![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 weeks ago
Last modified 6 weeks ago
#19191 feedback defect
Crash during/after session save
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.0.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x00000002028ad2c0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.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.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, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 61)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 1366,
"osVersion" : {
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"build" : "22A400",
"releaseType" : "User"
},
"captureTime" : "2025-10-20 17:36:16.4326 +0200",
"incident" : "4EEDB04A-0F8C-4B0F-9852-87C12BB35411",
"pid" : 36968,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-10-20 11:36:18.0108 +0200",
"procStartAbsTime" : 783093760103,
"procExitAbsTime" : 1261318356007,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"7EF6A097-F49F-56B3-8945-4C767B6B444F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "02E04C25-79CA-2EF6-F248-C1774882463F",
"wakeTime" : 6707,
"sleepWakeUUID" : "4193382B-9A3E-4838-9505-39892FEF8819",
"sip" : "disabled",
"vmRegionInfo" : "0x50e2d11efb28 is not in any region. Bytes after previous region: 88454064962345 Bytes before following region: 16618014967000\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000d0e2d11efb28","rawCodes":[1,229672589654824],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000d0e2d11efb28 -> 0x000050e2d11efb28 (possible pointer authentication failure)"},
"ktriageinfo" : "VM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\n",
"vmregioninfo" : "0x50e2d11efb28 is not in any region. Bytes after previous region: 88454064962345 Bytes before following region: 16618014967000\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/haandrew/Downloads/191025 scribo overlay figures .cxs" format
> session
Opened cryosparc_P1_J49_001_volume_map.mrc as #2.1, grid size 128,128,128,
pixel 3.32, shown at level 0.312, step 1, values float32
Opened cryosparc_P1_J49_001_volume_map_sharp.mrc as #2.2, grid size
128,128,128, pixel 3.32, shown at level 0.632, step 1, values float32
Opened ec8 ribso _ cryosparc_P26_J24_001_volume_map.mrc as #3, grid size
128,128,128, pixel 3.35, shown at level 0.906, step 1, values float32
Opened NU_cryosparc_P1_J23_002_volume_map_sharp.mrc as #1, grid size
128,128,128, pixel 3.35, shown at level 5.73, step 1, values float32
Opened NU_cryosparc_P1_J23_002_volume_map_sharp.mrc z flip as #4, grid size
128,128,128, pixel 3.35, shown at level 0.317, step 1, values float32
> set bgColor #ffffff00
opened ChimeraX session
> select add #8
204962 atoms, 220182 bonds, 5230 pseudobonds, 16898 residues, 7 models
selected
> surface hidePatches (#!8 & sel)
> select subtract #8
83 models selected
> ui tool show "Side View"
> lighting flat
> select #8/n
1624 atoms, 1814 bonds, 79 pseudobonds, 75 residues, 2 models selected
> surface (#!8 & sel)
> select #8/m
1611 atoms, 1799 bonds, 68 pseudobonds, 76 residues, 2 models selected
> surface (#!8 & sel)
> select #8/eI
1143 atoms, 1158 bonds, 154 residues, 1 model selected
> surface (#!8 & sel)
> select clear
> ui mousemode right zoom
> save /Users/haandrew/Desktop/image152.png supersample 3
> close session
> open "/Users/haandrew/Documents/progress/2025/Cryo-EM/100625
> /cryosparc_P1_J21_class_00_00082_volume.mrc"
> "/Users/haandrew/Documents/progress/2025/Cryo-EM/100625
> /cryosparc_P1_J21_class_01_00082_volume.mrc"
> "/Users/haandrew/Documents/progress/2025/Cryo-EM/100625
> /cryosparc_P1_J21_class_00_00082_volume_sharp.mrc"
> "/Users/haandrew/Documents/progress/2025/Cryo-EM/100625
> /cryosparc_P1_J21_class_01_00082_volume_sharp.mrc"
> "/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /ec8 ribso _
> cryosparc_P26_J24_001_volume_map.mrc"
Opened cryosparc_P1_J21_class_00_00082_volume.mrc as #1.1, grid size
128,128,128, pixel 3.32, shown at level 0.817, step 1, values float32
Opened cryosparc_P1_J21_class_01_00082_volume.mrc as #1.2, grid size
128,128,128, pixel 3.32, shown at level 0.964, step 1, values float32
Opened cryosparc_P1_J21_class_00_00082_volume_sharp.mrc as #1.3, grid size
128,128,128, pixel 3.32, shown at level 0.847, step 1, values float32
Opened cryosparc_P1_J21_class_01_00082_volume_sharp.mrc as #1.4, grid size
128,128,128, pixel 3.32, shown at level 1.06, step 1, values float32
Opened ec8 ribso _ cryosparc_P26_J24_001_volume_map.mrc as #1.5, grid size
128,128,128, pixel 3.35, shown at level 2.9, step 1, values float32
> hide #!1.4 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> volume #1.5 level 0.6201
> show #!1.1 models
> volume #1.5 level 1.867
> volume #1.1 level 0.07441
> select add #1.1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1.1,1,0,0,75.117,0,1,0,263.42,0,0,1,53.044
> volume #1.1 level 0.6988
> ui mousemode right "rotate selected models"
> view matrix models
> #1.1,0.89062,0.36667,-0.26897,74.938,-0.27965,0.90804,0.31188,274.37,0.35859,-0.20255,0.91126,42.56
> view matrix models
> #1.1,0.92266,0.37333,-0.096519,29.755,-0.33819,0.90369,0.26262,298.02,0.18527,-0.20967,0.96006,69.453
> view matrix models
> #1.1,-0.86775,0.050879,0.49439,343.64,0.011577,0.99655,-0.082238,279.48,-0.49687,-0.065638,-0.86534,571.42
> ui mousemode right "translate selected models"
> view matrix models
> #1.1,-0.86775,0.050879,0.49439,333.92,0.011577,0.99655,-0.082238,30.853,-0.49687,-0.065638,-0.86534,523.79
> view matrix models
> #1.1,-0.86775,0.050879,0.49439,295.18,0.011577,0.99655,-0.082238,28.515,-0.49687,-0.065638,-0.86534,541.89
> fitmap #1.1 inMap #1.5
Fit map cryosparc_P1_J21_class_00_00082_volume.mrc in map ec8 ribso _
cryosparc_P26_J24_001_volume_map.mrc using 35119 points
correlation = 0.721, correlation about mean = 0.03307, overlap = 3.689e+04
steps = 80, shift = 20.6, angle = 5.74 degrees
Position of cryosparc_P1_J21_class_00_00082_volume.mrc (#1.1) relative to ec8
ribso _ cryosparc_P26_J24_001_volume_map.mrc (#1.5) coordinates:
Matrix rotation and translation
-0.87904037 0.05814652 0.47318811 286.00293464
-0.02689875 0.98490425 -0.17099722 60.27817937
-0.47598788 -0.16304163 -0.86420654 543.34349682
Axis 0.00834784 0.99597531 -0.08923845
Axis point 212.07396948 0.00000000 237.97925158
Rotation angle (degrees) 151.54256293
Shift along axis 13.93595284
> flip vol #1.1
Unknown command: flip vol #1.1
> volume flip #1.1
Opened cryosparc_P1_J21_class_00_00082_volume.mrc z flip as #2, grid size
128,128,128, pixel 3.32, shown at step 1, values float32
> select subtract #1.1
Nothing selected
> select add #2
2 models selected
> view matrix models
> #2,-0.87904,0.058147,0.47319,67.46,-0.026899,0.9849,-0.171,74.449,-0.47599,-0.16304,-0.86421,426.46
> volume #1.5 level 2.843
> select subtract #2
Nothing selected
> select add #1.5
3 models selected
> view matrix models #1.5,1,0,0,53.199,0,1,0,-242.88,0,0,1,48.771
