outside contour = 687, contour level = 0.18652
Position of KP3-RBD-fromJN110.pdb (#9) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.51719138 -0.85423682 0.05284439 292.05593032
0.85586916 0.51613003 -0.03313272 -41.58743365
0.00102861 0.06236384 0.99805295 16.96539491
Axis 0.05573012 0.03023878 0.99798786
Axis point 183.26999714 236.22374077 0.00000000
Rotation angle (degrees) 58.95660203
Shift along axis 31.95001558
> delete sel
> hide #!4 models
> lighting soft
> set bgColor white
> color #9 #5e42ffff
> color #9 #211759ff
> graphics silhouettes true
> volume #3 level 0.2574
> volume #3 level 0.1865
> volume #3 level 0.2169
> ui tool show "Side View"
> volume #3 level 0.1702
> open /Users/hmed/Documents/SARS-CoV-2/KNP1/JN1-6/JN1-4/delta-rbd-
> JN1-4-p21_refine_7.pdb
Chain information for delta-rbd-JN1-4-p21_refine_7.pdb #10
---
Chain | Description
A | No description available
B L | No description available
E R | No description available
H | No description available
> select #9/H:96-109 /E
Nothing selected
> select #10/H:96-109 /E
1650 atoms, 1695 bonds, 210 residues, 1 model selected
> select ~sel & ##selected
8224 atoms, 8169 bonds, 2 pseudobonds, 1312 residues, 2 models selected
> delete sel
> mmaker #10 #7/A
> matchmaker #10 #7/A
Missing required "to" argument
> mmaker #10 to #7/A
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 KP3-RBD-fromJN110.pdb, chain A (#7) with delta-rbd-
JN1-4-p21_refine_7.pdb, chain E (#10), sequence alignment score = 823
RMSD between 178 pruned atom pairs is 0.726 angstroms; (across all 193 pairs:
1.223)
> fitmap #10 inMap #3
Fit molecule delta-rbd-JN1-4-p21_refine_7.pdb (#10) to map
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) using 1650 atoms
average map value = 0.1928, steps = 64
shifted from previous position = 0.252
rotated from previous position = 2.49 degrees
atoms outside contour = 693, contour level = 0.17016
Position of delta-rbd-JN1-4-p21_refine_7.pdb (#10) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.32839427 0.82376083 -0.46214209 272.40151182
0.02903450 -0.49784961 -0.86677723 226.77560065
-0.94409438 0.27122661 -0.18740844 218.87240943
Axis 0.77450706 0.32800896 -0.54087792
Axis point -0.00000000 -31.66179674 253.15605749
Rotation angle (degrees) 132.72122661
Shift along axis 166.97807084
> show #5,7,9#!8,10 cartoons
> hide #5,7,9#!8,10 atoms
> select #10/H:96-109
99 atoms, 99 bonds, 14 residues, 1 model selected
> select add #10
1650 atoms, 1695 bonds, 210 residues, 1 model selected
> select subtract #10
Nothing selected
> hide #7 models
> show #5,9#!8,10 atoms
> style #5,9#!8,10 stick
Changed 4963 atom styles
> fitmap #10 inMap #3
Fit molecule delta-rbd-JN1-4-p21_refine_7.pdb (#10) to map
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) using 1650 atoms
average map value = 0.1928, steps = 48
shifted from previous position = 0.0142
rotated from previous position = 0.0263 degrees
atoms outside contour = 694, contour level = 0.17016
Position of delta-rbd-JN1-4-p21_refine_7.pdb (#10) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.32821422 0.82379382 -0.46221117 272.40832670
0.02863067 -0.49776872 -0.86683712 226.76845461
-0.94416932 0.27127485 -0.18696055 218.86917963
Axis 0.77441096 0.32794109 -0.54105666
Axis point 0.00000000 -31.69700002 253.23002756
Rotation angle (degrees) 132.70762927
Shift along axis 166.90206110
> select #10/E
1551 atoms, 1596 bonds, 196 residues, 1 model selected
> fitmap #10 inMap #3
Fit molecule delta-rbd-JN1-4-p21_refine_7.pdb (#10) to map
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) using 1650 atoms
average map value = 0.1927, steps = 48
shifted from previous position = 0.0274
rotated from previous position = 0.0556 degrees
atoms outside contour = 694, contour level = 0.17016