> view matrix models #1.5,1,0,0,40.959,0,1,0,-178.06,0,0,1,11.287
> select subtract #1.5
Nothing selected
> select add #2
2 models selected
> view matrix models
> #2,-0.87904,0.058147,0.47319,252.32,-0.026899,0.9849,-0.171,128.98,-0.47599,-0.16304,-0.86421,502.29
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.80184,-0.38658,0.45564,337.81,-0.5176,0.83036,-0.20639,271.72,-0.29856,-0.40133,-0.86591,518.37
> select subtract #2
Nothing selected
> select add #1.5
3 models selected
> view matrix models
> #1.5,0.79342,-0.59427,-0.13166,244.2,0.60571,0.74948,0.2672,-306.26,-0.060109,-0.29175,0.9546,98.313
> view matrix models
> #1.5,0.97421,-0.22056,0.047738,85.168,0.21428,0.97047,0.11077,-239.99,-0.07076,-0.097684,0.9927,49.356
> volume #2 level 0.732
> volume #1.5 level 2.362
> select subtract #1.5
Nothing selected
> select add #2
2 models selected
> view matrix models
> #2,0.93117,-0.20995,-0.29807,96.375,0.10988,0.94114,-0.31966,140.99,0.34764,0.2649,0.89943,-126.85
> view matrix models
> #2,0.93098,-0.2458,-0.26992,98.476,0.15832,0.93807,-0.30816,129.27,0.32895,0.24416,0.91224,-121.07
> view matrix models
> #2,0.96837,-0.21465,0.12722,1.7723,0.23615,0.95307,-0.18944,85.326,-0.080583,0.21349,0.97362,-42.313
> view matrix models
> #2,0.73131,0.22218,-0.64484,114.38,-0.31172,0.94981,-0.026266,165.62,0.60664,0.22022,0.76386,-142.56
> view matrix models
> #2,0.97422,-0.097266,-0.20356,43.144,0.10501,0.99409,0.027563,58.557,0.19967,-0.048228,0.97867,-43.765
> ui mousemode right "move picked models"
> view matrix models
> #2,0.97422,-0.097266,-0.20356,94.227,0.10501,0.99409,0.027563,-205.79,0.19967,-0.048228,0.97867,-26.277
> fitmap #2 inMap #1.5
Fit map cryosparc_P1_J21_class_00_00082_volume.mrc z flip in map ec8 ribso _
cryosparc_P26_J24_001_volume_map.mrc using 30535 points
correlation = 0.9659, correlation about mean = 0.4349, overlap = 7.359e+04
steps = 108, shift = 24.4, angle = 13.3 degrees
Position of cryosparc_P1_J21_class_00_00082_volume.mrc z flip (#2) relative to
ec8 ribso _ cryosparc_P26_J24_001_volume_map.mrc (#1.5) coordinates:
Matrix rotation and translation
0.99210363 -0.04662971 -0.11643040 38.35017241
0.04643768 0.99891165 -0.00436286 -5.42524750
0.11650713 -0.00107835 0.99318926 -18.05192088
Axis 0.01309282 -0.92854496 0.37098900
Axis point 169.84644192 0.00000000 317.99388157
Rotation angle (degrees) 7.20567384
Shift along axis -1.15736590
> select subtract #2
Nothing selected
> show #!1.2 models
> volume flip #1.2
Opened cryosparc_P1_J21_class_01_00082_volume.mrc z flip as #3, grid size
128,128,128, pixel 3.32, shown at step 1, values float32
> select add #3
2 models selected
> view matrix models #3,1,0,0,-51.787,0,1,0,183.66,0,0,1,12.121
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.29762,-0.62657,0.7203,207.47,-0.6305,0.69554,0.34452,310.79,-0.71687,-0.35161,-0.60206,579.58
> view matrix models
> #3,-0.79389,0.20748,0.57157,164.24,0.306,0.94861,0.080688,112.58,-0.52545,0.23896,-0.81658,456.55
> view matrix models
> #3,0.83603,-0.48745,-0.25188,141.77,0.49588,0.86775,-0.033398,113.78,0.23485,-0.096978,0.96718,-9.9529
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.83603,-0.48745,-0.25188,221.39,0.49588,0.86775,-0.033398,-246.45,0.23485,-0.096978,0.96718,-18.822
> fitmap #3 inMap #1.5
Fit map cryosparc_P1_J21_class_01_00082_volume.mrc z flip in map ec8 ribso _
cryosparc_P26_J24_001_volume_map.mrc using 20947 points
correlation = 0.7591, correlation about mean = 0.07423, overlap = 3.427e+04
steps = 80, shift = 8.79, angle = 5.86 degrees
Position of cryosparc_P1_J21_class_01_00082_volume.mrc z flip (#3) relative to
ec8 ribso _ cryosparc_P26_J24_001_volume_map.mrc (#1.5) coordinates:
Matrix rotation and translation
0.85865824 -0.31609739 -0.40347053 168.15177579
0.31691075 0.94610174 -0.06677631 -42.35346314
0.40283199 -0.07052612 0.91255271 -54.79095459
Axis -0.00365798 -0.78655721 0.61750658
Axis point 208.86003374 0.00000000 343.58637281
Rotation angle (degrees) 30.83394954
Shift along axis -1.13544967
> select subtract #3
Nothing selected
> volume #3 level 0.1077
> volume #1.5 level 0.2597
> volume #2 level 0.1217
> hide #!1.5 models
> volume #2 level 0.1832
> select add #3
2 models selected
> view matrix models
> #3,0.78584,-0.51998,-0.33477,-22.182,0.53617,0.84262,-0.050178,-45.066,0.30818,-0.14006,0.94096,-91.786
> show #!1.5 models
> ui tool show "Side View"
> view matrix models
> #3,0.78584,-0.51998,-0.33477,68.311,0.53617,0.84262,-0.050178,39.274,0.30818,-0.14006,0.94096,-93.421
> ui tool show "Side View"
> hide #!1.5 models
> volume #2 level 0.7461
> volume #3 level 0.8397
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.49188,-0.85964,-0.13811,161.96,0.85823,0.50543,-0.089389,53.055,0.14665,-0.074564,0.98637,-83.332
> view matrix models
> #3,0.53436,-0.78593,-0.31108,173.83,0.84055,0.45531,0.29355,-13.815,-0.089072,-0.41834,0.90391,58.338
> view matrix models
> #3,0.47097,-0.86582,-0.16896,174.25,0.88156,0.46896,0.054206,25.516,0.032301,-0.17447,0.98413,-37.143
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.47097,-0.86582,-0.16896,363.62,0.88156,0.46896,0.054206,-278.85,0.032301,-0.17447,0.98413,34.992
> view matrix models
> #3,0.47097,-0.86582,-0.16896,570.06,0.88156,0.46896,0.054206,-82.55,0.032301,-0.17447,0.98413,65.599
> hide #!3 models
> select subtract #3
Nothing selected
> show #!1.2 models
> select add #1.2
2 models selected
> ui mousemode right "move picked models"
> view matrix models #1.2,1,0,0,-46.824,0,1,0,131.46,0,0,1,-39.466
> volume #1.2 level 0.7909
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2,-0.92575,0.32246,-0.19751,329.36,0.34939,0.92917,-0.12067,98.625,0.14461,-0.18072,-0.97284,382.12
> ui mousemode right "translate selected models"
> view matrix models
> #1.2,-0.92575,0.32246,-0.19751,374.11,0.34939,0.92917,-0.12067,-229.24,0.14461,-0.18072,-0.97284,419.22
> view matrix models
> #1.2,-0.92575,0.32246,-0.19751,412.63,0.34939,0.92917,-0.12067,-200.84,0.14461,-0.18072,-0.97284,432.74
> fitmap #1.2 inMap #1.5
Fit map cryosparc_P1_J21_class_01_00082_volume.mrc in map ec8 ribso _
cryosparc_P26_J24_001_volume_map.mrc using 34669 points
correlation = 0.9854, correlation about mean = 0.6691, overlap = 1.041e+05
steps = 140, shift = 18.2, angle = 26.6 degrees
Position of cryosparc_P1_J21_class_01_00082_volume.mrc (#1.2) relative to ec8
ribso _ cryosparc_P26_J24_001_volume_map.mrc (#1.5) coordinates:
Matrix rotation and translation
-0.99050071 0.13387079 0.03141579 389.76063571
0.13491486 0.99027827 0.03386622 -32.76627774
-0.02657668 0.03778297 -0.99893249 419.68182879
Axis 0.06737460 0.99756609 0.01795979
Axis point 199.04448103 0.00000000 207.29661360
Rotation angle (degrees) 178.33434993
Shift along axis 1.11083680
> select subtract #1.2
Nothing selected
> close #3
> volume #1.2 level 0.1511
> volume #1.1 level 0.2258
> hide #!1.1 models
> volume #2 level 0.2494
> hide #!1.2 models
> show #!1.2 models
> hide #!2 models
> show #!2 models
> hide #!1.2 models
> volume #2 level 0.1927
> show #!1.2 models
> hide #!2 models
> show #!2 models
> open "/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /3DV_tRNA/J39
> and exit focus mask /NU/cryosparc_P1_J49_001_volume_map.mrc"
Opened cryosparc_P1_J49_001_volume_map.mrc as #3, grid size 128,128,128, pixel
3.32, shown at level 1.03, step 1, values float32
> hide #!3 models
> show #!3 models
> select add #3
2 models selected
> view matrix models #3,1,0,0,24.71,0,1,0,202.88,0,0,1,-3.9617
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.072445,-0.97579,-0.20636,483.67,0.99716,0.066555,0.035351,179.9,-0.020761,-0.20833,0.97784,50.563
> volume #3 level 0.3494
> view matrix models
> #3,-0.41159,-0.8195,0.39876,421.88,0.88355,-0.25154,0.39505,194.36,-0.22344,0.51492,0.8276,-29.018
> view matrix models
> #3,-0.9777,0.18356,-0.10199,433.06,-0.19037,-0.56983,0.79941,398.73,0.088623,0.801,0.59207,-104.37
> view matrix models
> #3,-0.92618,-0.15855,-0.34212,546.29,-0.18482,-0.59997,0.77838,408.47,-0.32867,0.78415,0.52638,-0.13226
> view matrix models
> #3,-0.96475,-0.1531,-0.21405,525.82,-0.083596,-0.59296,0.80088,381.17,-0.24954,0.79054,0.55926,-24.935
> view matrix models
> #3,0.065037,-0.52256,-0.85012,526.2,-0.85526,-0.4681,0.22231,638.26,-0.51411,0.71261,-0.47737,267.68
> view matrix models
> #3,-0.37866,0.91122,-0.16217,166.87,-0.51508,-0.35304,-0.78106,757.2,-0.76897,-0.21222,0.60303,286.69
> view matrix models
> #3,-0.65303,-0.082836,-0.75279,561.08,0.66706,-0.53356,-0.51994,494.42,-0.35859,-0.84169,0.40369,377.78
> view matrix models
> #3,-0.82059,-0.57126,-0.017374,542.8,0.45342,-0.63221,-0.62827,582.85,0.34792,-0.52343,0.7778,83.646
> view matrix models
> #3,-0.88696,-0.37198,-0.27374,568.92,0.40585,-0.91064,-0.077575,534.43,-0.22042,-0.1799,0.95867,90.064
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.88696,-0.37198,-0.27374,565.38,0.40585,-0.91064,-0.077575,181.61,-0.22042,-0.1799,0.95867,112.03
> view matrix models
> #3,-0.88696,-0.37198,-0.27374,590.17,0.40585,-0.91064,-0.077575,183.55,-0.22042,-0.1799,0.95867,125.08
> fitmap #3 inMap #1.5
Fit map cryosparc_P1_J49_001_volume_map.mrc in map ec8 ribso _
cryosparc_P26_J24_001_volume_map.mrc using 90654 points
correlation = 0.6602, correlation about mean = 0.08202, overlap = 7.721e+04
steps = 144, shift = 15.9, angle = 17.5 degrees
Position of cryosparc_P1_J49_001_volume_map.mrc (#3) relative to ec8 ribso _
cryosparc_P26_J24_001_volume_map.mrc (#1.5) coordinates:
Matrix rotation and translation
-0.75272183 -0.65235640 -0.08854928 538.31741431
0.65377279 -0.75652257 0.01596052 242.32445992
-0.07740148 -0.04587728 0.99594392 36.95955406
Axis -0.04728963 -0.00852513 0.99884484
Axis point 224.87033254 221.69863149 0.00000000
Rotation angle (degrees) 139.16977402
Shift along axis 9.39417879
> show #!1.5 models
> hide #!2 models
> hide #!1.2 models
> view matrix models
> #3,-0.88119,-0.47086,-0.042241,905.59,0.4646,-0.87905,0.10684,151.65,-0.087437,0.074518,0.99338,56.411
> volume #1.5 level 2.453
> volume #3 level 1.048
> view matrix models
> #3,-0.88119,-0.47086,-0.042241,760.19,0.4646,-0.87905,0.10684,455.72,-0.087437,0.074518,0.99338,75.516
> view matrix models
> #3,-0.88119,-0.47086,-0.042241,601.31,0.4646,-0.87905,0.10684,424.41,-0.087437,0.074518,0.99338,2.4642
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.93658,0.26029,-0.23468,494.67,-0.31343,-0.92168,0.2286,578.73,-0.15679,0.28766,0.94481,-18.537
> view matrix models
> #3,0.22543,0.90968,-0.3488,122.55,-0.82218,0.3697,0.43283,366.49,0.52269,0.1892,0.83126,-122.28
> view matrix models
> #3,-0.10665,-0.49834,-0.8604,608.85,-0.91707,0.38367,-0.10855,497.64,0.3842,0.77747,-0.49793,58.455
> view matrix models
> #3,0.1994,-0.20678,-0.95785,498.74,-0.42933,-0.89711,0.1043,624.82,-0.88086,0.39044,-0.26766,371.75
> view matrix models
> #3,-0.35419,-0.37217,-0.85793,635.14,-0.23823,0.92304,-0.30207,272,0.90432,0.097394,-0.41559,75.171
> view matrix models
> #3,-0.33516,-0.39505,-0.85534,635.41,-0.32949,0.89967,-0.28642,293.81,0.88267,0.18582,-0.4317,64.05
> view matrix models
> #3,-0.92217,-0.31183,0.22885,518.91,-0.27877,0.94597,0.16564,177.94,-0.26813,0.088955,-0.95927,447.88
> view matrix models
> #3,-0.72055,0.68192,-0.12568,332.74,0.66151,0.73036,0.17024,17.777,0.20789,0.039528,-0.97735,358.08
> view matrix models
> #3,-0.70214,0.70382,-0.10788,320.21,0.70058,0.70993,0.071938,34.244,0.12722,-0.025071,-0.99156,392.79
> view matrix models
> #3,-0.67761,0.72981,-0.09065,305.57,0.73488,0.67666,-0.04557,58.575,0.028082,-0.097496,-0.99484,430.97
> view matrix models
> #3,-0.99089,0.043863,0.12734,477.84,0.030903,0.9943,-0.10202,155.6,-0.13109,-0.097159,-0.9866,464.06
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.99089,0.043863,0.12734,520.61,0.030903,0.9943,-0.10202,-129.69,-0.13109,-0.097159,-0.9866,513.36
> view matrix models
> #3,-0.99089,0.043863,0.12734,433.25,0.030903,0.9943,-0.10202,-161.96,-0.13109,-0.097159,-0.9866,471.61
> fitmap #3 inMap #1.5
Fit map cryosparc_P1_J49_001_volume_map.mrc in map ec8 ribso _
cryosparc_P26_J24_001_volume_map.mrc using 19724 points
correlation = 0.9856, correlation about mean = 0.5281, overlap = 7.675e+04
steps = 96, shift = 8.78, angle = 11.6 degrees
Position of cryosparc_P1_J49_001_volume_map.mrc (#3) relative to ec8 ribso _
cryosparc_P26_J24_001_volume_map.mrc (#1.5) coordinates:
Matrix rotation and translation
-0.99046393 0.13433827 0.03056879 389.92147029
0.13536522 0.99019673 0.03444858 -32.97413471
-0.02564135 0.03825803 -0.99893886 419.33006021
Axis 0.06760525 0.99754568 0.01822498
Axis point 199.03937544 0.00000000 207.21303899
Rotation angle (degrees) 178.38552271
Shift along axis 1.10981212
> select subtract #3
Nothing selected
> volume #3 level 0.3305
> volume #1.5 level 0.8304
> show #!2 models
> show #!1.2 models
> hide #!1.5 models
> volume #3 level 0.255
> volume #3 level 0.3242
> volume #1.2 level 0.2487
> hide #!2 models
> hide #!1.2 models
> volume #3 level 0.2613
> volume #3 level 0.3494
> show #!1.2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!1.2 models
> volume #2 level 0.169
> show #!1.4 models
> hide #!1.4 models
> show #!1.5 models
> hide #!2 models
> show #!2 models
> hide #!1.5 models
> show #!1.2 models
> hide #!2 models
> open /Users/haandrew/Downloads/4v88-assembly1.cif
Summary of feedback from opening /Users/haandrew/Downloads/4v88-assembly1.cif
---
warnings | Ignoring microheterogeneity for label_seq_id 3 in chain BO
Ignoring microheterogeneity for label_seq_id 4 in chain BO
Ignoring microheterogeneity for label_seq_id 11 in chain BO
Ignoring microheterogeneity for label_seq_id 13 in chain BO
Ignoring microheterogeneity for label_seq_id 16 in chain BO
15 messages similar to the above omitted
notes | Fetching CCD OHX from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/OHX/OHX.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
4v88-assembly1.cif title:
The structure of the eukaryotic ribosome at 3.0 A resolution. [more info...]