Position of delta-rbd-JN1-4-p21_refine_7.pdb (#10) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.32832911 0.82369649 -0.46230302 272.40325805
0.02948838 -0.49813562 -0.86659757 226.77566473
-0.94410298 0.27089664 -0.18784190 218.85300924
Axis 0.77454237 0.32806715 -0.54079206
Axis point -0.00000000 -31.60088311 253.08230654
Rotation angle (degrees) 132.75183036
Shift along axis 167.03154277
> fitmap #10 inMap #3
Fit molecule delta-rbd-JN1-4-p21_refine_7.pdb (#10) to map
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) using 1650 atoms
average map value = 0.1928, steps = 44
shifted from previous position = 0.0199
rotated from previous position = 0.0376 degrees
atoms outside contour = 694, contour level = 0.17016
Position of delta-rbd-JN1-4-p21_refine_7.pdb (#10) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.32838624 0.82375290 -0.46216192 272.40660008
0.02893636 -0.49784060 -0.86678569 226.77566842
-0.94410019 0.27126720 -0.18732041 218.87500120
Axis 0.77449713 0.32798107 -0.54090907
Axis point 0.00000000 -31.66717120 253.17302528
Rotation angle (degrees) 132.71775612
Shift along axis 166.96478366
> fitmap #10 inMap #3
Fit molecule delta-rbd-JN1-4-p21_refine_7.pdb (#10) to map
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) using 1650 atoms
average map value = 0.1927, steps = 48
shifted from previous position = 0.0273
rotated from previous position = 0.061 degrees
atoms outside contour = 692, contour level = 0.17016
Position of delta-rbd-JN1-4-p21_refine_7.pdb (#10) relative to
cryosparc_P17_J31_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.32876096 0.82377326 -0.46185912 272.41539897
0.02991757 -0.49788233 -0.86672840 226.78962114
-0.94393918 0.27112876 -0.18832957 218.87443505
Axis 0.77469323 0.32821708 -0.54048491
Axis point -0.00000000 -31.62423291 253.00762668
Rotation angle (degrees) 132.74412692
Shift along axis 167.17626385
> select add #10
1650 atoms, 1695 bonds, 210 residues, 1 model selected
> select subtract #10
Nothing selected
> open /Users/hmed/Downloads/cryosparc_P15_J63_004_volume_map_sharp.mrc
Opened cryosparc_P15_J63_004_volume_map_sharp.mrc as #11, grid size
560,560,560, pixel 0.829, shown at level 0.0176, step 4, values float32
> volume #11 level 0.05163
> volume #11 step 1
> volume #11 level 0.06556
> hide #5 models
> hide #!8 models
> hide #9 models
> hide #!10 models
> volume #11 level 0.07717
> volume #11 level 0.08181
> volume #11 level 0.09088
> open /Users/hmed/Documents/SARS-CoV-2/JN1fabs/JN1-10/RBD-AF-
> JN10_fit2JN10globalmap-coot-3.pdb /Users/hmed/Documents/SARS-
> CoV-2/JN1fabs/JN1-10/RBD-AF-JN10_fit2JN10globalmap-coot-2.pdb
> /Users/hmed/Documents/SARS-CoV-2/JN1fabs/JN1-10/RBD-AF-
> JN10_fit2JN10globalmap-coot-1.pdb
Summary of feedback from opening /Users/hmed/Documents/SARS-
CoV-2/JN1fabs/JN1-10/RBD-AF-JN10_fit2JN10globalmap-coot-3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 6 6 GLY A 499 HIS A 502 1 4
Start residue of secondary structure not found: SHEET 1 1 1 ARG A 316 ARG A
316 0
Start residue of secondary structure not found: SHEET 2 2 2 GLU A 321 ARG A
325 0
End residue of secondary structure not found: SHEET 7 7 7 ASN A 391 ARG A 400
0
Start residue of secondary structure not found: SHEET 9 9 9 GLN A 449 ARG A
451 0
Start residue of secondary structure not found: SHEET 11 1111 CYS A 485 TYR A
486 0
Start residue of secondary structure not found: SHEET 12 1212 LEU A 489 SER A
491 0
Start residue of secondary structure not found: SHEET 13 1313 PRO A 504 GLU A
513 0
Start residue of secondary structure not found: SHEET 14 1414 VAL A 521 CYS A
522 0
5 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (522 )
Cannot find LINK/SSBOND residue CYS (485 )
Cannot find LINK/SSBOND residue CYS (535 )
Summary of feedback from opening /Users/hmed/Documents/SARS-