Chain information for 4v88-assembly1.cif #4
---
Chain | Description
A1 | 25S rRNA
A2 | 18S RIBOSOMAL RNA
A3 | 5S rRNA
A4 | 5.8S rRNA
AA | 40S ribosomal protein S0-A
AB | 40S ribosomal protein S1-A
AC | 40S ribosomal protein S2
AD | 40S ribosomal protein S3
AE | 40S ribosomal protein S4-A
AF | 40S ribosomal protein S5
AG | 40S ribosomal protein S6-A
AH | 40S ribosomal protein S7-A
AI | 40S ribosomal protein S8-A
AJ | 40S ribosomal protein S9-A
AK | 40S ribosomal protein S10-A
AL | 40S ribosomal protein S11-A
AM | 40S ribosomal protein S12
AN | 40S ribosomal protein S13
AO | 40S ribosomal protein S14-A
AP | 40S ribosomal protein S15
AQ | 40S ribosomal protein S16-A
AR | 40S ribosomal protein S17-A
AS | 40S ribosomal protein S18-A
AT | 40S ribosomal protein S19-A
AU | 40S ribosomal protein S20
AV | 40S ribosomal protein S21-A
AW | 40S ribosomal protein S22-A
AX | 40S ribosomal protein S23-A
AY | 40S ribosomal protein S24-A
AZ | 40S ribosomal protein S25-A
Aa | 40S ribosomal protein S26-A
Ab | 40S ribosomal protein S27-A
Ac | 40S ribosomal protein S28-A
Ad | 40S ribosomal protein S29-A
Ae | 40S ribosomal protein S30-A
Af | 40S ribosomal protein S31
Ag | Guanine nucleotide-binding protein subunit beta-like protein (ASC1, RACK1)
Ah | Suppressor protein STM1
BA | 60S ribosomal protein L2-A
BB | 60S ribosomal protein L3
BC | 60S ribosomal protein L4-A
BD | 60S ribosomal protein L5
BE | 60S ribosomal protein L6-A
BF | 60S ribosomal protein L7-A
BG | 60S ribosomal protein L8-A
BH | 60S ribosomal protein L9-A
BI | 60S ribosomal protein L10
BJ | 60S ribosomal protein L11-A
BL | 60S ribosomal protein L13-A
BM | 60S ribosomal protein L14-A
BN | 60S ribosomal protein L15-A
BO | 60S ribosomal protein L16-A, 60S ribosomal protein L16-B
BP | 60S ribosomal protein L17-A
BQ | 60S ribosomal protein L18-A
BR | 60S ribosomal protein L19-A
BS | 60S ribosomal protein L20-A
BT | 60S ribosomal protein L21-A
BU | 60S ribosomal protein L22-A
BV | 60S ribosomal protein L23-A
BW | 60S ribosomal protein L24-A
BX | 60S ribosomal protein L25
BY | 60S ribosomal protein L26-A
BZ | 60S ribosomal protein L27-A
Ba | 60S ribosomal protein L28
Bb | 60S ribosomal protein L29
Bc | 60S ribosomal protein L30
Bd | 60S ribosomal protein L31-A
Be | 60S ribosomal protein L32
Bf | 60S ribosomal protein L33-A
Bg | 60S ribosomal protein L34-A
Bh | 60S ribosomal protein L35-A
Bi | 60S ribosomal protein L36-A
Bj | 60S ribosomal protein L37-A
Bk | 60S ribosomal protein L38
Bl | 60S ribosomal protein L39
Bm | 60S ribosomal protein L40
Bn | 60S ribosomal protein L41-A
Bo | 60S ribosomal protein L42-A
Bp | 60S ribosomal protein L43-A
Non-standard residues in 4v88-assembly1.cif #4
---
MG — magnesium ion
OHX — osmium (III) hexammine (osmium(6+) hexaazanide)
ZN — zinc ion
1577 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!3 models
> volume #1.2 level 0.8994
> select add #4
205475 atoms, 214568 bonds, 3951 pseudobonds, 18187 residues, 3 models
selected
> view matrix models #4,1,0,0,-103.03,0,1,0,229.25,0,0,1,68.795
> view matrix models #4,1,0,0,-67.156,0,1,0,273.98,0,0,1,71.597
> view matrix models #4,1,0,0,28.314,0,1,0,195.21,0,0,1,102.81
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.68155,-0.40396,0.61017,-13.39,-0.67484,-0.024512,0.73756,148.54,-0.28299,-0.91445,-0.28931,203.28
> view matrix models
> #4,0.70085,-0.65415,0.28442,13.609,-0.65804,-0.43905,0.61174,163.84,-0.27529,-0.6159,-0.73816,230.63
> view matrix models
> #4,0.4176,0.90014,0.1239,-2.3526,0.075415,-0.17023,0.98251,144.4,0.90549,-0.40096,-0.13897,202.41
> view matrix models
> #4,-0.10506,0.407,0.90736,-57.945,-0.62619,-0.73589,0.25758,193.72,0.77256,-0.54112,0.33218,169.3
> view matrix models
> #4,0.3048,-0.010693,0.95236,-48.906,-0.14709,-0.98847,0.035977,220.13,0.94099,-0.15105,-0.30286,210.77
> view matrix models
> #4,0.51209,0.83619,-0.19633,22.582,0.017158,-0.23848,-0.971,282.43,-0.85876,0.49387,-0.13647,163.1
> view matrix models
> #4,0.065708,0.97377,-0.21784,15.523,-0.44681,-0.16649,-0.879,268.08,-0.89221,0.15509,0.42415,128.09
> view matrix models
> #4,0.27476,0.89196,-0.35905,29.765,-0.5329,-0.16956,-0.82902,263.34,-0.80033,0.41912,0.42873,125.18
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.27476,0.89196,-0.35905,240.37,-0.5329,-0.16956,-0.82902,48.378,-0.80033,0.41912,0.42873,176
> fitmap #4 inMap #1.5
Fit molecule 4v88-assembly1.cif (#4) to map ec8 ribso _
cryosparc_P26_J24_001_volume_map.mrc (#1.5) using 205475 atoms
average map value = 2.194, steps = 176
shifted from previous position = 69.6
rotated from previous position = 18.1 degrees
atoms outside contour = 14569, contour level = 0.83042
Position of 4v88-assembly1.cif (#4) relative to ec8 ribso _
cryosparc_P26_J24_001_volume_map.mrc (#1.5) coordinates:
Matrix rotation and translation
0.10831814 0.66978833 -0.73460926 267.65012188
-0.36158849 -0.66179743 -0.65671754 267.04321614
-0.92602427 0.33676068 0.17050308 200.06741212
Axis 0.68763492 0.13248770 -0.71386640
Axis point 307.02674187 87.78252752 0.00000000
Rotation angle (degrees) 133.74802072
Shift along axis 76.60410742
> select subtract #4
Nothing selected
> volume #1.2 level 0.2108
> color #4 #666666ff
> colour zone #1.2 onmap #4 distance 5
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> colour zone #1.2 onmap #4
> color zone #1.2 onmap #4
Expected a keyword
> colour zone #1.2 onmap #4 distance 5
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> colour zone #1.2 onmap #4 distance 5
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> colour zone #1.2 onmap #4 distance 5
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> colour zone #1.2 onmap #4 distance 5
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> colour zone #1.2 onmap #4 distance 5
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> colour zone #1.2 onmap #4 distance 5
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> colour zone #1.2 onmap #4 distance 5
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> colour zone #1.2 onmap #4 distance 5
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> colour zone #1.2 onmap #4 distance 5
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> colour zone #1.2 onmap #4 distance 5
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> colour zone #1.2 onmap #4 distance 5
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> colour zone #1.2 onmap #4 distance 5
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> colour zone #1.2 onmap #4 distance 5
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> colour zone #1.2 onmap #4 distance 5
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> save "/Users/haandrew/Downloads/class 0 and 1 .cxs"
> close session
> open "/Users/haandrew/Downloads/191025 scribo overlay figures .cxs" format
> session
Opened cryosparc_P1_J49_001_volume_map.mrc as #2.1, grid size 128,128,128,
pixel 3.32, shown at level 0.312, step 1, values float32
Opened cryosparc_P1_J49_001_volume_map_sharp.mrc as #2.2, grid size
128,128,128, pixel 3.32, shown at level 0.632, step 1, values float32
Opened ec8 ribso _ cryosparc_P26_J24_001_volume_map.mrc as #3, grid size
128,128,128, pixel 3.35, shown at level 0.906, step 1, values float32
Opened NU_cryosparc_P1_J23_002_volume_map_sharp.mrc as #1, grid size
128,128,128, pixel 3.35, shown at level 5.73, step 1, values float32
Opened NU_cryosparc_P1_J23_002_volume_map_sharp.mrc z flip as #4, grid size
128,128,128, pixel 3.35, shown at level 0.317, step 1, values float32
opened ChimeraX session
> select up
204962 atoms, 220182 bonds, 5200 pseudobonds, 16898 residues, 2 models
selected
> select up
569952 atoms, 605180 bonds, 5200 pseudobonds, 49343 residues, 12 models
selected
> select up
569952 atoms, 605180 bonds, 7346 pseudobonds, 49343 residues, 170 models
selected
> select up
569952 atoms, 605180 bonds, 7376 pseudobonds, 49343 residues, 172 models
selected
> select up
569952 atoms, 605180 bonds, 7376 pseudobonds, 49343 residues, 172 models
selected
> select up
569952 atoms, 605180 bonds, 7376 pseudobonds, 49343 residues, 172 models
selected
> select up
569952 atoms, 605180 bonds, 7376 pseudobonds, 49343 residues, 172 models
selected
> select up
569952 atoms, 605180 bonds, 7376 pseudobonds, 49343 residues, 172 models
selected
> select up
569952 atoms, 605180 bonds, 7376 pseudobonds, 49343 residues, 172 models
selected
> select up
569952 atoms, 605180 bonds, 7376 pseudobonds, 49343 residues, 172 models
selected
> select up
569952 atoms, 605180 bonds, 7376 pseudobonds, 49343 residues, 172 models
selected
> select up
569952 atoms, 605180 bonds, 7376 pseudobonds, 49343 residues, 172 models
selected
> select up
569952 atoms, 605180 bonds, 7376 pseudobonds, 49343 residues, 172 models
selected
> close session
> open "/Users/haandrew/Downloads/class 0 and 1 .cxs" format session
Opened cryosparc_P1_J21_class_00_00082_volume.mrc as #1.1, grid size
128,128,128, pixel 3.32, shown at level 0.226, step 1, values float32
Opened cryosparc_P1_J21_class_01_00082_volume.mrc as #1.2, grid size
128,128,128, pixel 3.32, shown at level 0.211, step 1, values float32
Opened cryosparc_P1_J21_class_00_00082_volume_sharp.mrc as #1.3, grid size
128,128,128, pixel 3.32, shown at level 0.847, step 1, values float32
Opened cryosparc_P1_J21_class_01_00082_volume_sharp.mrc as #1.4, grid size
128,128,128, pixel 3.32, shown at level 1.06, step 1, values float32
Opened ec8 ribso _ cryosparc_P26_J24_001_volume_map.mrc as #1.5, grid size
128,128,128, pixel 3.35, shown at level 0.83, step 1, values float32
Opened cryosparc_P1_J21_class_00_00082_volume.mrc z flip as #2, grid size
128,128,128, pixel 3.32, shown at level 0.169, step 1, values float32
Opened cryosparc_P1_J49_001_volume_map.mrc as #3, grid size 128,128,128, pixel
3.32, shown at level 0.349, step 1, values float32
opened ChimeraX session
> color #1.2 on #4 distance 5
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> ui tool show "Color Actions"
> color zonee #1.2 onmap #4 distance 5
Expected a keyword
> color zone #1.2 onmap #4 distance 5
Expected a keyword
> select add #4
205475 atoms, 214568 bonds, 3951 pseudobonds, 18187 residues, 3 models
selected
> show sel cartoons
> hide sel atoms
> hide sel surfaces
> select subtract #4
Nothing selected
> color zone #1.2 near #4 distance 10
> hide #!1.2 models
> hide #!4 models
> show #!1.5 models
> hide #!1.5 models
> show #!3 models
> open "/Users/haandrew/Documents/SND constructs /PDB/scSnd1.pdb"
scSnd1.pdb title:
Alphafold monomer V2.0 prediction for SRP-independent targeting protein 1
(Q04007) [more info...]
Chain information for scSnd1.pdb #5
---
Chain | Description | UniProt
A | SRP-independent targeting protein 1 | SND1_YEAST 1-877
> select add #5
6914 atoms, 7029 bonds, 877 residues, 1 model selected
> view matrix models #5,1,0,0,27.262,0,1,0,320.98,0,0,1,262.31
> select subtract #5
Nothing selected
> select add #5
6914 atoms, 7029 bonds, 877 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.19697,0.28176,-0.93905,9.5755,-0.28139,0.93376,0.22116,325.14,0.93916,0.22068,0.26321,248.45
> view matrix models
> #5,0.52948,0.84804,0.021896,24.728,-0.78207,0.47796,0.3999,329.89,0.32867,-0.22886,0.9163,261.62
> view matrix models
> #5,0.36436,-0.80402,-0.46989,21.664,0.92866,0.27605,0.24776,327.89,-0.069494,-0.52665,0.84724,261.41
> view matrix models
> #5,0.48766,0.14482,-0.86094,11.439,0.78743,0.35289,0.50538,332.21,0.37701,-0.92439,0.058054,248.74
> view matrix models
> #5,0.44428,0.033023,-0.89528,11.213,0.8269,0.36943,0.42397,330.7,0.34475,-0.92867,0.13683,250.15
> view matrix models
> #5,-0.72517,-0.48269,-0.49106,20.173,0.6878,-0.54158,-0.48335,317.69,-0.03264,-0.68826,0.72473,259.79
> view matrix models
> #5,-0.11889,0.99248,-0.029135,23.318,-0.18192,-0.05062,-0.98201,307.12,-0.9761,-0.11145,0.18657,248.22
> view matrix models
> #5,0.88647,0.12001,-0.44696,18.894,-0.40499,-0.26624,-0.8747,309.77,-0.22397,0.95641,-0.1874,237.89
> view matrix models
> #5,-0.69964,-0.24899,-0.6697,16.189,-0.68246,-0.044627,0.72956,337.56,-0.21154,0.96748,-0.1387,238.72
> view matrix models
> #5,0.67181,0.10989,-0.73253,13.846,-0.64804,-0.39178,-0.65311,314.15,-0.35876,0.91347,-0.19198,237.96
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.67181,0.10989,-0.73253,0.90286,-0.64804,-0.39178,-0.65311,96.575,-0.35876,0.91347,-0.19198,227.77
> view matrix models
> #5,0.67181,0.10989,-0.73253,213.66,-0.64804,-0.39178,-0.65311,60.723,-0.35876,0.91347,-0.19198,191.4
> view matrix models
> #5,0.67181,0.10989,-0.73253,218.28,-0.64804,-0.39178,-0.65311,66.107,-0.35876,0.91347,-0.19198,205.5
> hide #!3 models
> select clear
> ui mousemode right zoom
> select #5:1-270
2168 atoms, 2205 bonds, 270 residues, 1 model selected
> show #!3 models
> hide #!3 models
> show #!3 models
> fitmap sel inMap @#
Invalid "inMap" argument: invalid density map specifier
> fitmap sel inMap @#
Invalid "inMap" argument: invalid density map specifier
> fitmap sel inMap #3
Fit molecule scSnd1.pdb (#5) to map cryosparc_P1_J49_001_volume_map.mrc (#3)
using 2168 atoms
average map value = 0.4293, steps = 64
shifted from previous position = 9.98
rotated from previous position = 23.7 degrees
atoms outside contour = 846, contour level = 0.34937
Position of scSnd1.pdb (#5) relative to cryosparc_P1_J49_001_volume_map.mrc
(#3) coordinates:
Matrix rotation and translation
-0.42545675 0.26794900 0.86440147 243.69999112
-0.80583069 -0.54686148 -0.22711104 238.87574228
0.41185369 -0.79318716 0.44858744 224.62274710
Axis -0.43696557 0.34933075 -0.82887220
Axis point 131.82670135 133.00131531 0.00000000
Rotation angle (degrees) 139.62892411
Shift along axis -209.22541132
> select clear
> transparency #3 50
> transparency #3 0
> rename #5 "scSnd1 Tunnel .pdb"
> open "/Users/haandrew/Documents/SND constructs /PDB/scSnd1.pdb"
scSnd1.pdb title:
Alphafold monomer V2.0 prediction for SRP-independent targeting protein 1
(Q04007) [more info...]