CoV-2/JN1fabs/JN1-10/RBD-AF-JN10_fit2JN10globalmap-coot-2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 6 6 GLY A 499 HIS A 502 1 4
Start residue of secondary structure not found: SHEET 1 1 1 ARG A 316 ARG A
316 0
Start residue of secondary structure not found: SHEET 2 2 2 GLU A 321 ARG A
325 0
End residue of secondary structure not found: SHEET 7 7 7 ASN A 391 ARG A 400
0
Start residue of secondary structure not found: SHEET 9 9 9 GLN A 449 ARG A
451 0
Start residue of secondary structure not found: SHEET 11 1111 CYS A 485 TYR A
486 0
Start residue of secondary structure not found: SHEET 12 1212 LEU A 489 SER A
491 0
Start residue of secondary structure not found: SHEET 13 1313 PRO A 504 GLU A
513 0
Start residue of secondary structure not found: SHEET 14 1414 VAL A 521 CYS A
522 0
5 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (522 )
Cannot find LINK/SSBOND residue CYS (485 )
Cannot find LINK/SSBOND residue CYS (535 )
Summary of feedback from opening /Users/hmed/Documents/SARS-
CoV-2/JN1fabs/JN1-10/RBD-AF-JN10_fit2JN10globalmap-coot-1.pdb
---
warnings | Start residue of secondary structure not found: SHEET 1 1 1 ARG A 316 ARG A 316 0
Start residue of secondary structure not found: SHEET 2 2 2 GLU A 321 ARG A
325 0
Start residue of secondary structure not found: SHEET 15 1515 CYS A 535 PHE A
540 0
Start residue of secondary structure not found: SHEET 16 1616 LEU A 543 GLU A
551 0
Start residue of secondary structure not found: SHEET 17 1717 PHE A 562 GLY A
563 0
2 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (535 )
RBD-AF-JN10_fit2JN10globalmap-coot-3.pdb title:
Ba.2-07 fab In complex with sars-cov-2 Ba.2.12.1 spike glycoprotein [more
info...]
Chain information for RBD-AF-JN10_fit2JN10globalmap-coot-3.pdb #12
---
Chain | Description | UniProt
A | spike glycoprotein,fibritin | SPIKE_SARS2 1-1205, WAC_BPT4 1208-1234
B | spike glycoprotein,fibritin |
C | spike glycoprotein,fibritin |
RBD-AF-JN10_fit2JN10globalmap-coot-2.pdb title:
Ba.2-07 fab In complex with sars-cov-2 Ba.2.12.1 spike glycoprotein [more
info...]
Chain information for RBD-AF-JN10_fit2JN10globalmap-coot-2.pdb #13
---
Chain | Description | UniProt
A | spike glycoprotein,fibritin | SPIKE_SARS2 1-1205, WAC_BPT4 1208-1234
B | spike glycoprotein,fibritin |
C | spike glycoprotein,fibritin |
RBD-AF-JN10_fit2JN10globalmap-coot-1.pdb title:
Ba.2-07 fab In complex with sars-cov-2 Ba.2.12.1 spike glycoprotein [more
info...]
Chain information for RBD-AF-JN10_fit2JN10globalmap-coot-1.pdb #14
---
Chain | Description | UniProt
A | spike glycoprotein,fibritin | SPIKE_SARS2 1-1205, WAC_BPT4 1208-1234
B | spike glycoprotein,fibritin |
C | spike glycoprotein,fibritin |
> select add #11
4 models selected
> select add #12
3344 atoms, 3442 bonds, 430 residues, 5 models selected
> select add #13
6688 atoms, 6884 bonds, 860 residues, 6 models selected
> select add #14
10008 atoms, 10299 bonds, 1288 residues, 7 models selected
> select subtract #11
10008 atoms, 10299 bonds, 1288 residues, 3 models selected
> view matrix models
> #12,0.019905,-0.89142,-0.45274,511,-0.99516,0.025902,-0.094753,438.34,0.096192,0.45244,-0.88659,375.82,#13,0.019905,-0.89142,-0.45274,511,-0.99516,0.025902,-0.094753,438.34,0.096192,0.45244,-0.88659,375.82,#14,0.019905,-0.89142,-0.45274,511,-0.99516,0.025902,-0.094753,438.34,0.096192,0.45244,-0.88659,375.82
> view matrix models
> #12,-0.58592,0.65639,-0.47523,327.67,0.27313,0.71209,0.64679,-167.05,0.76295,0.24917,-0.59651,199.65,#13,-0.58592,0.65639,-0.47523,327.67,0.27313,0.71209,0.64679,-167.05,0.76295,0.24917,-0.59651,199.65,#14,-0.58592,0.65639,-0.47523,327.67,0.27313,0.71209,0.64679,-167.05,0.76295,0.24917,-0.59651,199.65
> select subtract #12
6664 atoms, 6857 bonds, 858 residues, 2 models selected
> select subtract #13
3320 atoms, 3415 bonds, 428 residues, 1 model selected
> select subtract #14