Chain information for scSnd1.pdb #6
---
Chain | Description | UniProt
A | SRP-independent targeting protein 1 | SND1_YEAST 1-877
> rename #6 "scSnd1 exit .pdb"
> select add #6
6914 atoms, 7029 bonds, 877 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-7.3885,0,1,0,-212.53,0,0,1,171.33
> view matrix models #6,1,0,0,135.29,0,1,0,-136.08,0,0,1,200.08
> view matrix models #6,1,0,0,217.6,0,1,0,-192.08,0,0,1,202.2
> view matrix models #6,1,0,0,322.46,0,1,0,-66.218,0,0,1,232
> view matrix models #6,1,0,0,339.96,0,1,0,-59.021,0,0,1,218.07
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.64243,-0.54292,-0.54086,332.2,0.45908,0.83776,-0.29565,-63.72,0.61362,-0.058364,0.78744,214.49
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.64243,-0.54292,-0.54086,330.06,0.45908,0.83776,-0.29565,-61.522,0.61362,-0.058364,0.78744,218.77
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.59716,-0.38192,-0.70536,326.58,0.26768,0.92385,-0.2736,-61.428,0.75614,-0.025426,0.65392,216.29
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.59716,-0.38192,-0.70536,330.13,0.26768,0.92385,-0.2736,-64.99,0.75614,-0.025426,0.65392,214.53
> select #6:1-270
2168 atoms, 2205 bonds, 270 residues, 1 model selected
> fitmap sel inMap #3
Fit molecule scSnd1 exit .pdb (#6) to map cryosparc_P1_J49_001_volume_map.mrc
(#3) using 2168 atoms
average map value = 0.5961, steps = 244
shifted from previous position = 65.4
rotated from previous position = 19.1 degrees
atoms outside contour = 699, contour level = 0.34937
Position of scSnd1 exit .pdb (#6) relative to
cryosparc_P1_J49_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.63786364 0.28488752 0.71552014 197.83618175
0.38874939 0.92112226 -0.02019109 135.70105868
-0.66483372 0.26527886 -0.69830025 192.84507026
Axis 0.20197607 0.97662976 0.07348449
Axis point 122.84099921 0.00000000 57.38660800
Rotation angle (degrees) 135.03355832
Shift along axis 186.65898915
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.52551,0.44579,0.72464,349.16,-0.27548,-0.89501,0.35083,-44.057,0.80496,-0.015261,0.59314,215.17
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.52551,0.44579,0.72464,325.47,-0.27548,-0.89501,0.35083,-54.982,0.80496,-0.015261,0.59314,220.38
> view matrix models
> #6,-0.52551,0.44579,0.72464,329.44,-0.27548,-0.89501,0.35083,-58.548,0.80496,-0.015261,0.59314,215.65
> view matrix models
> #6,-0.52551,0.44579,0.72464,330.5,-0.27548,-0.89501,0.35083,-56.042,0.80496,-0.015261,0.59314,225.18
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.52551,0.44579,0.72464,330.56,-0.27548,-0.89501,0.35083,-56.565,0.80496,-0.015261,0.59314,221.78
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.64352,0.60926,0.46334,325.34,-0.2389,-0.73496,0.63463,-52.065,0.7272,0.2977,0.61851,221.15
> fitmap sel inMap #3
Fit molecule scSnd1 exit .pdb (#6) to map cryosparc_P1_J49_001_volume_map.mrc
(#3) using 6914 atoms
average map value = 0.5294, steps = 176
shifted from previous position = 69.6
rotated from previous position = 18.8 degrees
atoms outside contour = 2624, contour level = 0.34937
Position of scSnd1 exit .pdb (#6) relative to
cryosparc_P1_J49_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.68643598 -0.68477187 -0.24473070 178.21654015
-0.31629688 -0.58419470 0.74744419 187.59839367
-0.65479914 -0.43566503 -0.61760347 226.43924513
Axis -0.90642351 0.31416853 0.28230225
Axis point 0.00000000 173.29890639 100.06025320
Rotation angle (degrees) 139.26019335
Shift along axis -38.67784320
> view matrix models
> #6,-0.54802,-0.41062,0.72875,333.58,0.60956,-0.79265,0.011766,-62.944,0.57281,0.45066,0.68468,221.8
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.54802,-0.41062,0.72875,366.97,0.60956,-0.79265,0.011766,-91.375,0.57281,0.45066,0.68468,235.56
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.42048,-0.5683,-0.70727,341.97,0.52302,0.7888,-0.32287,-102.78,0.74139,-0.23416,0.6289,236.93
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.42048,-0.5683,-0.70727,358.22,0.52302,0.7888,-0.32287,-112.37,0.74139,-0.23416,0.6289,194.93
> transparency #3 60
> transparency #3 30
> transparency #3 10
> transparency #3 0
> transparency #3 10
> view matrix models
> #6,0.42048,-0.5683,-0.70727,353.53,0.52302,0.7888,-0.32287,-83.639,0.74139,-0.23416,0.6289,239.13
> view matrix models
> #6,0.42048,-0.5683,-0.70727,326.41,0.52302,0.7888,-0.32287,-73.889,0.74139,-0.23416,0.6289,223.28
> view matrix models
> #6,0.42048,-0.5683,-0.70727,344.61,0.52302,0.7888,-0.32287,-55.746,0.74139,-0.23416,0.6289,225.12
> view matrix models
> #6,0.42048,-0.5683,-0.70727,341.8,0.52302,0.7888,-0.32287,-56.174,0.74139,-0.23416,0.6289,218.64
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.84646,0.41484,-0.33379,345.07,0.10545,-0.74507,-0.65859,-56.869,-0.52191,0.52227,-0.67442,192.83
> view matrix models
> #6,0.62683,0.54068,-0.56103,340.59,0.39779,-0.8412,-0.36626,-51.334,-0.66997,0.0064077,-0.74236,193.39
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.62683,0.54068,-0.56103,335.91,0.39779,-0.8412,-0.36626,-49.138,-0.66997,0.0064077,-0.74236,210.42
> view matrix models
> #6,0.62683,0.54068,-0.56103,340.78,0.39779,-0.8412,-0.36626,-50.178,-0.66997,0.0064077,-0.74236,205.26
> view matrix models
> #6,0.62683,0.54068,-0.56103,335.5,0.39779,-0.8412,-0.36626,-52.255,-0.66997,0.0064077,-0.74236,214.57
> fitmap sel inMap #3
Fit molecule scSnd1 exit .pdb (#6) to map cryosparc_P1_J49_001_volume_map.mrc
(#3) using 6914 atoms
average map value = 0.4157, steps = 168
shifted from previous position = 63.7
rotated from previous position = 35 degrees
atoms outside contour = 3454, contour level = 0.34937
Position of scSnd1 exit .pdb (#6) relative to
cryosparc_P1_J49_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.78270093 -0.09427237 0.61521700 194.90409041
-0.19241356 -0.90339080 -0.38322586 147.75436997
0.59190899 -0.41832733 0.68894554 200.89011186
Axis -0.32865357 0.21823179 -0.91889157
Axis point 64.36144725 95.93265715 0.00000000
Rotation angle (degrees) 176.93883796
Shift along axis -216.40745511
> view matrix models
> #6,0.62683,0.54068,-0.56103,338.35,0.39779,-0.8412,-0.36626,-63.029,-0.66997,0.0064077,-0.74236,216.28
> fitmap sel inMap #3
Fit molecule scSnd1 exit .pdb (#6) to map cryosparc_P1_J49_001_volume_map.mrc
(#3) using 6914 atoms
average map value = 0.383, steps = 164