Nothing selected
> show #!6 models
> select add #6
24841 atoms, 25416 bonds, 32 pseudobonds, 3163 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.96091,0.27672,0.0085009,103.67,-0.20278,0.6826,0.7021,98.119,0.18848,-0.67638,0.71203,215.59
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.96091,0.27672,0.0085009,100.89,-0.20278,0.6826,0.7021,105.62,0.18848,-0.67638,0.71203,224.76
> view matrix models
> #6,0.96091,0.27672,0.0085009,95.643,-0.20278,0.6826,0.7021,102.79,0.18848,-0.67638,0.71203,223.48
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.94283,0.31557,-0.10716,106.42,-0.10058,0.57599,0.81124,92.547,0.31773,-0.75409,0.5748,236.13
> view matrix models
> #6,0.90242,0.37959,-0.20385,114.12,-0.10477,0.65223,0.75075,90.735,0.41793,-0.65613,0.62835,207.42
> view matrix models
> #6,0.93686,0.3263,-0.12576,107.91,-0.19199,0.78053,0.5949,102.31,0.29228,-0.5332,0.7939,185.44
> view matrix models
> #6,0.9168,0.36503,-0.16199,109.48,-0.21209,0.78873,0.57699,105.48,0.33838,-0.49463,0.80052,175.17
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.9168,0.36503,-0.16199,102.17,-0.21209,0.78873,0.57699,101.45,0.33838,-0.49463,0.80052,178.23
> view matrix models
> #6,0.9168,0.36503,-0.16199,105.87,-0.21209,0.78873,0.57699,100.71,0.33838,-0.49463,0.80052,174.87
> fitmap #6 inMap #11
Fit molecule 6zb4.pdb (#6) to map cryosparc_P15_J63_004_volume_map_sharp.mrc
(#11) using 24841 atoms
average map value = 0.07165, steps = 112
shifted from previous position = 6.16
rotated from previous position = 4.27 degrees
atoms outside contour = 16605, contour level = 0.090884
Position of 6zb4.pdb (#6) relative to
cryosparc_P15_J63_004_volume_map_sharp.mrc (#11) coordinates:
Matrix rotation and translation
0.90008770 0.42014723 -0.11540560 92.34350277
-0.27684266 0.75600657 0.59313762 108.82688704
0.33645251 -0.50192668 0.79678689 171.61041132
Axis -0.79672410 -0.32875352 -0.50710140
Axis point 0.00000000 148.92025153 -13.37442975
Rotation angle (degrees) 43.41118160
Shift along axis -196.37339679
> select subtract #6
Nothing selected
> volume #11 level 0.06934
> transparency #11.1 50
> hide #13 models
> hide #14 models
> mmaker #12 to #6/B
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 6zb4.pdb, chain B (#6) with RBD-AF-JN10_fit2JN10globalmap-
coot-3.pdb, chain A (#12), sequence alignment score = 870.8
RMSD between 177 pruned atom pairs is 0.985 angstroms; (across all 200 pairs:
1.359)
> show #!11 models
> color #12#!6 bychain
> hide #!6 models
> select #12/B #12/C
1737 atoms, 1780 bonds, 230 residues, 1 model selected
> delete sel
> open "/Users/hmed/Documents/SARS-CoV-2/JN1fabs/JN1-3/fold_2025_01_29_18_20
> (1)/fold_2025_01_29_18_20_model_0.cif"
Chain information for fold_2025_01_29_18_20_model_0.cif #15
---
Chain | Description
A | .
B | .
Computing secondary structure
> select add #15
1793 atoms, 1839 bonds, 230 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #15,1,0,0,198.89,0,1,0,358.05,0,0,1,56.753
> view matrix models #15,1,0,0,219.28,0,1,0,285.77,0,0,1,176.46
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.65797,0.038298,0.75207,216.06,0.33611,-0.90864,-0.24778,281.76,0.67388,0.41581,-0.61073,184.69
> view matrix models
> #15,0.79318,-0.43326,0.42796,216.16,-0.43088,-0.89588,-0.10836,280.44,0.43035,-0.098448,-0.89728,184.13
> view matrix models
> #15,0.86779,0.24918,0.42994,218.14,-0.25911,-0.51138,0.81936,278.03,0.42403,-0.82244,-0.37921,180.06
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.86779,0.24918,0.42994,212.38,-0.25911,-0.51138,0.81936,270.93,0.42403,-0.82244,-0.37921,175.74
> view matrix models
> #15,0.86779,0.24918,0.42994,218.2,-0.25911,-0.51138,0.81936,267.61,0.42403,-0.82244,-0.37921,168.72
> view matrix models
> #15,0.86779,0.24918,0.42994,224.19,-0.25911,-0.51138,0.81936,264.53,0.42403,-0.82244,-0.37921,178.77
> view matrix models
> #15,0.86779,0.24918,0.42994,224.92,-0.25911,-0.51138,0.81936,264.34,0.42403,-0.82244,-0.37921,178.67
> view matrix models
> #15,0.86779,0.24918,0.42994,226.4,-0.25911,-0.51138,0.81936,263.28,0.42403,-0.82244,-0.37921,179.13
> view matrix models
> #15,0.86779,0.24918,0.42994,226.93,-0.25911,-0.51138,0.81936,264.54,0.42403,-0.82244,-0.37921,177.79
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.84404,-0.047887,-0.53413,228.11,0.32726,0.74305,-0.58376,274.21,0.42484,-0.66752,-0.6115,179.14
> view matrix models
> #15,-0.69089,-0.25712,-0.67569,228.25,0.12948,0.8755,-0.46554,273.9,0.71127,-0.40913,-0.57159,180.01
> view matrix models
> #15,0.9398,-0.14043,0.31154,226.38,-0.32301,-0.66264,0.6757,264.62,0.11155,-0.73566,-0.66811,178.85
> view matrix models
> #15,0.83443,0.2725,0.47904,226.77,-0.20912,-0.64765,0.73268,264.56,0.5099,-0.71154,-0.48343,178.6
> view matrix models
> #15,0.92837,0.11403,0.35372,226.92,-0.29239,-0.36342,0.88455,264.66,0.22941,-0.92462,-0.30405,177
> fitmap #15 inMap #11
Fit molecule fold_2025_01_29_18_20_model_0.cif (#15) to map
cryosparc_P15_J63_004_volume_map_sharp.mrc (#11) using 1793 atoms
average map value = 0.06048, steps = 120
shifted from previous position = 8.6
rotated from previous position = 7.84 degrees
atoms outside contour = 1126, contour level = 0.069335
Position of fold_2025_01_29_18_20_model_0.cif (#15) relative to
cryosparc_P15_J63_004_volume_map_sharp.mrc (#11) coordinates:
Matrix rotation and translation
0.93258477 0.15457222 0.32617951 228.52945250
-0.28532482 -0.23779278 0.92846342 260.04835310
0.22107779 -0.95893796 -0.17765864 183.94255969
Axis -0.97246884 0.05415284 -0.22665352
Axis point 0.00000000 187.55594009 -44.61443343
Rotation angle (degrees) 103.97115200
Shift along axis -249.84664301
> fitmap #12 inMap #11
Fit molecule RBD-AF-JN10_fit2JN10globalmap-coot-3.pdb (#12) to map
cryosparc_P15_J63_004_volume_map_sharp.mrc (#11) using 1607 atoms
average map value = 0.07725, steps = 76
shifted from previous position = 4.6
rotated from previous position = 2.1 degrees
atoms outside contour = 731, contour level = 0.069335
Position of RBD-AF-JN10_fit2JN10globalmap-coot-3.pdb (#12) relative to
cryosparc_P15_J63_004_volume_map_sharp.mrc (#11) coordinates:
Matrix rotation and translation
-0.88225961 0.44731449 0.14672333 295.12374959
0.43240956 0.89323628 -0.12308911 -12.43377372
-0.18611815 -0.04515198 -0.98148935 497.60651162
Axis 0.22777363 0.97273927 -0.04356012
Axis point 171.12430063 0.00000000 235.78945556
Rotation angle (degrees) 170.14911203
Shift along axis 33.45079157
> select subtract #15
Nothing selected
> ui tool show "Side View"
> view orient
> color #11 #e5ffff80 models
> color #11 #bed4d480 models
> lighting full
> volume #11 level 0.07748
> lighting soft
> lighting full
> lighting simple
> show #12,15 atoms
> open /Users/hmed/Downloads/cryosparc_P15_J63_005_volume_map_sharp.mrc
Opened cryosparc_P15_J63_005_volume_map_sharp.mrc as #16, grid size
560,560,560, pixel 0.829, shown at level 0.0182, step 4, values float32
> select add #15
1793 atoms, 1839 bonds, 230 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.58494,-0.4014,0.70479,225.02,0.24606,-0.74018,-0.62577,264.27,0.77286,0.53946,-0.33419,190.04
> view matrix models
> #15,0.27954,-0.83527,-0.47348,227.37,-0.93316,-0.12028,-0.33875,264.23,0.226,0.53653,-0.81306,191.18
> view matrix models
> #15,-0.4923,-0.86717,-0.075175,225.15,-0.65514,0.42602,-0.62394,267.32,0.57309,-0.25792,-0.77785,188.72
> view matrix models
> #15,-0.67577,-0.60445,-0.42188,227.06,-0.50968,0.79663,-0.32497,267.67,0.53251,-0.004582,-0.84641,189.77
> view matrix models
> #15,-0.68086,-0.63405,-0.36661,226.76,-0.55553,0.77328,-0.30566,267.48,0.4773,-0.004449,-0.87873,189.83
> view matrix models