shifted from previous position = 65.5
rotated from previous position = 33 degrees
atoms outside contour = 3731, contour level = 0.34937
Position of scSnd1 exit .pdb (#6) relative to
cryosparc_P1_J49_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.89948800 -0.20352674 0.38664995 194.63870749
-0.01689834 -0.86802755 -0.49622837 137.09235505
0.43661856 -0.45288522 0.77734110 217.45527239
Axis 0.21890021 -0.25236140 0.94254783
Axis point 67.04452093 101.55376679 0.00000000
Rotation angle (degrees) 174.31829093
Shift along axis 212.97163154
> view matrix models
> #6,0.62683,0.54068,-0.56103,330.16,0.39779,-0.8412,-0.36626,-60.634,-0.66997,0.0064077,-0.74236,204.95
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.98696,-0.078037,-0.1408,339.77,-0.13672,-0.86806,-0.47726,-62.521,-0.084977,0.49028,-0.86741,201.07
> view matrix models
> #6,0.77103,0.6325,-0.073867,338.52,0.63676,-0.76456,0.09994,-52.601,0.0067372,-0.12409,-0.99225,200.96
> ui mousemode right "translate selected models"
> transparency #3 0
> ui mousemode right "move picked models"
> view matrix models
> #6,0.77103,0.6325,-0.073867,319.38,0.63676,-0.76456,0.09994,-105.16,0.0067372,-0.12409,-0.99225,160.25
> view matrix models
> #6,0.77103,0.6325,-0.073867,342.54,0.63676,-0.76456,0.09994,-59.856,0.0067372,-0.12409,-0.99225,215.1
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.91911,0.1332,0.3708,352.17,0.37383,0.0023894,-0.92749,-80.782,-0.12443,0.99109,-0.0476,228.07
> view matrix models
> #6,0.73904,0.56501,-0.36687,337.55,0.47596,-0.82332,-0.30919,-66.935,-0.47675,0.053891,-0.87739,216.53
> ui mousemode right "move picked models"
> view matrix models
> #6,0.73904,0.56501,-0.36687,341.25,0.47596,-0.82332,-0.30919,-68.305,-0.47675,0.053891,-0.87739,211.52
> view matrix models
> #3,-0.99599,-0.085696,-0.025505,491.37,-0.083713,0.99398,-0.070671,-140.44,0.031408,-0.068253,-0.99717,440.21
> undo
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.75183,0.64057,-0.15626,341.04,0.59657,-0.7618,-0.25252,-66.138,-0.2808,0.096633,-0.95489,215.01
> ui mousemode right "move picked models"
> view matrix models
> #6,0.75183,0.64057,-0.15626,337.79,0.59657,-0.7618,-0.25252,-58.131,-0.2808,0.096633,-0.95489,210.23
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.83924,0.53447,0.10006,342.72,0.41818,-0.51679,-0.74703,-67.776,-0.34756,0.66878,-0.65722,213.56
> view matrix models
> #6,0.8347,0.45608,-0.30864,335.71,0.38242,-0.88333,-0.27107,-58.045,-0.39626,0.10823,-0.91174,210.96
> view matrix models
> #6,0.88955,0.41531,-0.19031,337.96,0.27925,-0.82402,-0.49297,-62.198,-0.36155,0.38538,-0.84898,211.12
> ui mousemode right "move picked models"
> view matrix models
> #3,-0.99599,-0.085696,-0.025505,493.35,-0.083713,0.99398,-0.070671,-144.11,0.031408,-0.068253,-0.99717,442.98
> undo
> view matrix models
> #6,0.88955,0.41531,-0.19031,334.12,0.27925,-0.82402,-0.49297,-54.974,-0.36155,0.38538,-0.84898,205.05
> fitmap sel inMap #3
Fit molecule scSnd1 exit .pdb (#6) to map cryosparc_P1_J49_001_volume_map.mrc
(#3) using 6914 atoms
average map value = 0.4268, steps = 184
shifted from previous position = 64.2
rotated from previous position = 25.2 degrees
atoms outside contour = 3479, contour level = 0.34937
Position of scSnd1 exit .pdb (#6) relative to
cryosparc_P1_J49_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.92405958 -0.34829964 0.15748404 195.75148218
0.11204513 -0.64070257 -0.75956966 135.43400986
0.36545828 -0.68424232 0.63107264 204.44994527
Axis 0.14748966 -0.40721001 0.90134722
Axis point 66.76018211 126.32027890 0.00000000
Rotation angle (degrees) 165.20479532
Shift along axis 158.00162316
> undo
> select subtract #6
Nothing selected
> select add #6
6914 atoms, 7029 bonds, 877 residues, 1 model selected
> select subtract #6
Nothing selected
> select #6:1-270
2168 atoms, 2205 bonds, 270 residues, 1 model selected
> hide ~sel
> view matrix models
> #3,-0.99599,-0.085696,-0.025505,492.18,-0.083713,0.99398,-0.070671,-145.16,0.031408,-0.068253,-0.99717,440.78
> undo
> view matrix models
> #6,0.88955,0.41531,-0.19031,339.91,0.27925,-0.82402,-0.49297,-61.58,-0.36155,0.38538,-0.84898,208
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.74658,0.5424,-0.38526,336.01,0.2806,-0.78177,-0.55687,-62.863,-0.60323,0.30765,-0.73585,210.28
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.74658,0.5424,-0.38526,338.51,0.2806,-0.78177,-0.55687,-61.723,-0.60323,0.30765,-0.73585,213.91
> fitmap sel inMap #3
Fit molecule scSnd1 exit .pdb (#6) to map cryosparc_P1_J49_001_volume_map.mrc
(#3) using 2168 atoms
average map value = 0.5696, steps = 196
shifted from previous position = 63.2
rotated from previous position = 45.6 degrees
atoms outside contour = 747, contour level = 0.34937
Position of scSnd1 exit .pdb (#6) relative to
cryosparc_P1_J49_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.44379326 0.01639799 0.89597914 196.07385698
-0.24567718 -0.96375120 -0.10404962 133.30835677
0.86179478 -0.26629816 0.43173491 208.31126822
Axis -0.52317403 0.11022824 -0.84506726
Axis point 41.05009621 77.56333829 0.00000000
Rotation angle (degrees) 171.07962390
Shift along axis -263.92343746
> undo
> view matrix models
> #6,0.74658,0.5424,-0.38526,346.56,0.2806,-0.78177,-0.55687,-56.153,-0.60323,0.30765,-0.73585,219.99
> view matrix models
> #6,0.74658,0.5424,-0.38526,344.42,0.2806,-0.78177,-0.55687,-55.329,-0.60323,0.30765,-0.73585,204.6
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.50635,0.77072,-0.38678,343.61,0.22927,-0.55271,-0.80121,-60.467,-0.83129,0.31702,-0.45657,209.53
> fitmap sel inMap #3
Fit molecule scSnd1 exit .pdb (#6) to map cryosparc_P1_J49_001_volume_map.mrc
(#3) using 2168 atoms
average map value = 0.333, steps = 112
shifted from previous position = 39.7
rotated from previous position = 35.1 degrees
atoms outside contour = 1366, contour level = 0.34937
Position of scSnd1 exit .pdb (#6) relative to
cryosparc_P1_J49_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.80357006 -0.17961805 0.56746143 168.18281662
-0.12482347 -0.88132508 -0.45572489 121.38337638
0.58197442 -0.43703940 0.68578591 229.35036358
Axis 0.31307195 -0.24316241 0.91807298
Axis point 43.53752813 91.83707933 0.00000000
Rotation angle (degrees) 178.28991571
Shift along axis 233.69781927
> transparency #3 10
> view matrix models