> #15,-0.72267,-0.58577,-0.36691,226.89,-0.53488,0.81016,-0.23989,267.39,0.43778,0.022892,-0.89879,189.95
> view matrix models
> #15,-0.60901,-0.7828,0.12781,224.61,-0.75727,0.62177,0.19986,265.02,-0.23592,0.024931,-0.97145,189.57
> view matrix models
> #15,-0.79201,-0.61035,-0.013843,225.51,-0.60977,0.79197,-0.031206,266.54,0.03001,-0.016274,-0.99942,189.78
> view matrix models
> #15,-0.92564,-0.36609,0.095711,225.82,-0.34459,0.92004,0.1865,266.46,-0.15633,0.13965,-0.97778,190.06
> view matrix models
> #15,-0.98323,-0.10162,0.15146,226.46,-0.13783,0.95782,-0.25216,268.31,-0.11945,-0.2688,-0.95576,188.64
> view matrix models
> #15,-0.7211,0.024546,0.6924,225.26,-0.24701,0.92459,-0.29003,268.22,-0.6473,-0.38017,-0.66066,186.74
> view matrix models
> #15,-0.61653,-0.60564,0.50308,223.9,-0.62102,0.76684,0.16211,265.77,-0.48396,-0.21248,-0.8489,188.12
> view matrix models
> #15,-0.68571,-0.54032,0.48771,224.1,-0.57483,0.81302,0.092525,266.21,-0.44651,-0.2169,-0.86809,188.2
> view matrix models
> #15,-0.73727,-0.50977,0.44337,224.31,-0.52264,0.8462,0.10384,266.33,-0.42811,-0.15516,-0.8903,188.51
> view matrix models
> #15,-0.72597,-0.57663,0.3748,224.34,-0.57712,0.80719,0.12402,266.08,-0.37405,-0.12627,-0.91877,188.75
> fitmap #15 inMap #11
Fit molecule fold_2025_01_29_18_20_model_0.cif (#15) to map
cryosparc_P15_J63_004_volume_map_sharp.mrc (#11) using 1793 atoms
average map value = 0.06184, steps = 160
shifted from previous position = 6.67
rotated from previous position = 27.6 degrees
atoms outside contour = 1264, contour level = 0.077475
Position of fold_2025_01_29_18_20_model_0.cif (#15) relative to
cryosparc_P15_J63_004_volume_map_sharp.mrc (#11) coordinates:
Matrix rotation and translation
-0.89572668 -0.33485892 0.29247770 229.26512856
-0.21542212 0.90233390 0.37334545 260.39744845
-0.38893061 0.27140932 -0.88038057 190.34037280
Axis -0.14577583 0.97446177 0.17080302
Axis point 147.73958778 0.00000000 47.70026056
Rotation angle (degrees) 159.53512022
Shift along axis 252.83675398
> undo
> redo
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.68086,-0.63405,-0.36661,223.67,-0.55553,0.77328,-0.30566,268.02,0.4773,-0.004449,-0.87873,187.94
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.21383,-0.13784,-0.9671,227.87,-0.087472,0.98872,-0.12159,268.55,0.97295,0.058596,-0.22347,186.34
> view matrix models
> #15,-0.22809,-0.14756,-0.96239,227.81,-0.080994,0.9879,-0.13228,268.59,0.97027,0.047778,-0.23728,186.35
> view matrix models
> #15,-0.38819,-0.85305,0.34874,220.73,-0.76207,0.50992,0.39903,264.49,-0.51823,-0.11086,-0.84803,186.54
> view matrix models
> #15,0.23677,-0.85974,0.45253,220.94,-0.66097,0.19883,0.72359,262.41,-0.71208,-0.47043,-0.52118,184.01
> view matrix models
> #15,0.43245,-0.79701,0.42162,221.44,-0.60194,0.092953,0.79312,261.87,-0.67131,-0.59677,-0.43955,183.34
> fitmap #15 inMap #11
Fit molecule fold_2025_01_29_18_20_model_0.cif (#15) to map
cryosparc_P15_J63_004_volume_map_sharp.mrc (#11) using 1793 atoms
average map value = 0.05264, steps = 120
shifted from previous position = 5.01
rotated from previous position = 19.4 degrees
atoms outside contour = 1421, contour level = 0.077475
Position of fold_2025_01_29_18_20_model_0.cif (#15) relative to
cryosparc_P15_J63_004_volume_map_sharp.mrc (#11) coordinates:
Matrix rotation and translation
0.66543906 -0.72173863 0.19048413 226.01574689
-0.40695859 -0.13685421 0.90313655 261.01103424
-0.62575998 -0.67850149 -0.38478587 184.75581762
Axis -0.87506007 0.45159677 0.17415580
Axis point 0.00000000 258.63697662 12.69696718
Rotation angle (degrees) 115.34707400
Shift along axis -47.72931792
> view matrix models
> #15,0.81064,-0.30318,0.50094,226.48,-0.53472,-0.034694,0.84431,261.44,-0.2386,-0.9523,-0.19024,183.53
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.81064,-0.30318,0.50094,220.01,-0.53472,-0.034694,0.84431,266.16,-0.2386,-0.9523,-0.19024,181.6
> view matrix models
> #15,0.81064,-0.30318,0.50094,225.2,-0.53472,-0.034694,0.84431,265.04,-0.2386,-0.9523,-0.19024,177.58
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.94338,-0.098305,0.31681,226.66,-0.32224,-0.044922,0.94559,264.85,-0.078725,-0.99414,-0.074056,177.19
> view matrix models
> #15,0.90352,0.03591,0.42704,226.69,-0.41732,-0.15291,0.8958,264.57,0.097467,-0.98759,-0.12317,177.55
> view matrix models
> #15,0.91096,0.15633,0.38171,227.26,-0.37819,-0.052922,0.92422,264.84,0.16468,-0.98629,0.010911,177.15
> fitmap #15 inMap #11
Fit molecule fold_2025_01_29_18_20_model_0.cif (#15) to map
cryosparc_P15_J63_004_volume_map_sharp.mrc (#11) using 1793 atoms
average map value = 0.06048, steps = 116
shifted from previous position = 8.18
rotated from previous position = 11.9 degrees
atoms outside contour = 1287, contour level = 0.077475
Position of fold_2025_01_29_18_20_model_0.cif (#15) relative to
cryosparc_P15_J63_004_volume_map_sharp.mrc (#11) coordinates:
Matrix rotation and translation
0.93267359 0.15422076 0.32609188 228.53265501
-0.28522964 -0.23810897 0.92841163 260.04387400
0.22082575 -0.95891609 -0.17808961 183.94379705
Axis -0.97251302 0.05424213 -0.22644252
Axis point 0.00000000 187.56985488 -44.55087319
Rotation angle (degrees) 103.99058755
Shift along axis -249.79834488
> select subtract #15
Nothing selected
> select add #15
1793 atoms, 1839 bonds, 230 residues, 1 model selected
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.81632,-0.21619,0.53561,226.45,-0.56571,-0.11213,0.81694,260.59,-0.11656,-0.96989,-0.21383,183.71
> view matrix models
> #15,0.80302,-0.26555,0.53353,226.28,-0.58084,-0.14834,0.80039,260.51,-0.13339,-0.95262,-0.27336,183.96
> view matrix models
> #15,0.7955,-0.2717,0.54162,226.22,-0.59277,-0.1635,0.7886,260.49,-0.12571,-0.94839,-0.29112,184.04
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.7955,-0.2717,0.54162,224.55,-0.59277,-0.1635,0.7886,263.07,-0.12571,-0.94839,-0.29112,182.68
> view matrix models
> #15,0.7955,-0.2717,0.54162,224.59,-0.59277,-0.1635,0.7886,263.08,-0.12571,-0.94839,-0.29112,182.69
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.80383,-0.15607,0.57402,224.87,-0.59235,-0.1215,0.79647,263.19,-0.054563,-0.98024,-0.19012,182.3
> view matrix models
> #15,0.85947,0.27381,0.43168,226.87,-0.21121,-0.57881,0.78764,262.05,0.46552,-0.76812,-0.43964,184.37
> view matrix models
> #15,0.90355,0.22089,0.36716,226.95,-0.2911,-0.31231,0.90428,262.46,0.31441,-0.92394,-0.21789,182.94
> view matrix models
> #15,0.78267,-0.019487,0.62213,225.15,-0.55687,-0.46844,0.6859,262.45,0.27807,-0.88328,-0.37749,183.59
> view matrix models
> #15,-0.54704,-0.19359,-0.81442,228.3,0.47766,0.72678,-0.4936,271.54,0.68746,-0.65903,-0.3051,184.48
> view matrix models
> #15,0.89968,0.36599,0.23798,227.89,-0.06331,-0.42999,0.90061,262.3,0.43194,-0.82532,-0.36368,183.89
> view matrix models
> #15,0.97698,0.10104,0.18788,227.24,-0.14668,-0.32132,0.93554,262.46,0.15489,-0.94157,-0.2991,183.01
> fitmap #15 inMap #11
Fit molecule fold_2025_01_29_18_20_model_0.cif (#15) to map
cryosparc_P15_J63_004_volume_map_sharp.mrc (#11) using 1793 atoms
average map value = 0.06049, steps = 88
shifted from previous position = 3.24
rotated from previous position = 10.7 degrees
atoms outside contour = 1291, contour level = 0.077475
Position of fold_2025_01_29_18_20_model_0.cif (#15) relative to
cryosparc_P15_J63_004_volume_map_sharp.mrc (#11) coordinates:
Matrix rotation and translation
0.93249651 0.15444642 0.32649127 228.54348459
-0.28559747 -0.23805715 0.92831184 260.05221918
0.22109802 -0.95889263 -0.17787795 183.93467594
Axis -0.97243873 0.05430704 -0.22674581
Axis point 0.00000000 187.55186662 -44.61832992
Rotation angle (degrees) 103.98803682
Shift along axis -249.82828772
> select subtract #15
Nothing selected
> select add #15
1793 atoms, 1839 bonds, 230 residues, 1 model selected
> view matrix models
> #15,0.98301,0.054479,0.17527,228.78,-0.17097,-0.075544,0.98238,260.52,0.066759,-0.99565,-0.064946,183.27
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.98301,0.054479,0.17527,228.51,-0.17097,-0.075544,0.98238,261.59,0.066759,-0.99565,-0.064946,180.15
> view matrix models
> #15,0.98301,0.054479,0.17527,228.89,-0.17097,-0.075544,0.98238,262.69,0.066759,-0.99565,-0.064946,179.7
> view matrix models
> #15,0.98301,0.054479,0.17527,228.75,-0.17097,-0.075544,0.98238,262.56,0.066759,-0.99565,-0.064946,179.94
> view matrix models
> #15,0.98301,0.054479,0.17527,228.47,-0.17097,-0.075544,0.98238,262.56,0.066759,-0.99565,-0.064946,179.5
> view matrix models
> #15,0.98301,0.054479,0.17527,228.64,-0.17097,-0.075544,0.98238,262.42,0.066759,-0.99565,-0.064946,178.45
> view matrix models
> #15,0.98301,0.054479,0.17527,228.38,-0.17097,-0.075544,0.98238,262.61,0.066759,-0.99565,-0.064946,178.52
> select subtract #15
Nothing selected
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!8 models
> show #!6 models
> hide #15 models
> show #15 models
> hide #!6 models
> show #!3 models
> hide #15 models
> hide #12 models
> hide #!11 models
> volume #3 level 0.2867
> volume #3 level 0.2604
> open /Users/hmed/Downloads/cryosparc_P13_J16_class_00_00082_volume_sharp.mrc
Opened cryosparc_P13_J16_class_00_00082_volume_sharp.mrc as #17, grid size
128,128,128, pixel 3.11, shown at level 0.238, step 1, values float32
> volume #17 level 0.6269
> volume #17 level 0.3066
> volume #17 level 0.421
> open /Users/hmed/Downloads/cryosparc_P13_J13_class_00_final_volume.mrc
Opened cryosparc_P13_J13_class_00_final_volume.mrc as #18, grid size
120,120,120, pixel 3.32, shown at level 0.163, step 1, values float32
> volume #18 level 0.3146
> volume #18 level 0.3566
> open /Users/hmed/Downloads/cryosparc_P17_J32_002_volume_map_sharp.mrc
Opened cryosparc_P17_J32_002_volume_map_sharp.mrc as #19, grid size
140,140,140, pixel 3.32, shown at level 0.192, step 1, values float32
> volume #19 level 0.4153
> volume #19 level 0.5644
> volume #19 level 0.4898
> volume #19 level 0.5005
> volume #19 level 0.6177
> volume #19 level 0.7242
> volume #19 level 0.6709
> open /Users/hmed/Downloads/cryosparc_P12_J50_002_volume_map_sharp.mrc
Opened cryosparc_P12_J50_002_volume_map_sharp.mrc as #20, grid size
120,120,120, pixel 3.32, shown at level 0.313, step 1, values float32
> volume #20 level 0.8616
> lighting soft
> close #19
> close #18
> close #17
> volume #16 step 1
> volume #16 level 0.0438
> volume #16 level 0.0807
> volume #16 level 0.09198
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 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: Mac14,9
Model Number: MPHF3B/A
Chip: Apple M2 Pro
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.121.1
OS Loader Version: 8422.141.2.700.1
Software:
System Software Overview:
System Version: macOS 13.6.7 (22G720)
Kernel Version: Darwin 22.6.0
Time since boot: 1 hour, 17 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 19
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
DELL U2717D:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 9 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 , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The message in the Report a Bug panel (shown in red) when you reported this explains what we know about this crash:
"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."
We plan to update the ChimeraX daily build to a new version of the Qt window toolkit in about a week (when PyQt 6.8.2 comes out) which may fix the Mac multi-display crashes.
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Reported by Helen Duyvesteyn