> #6,0.7858,0.36158,-0.50178,308.98,-0.024053,-0.79282,-0.60898,-52.818,-0.61802,0.4906,-0.6143,209.92
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.7858,0.36158,-0.50178,335.41,-0.024053,-0.79282,-0.60898,-55.668,-0.61802,0.4906,-0.6143,214.42
> transparency #3 0
> view matrix models
> #6,0.7858,0.36158,-0.50178,332.24,-0.024053,-0.79282,-0.60898,-57.334,-0.61802,0.4906,-0.6143,213.87
> fitmap sel inMap #3
Fit molecule scSnd1 exit .pdb (#6) to map cryosparc_P1_J49_001_volume_map.mrc
(#3) using 2168 atoms
average map value = 0.5731, steps = 172
shifted from previous position = 54.8
rotated from previous position = 28 degrees
atoms outside contour = 738, contour level = 0.34937
Position of scSnd1 exit .pdb (#6) relative to
cryosparc_P1_J49_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.53782345 -0.18399138 0.82273512 192.55860844
-0.43204200 -0.77785351 -0.45638098 135.04797664
0.72393758 -0.60090853 0.33885586 205.44665902
Axis -0.47603223 0.32541071 -0.81700746
Axis point 46.01441257 104.23605601 0.00000000
Rotation angle (degrees) 171.26849268
Shift along axis -215.56949955
> undo
> view matrix models
> #6,0.7858,0.36158,-0.50178,337.39,-0.024053,-0.79282,-0.60898,-62.048,-0.61802,0.4906,-0.6143,223.28
> view matrix models
> #6,0.7858,0.36158,-0.50178,345.87,-0.024053,-0.79282,-0.60898,-61.784,-0.61802,0.4906,-0.6143,212.29
> view matrix models
> #6,0.7858,0.36158,-0.50178,344.61,-0.024053,-0.79282,-0.60898,-61.695,-0.61802,0.4906,-0.6143,214.16
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.33974,-0.52386,-0.78112,342.69,0.76814,0.63379,-0.090958,-57.383,0.54271,-0.56911,0.61772,239.74
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.33974,-0.52386,-0.78112,344.27,0.76814,0.63379,-0.090958,-63.011,0.54271,-0.56911,0.61772,227.02
> view matrix models
> #6,0.33974,-0.52386,-0.78112,343.8,0.76814,0.63379,-0.090958,-63.129,0.54271,-0.56911,0.61772,227.43
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.074286,-0.59705,-0.79875,343.73,0.80031,0.51357,-0.30945,-66.603,0.59497,-0.61626,0.51598,225.78
> view matrix models
> #6,0.29527,-0.75289,-0.58819,348.02,0.63726,0.61388,-0.46588,-69.733,0.71183,-0.23727,0.66106,227.06
> view matrix models
> #6,0.73157,-0.61692,-0.2902,352.86,0.50474,0.77624,-0.37774,-68.725,0.4583,0.12986,0.87926,229.67
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.73157,-0.61692,-0.2902,349.17,0.50474,0.77624,-0.37774,-62.433,0.4583,0.12986,0.87926,224.35
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.42175,-0.62571,-0.65621,342.69,0.4225,0.77597,-0.46836,-64.046,0.80226,-0.079715,0.59163,219.96
> ui mousemode right "move picked models"
> view matrix models
> #6,0.42175,-0.62571,-0.65621,346.56,0.4225,0.77597,-0.46836,-59.102,0.80226,-0.079715,0.59163,219.42
> fitmap sel inMap #3
Fit molecule scSnd1 exit .pdb (#6) to map cryosparc_P1_J49_001_volume_map.mrc
(#3) using 2168 atoms
average map value = 0.5144, steps = 168
shifted from previous position = 57.2
rotated from previous position = 32.2 degrees
atoms outside contour = 860, contour level = 0.34937
Position of scSnd1 exit .pdb (#6) relative to
cryosparc_P1_J49_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.20062966 0.15609140 0.96715210 181.80758861
0.37309329 0.92500419 -0.07189316 130.31783010
-0.90584166 0.34641407 -0.24381993 191.58285775
Axis 0.21658615 0.96977648 0.11235666
Axis point 143.75544692 0.00000000 32.41693340
Rotation angle (degrees) 105.05360888
Shift along axis 187.28178242
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.83123,0.49779,0.24753,354.91,0.31739,-0.059362,-0.94644,-69.677,-0.45643,0.86526,-0.20734,202.48
> view matrix models
> #6,0.29464,0.85783,-0.42109,341.76,0.73449,-0.48519,-0.47447,-59.81,-0.61132,-0.16949,-0.77302,195.97
> ui mousemode right "move picked models"
> view matrix models
> #3,-0.99599,-0.085696,-0.025505,491.41,-0.083713,0.99398,-0.070671,-142.19,0.031408,-0.068253,-0.99717,449.77
> undo
> view matrix models
> #3,-0.99599,-0.085696,-0.025505,491.74,-0.083713,0.99398,-0.070671,-142.32,0.031408,-0.068253,-0.99717,444.86
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.29464,0.85783,-0.42109,340.06,0.73449,-0.48519,-0.47447,-60.429,-0.61132,-0.16949,-0.77302,209.82
> fitmap sel inMap #3
Fit molecule scSnd1 exit .pdb (#6) to map cryosparc_P1_J49_001_volume_map.mrc
(#3) using 2168 atoms
average map value = 0.5703, steps = 184
shifted from previous position = 69.3
rotated from previous position = 76.7 degrees
atoms outside contour = 735, contour level = 0.34937
Position of scSnd1 exit .pdb (#6) relative to
cryosparc_P1_J49_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.47720098 0.32697290 0.81570088 197.39954384
0.45144153 -0.70515898 0.54676442 134.89038267
0.75397596 0.62915778 0.18889341 211.37962752
Axis 0.51008933 0.38213300 0.77057332
Axis point 28.35742894 15.99497783 -0.00000000
Rotation angle (degrees) 175.36753817
Shift along axis 315.12096977
> view matrix models
> #6,0.29464,0.85783,-0.42109,340.75,0.73449,-0.48519,-0.47447,-59.101,-0.61132,-0.16949,-0.77302,213.59
> fitmap sel inMap #3
Fit molecule scSnd1 exit .pdb (#6) to map cryosparc_P1_J49_001_volume_map.mrc
(#3) using 2168 atoms
average map value = 0.5912, steps = 196
shifted from previous position = 77.4
rotated from previous position = 31.2 degrees
atoms outside contour = 724, contour level = 0.34937
Position of scSnd1 exit .pdb (#6) relative to
cryosparc_P1_J49_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.63493908 -0.53272472 0.55951472 202.17906207
0.69886819 -0.70475777 0.12206441 145.20900449
0.32929562 0.46853050 0.81978262 204.82825428
Axis 0.26652336 0.17709891 0.94741821
Axis point 53.42299638 78.65034143 0.00000000
Rotation angle (degrees) 139.46041788
Shift along axis 273.65981887
> view matrix models
> #6,0.29464,0.85783,-0.42109,338.57,0.73449,-0.48519,-0.47447,-76.431,-0.61132,-0.16949,-0.77302,123.31
> view matrix models
> #6,0.29464,0.85783,-0.42109,311.44,0.73449,-0.48519,-0.47447,-27.077,-0.61132,-0.16949,-0.77302,166.15
> view matrix models
> #6,0.29464,0.85783,-0.42109,327.81,0.73449,-0.48519,-0.47447,-72.835,-0.61132,-0.16949,-0.77302,189.65
> view matrix models
> #6,0.29464,0.85783,-0.42109,335.36,0.73449,-0.48519,-0.47447,-64.224,-0.61132,-0.16949,-0.77302,204.46
> view matrix models
> #6,0.29464,0.85783,-0.42109,324.82,0.73449,-0.48519,-0.47447,-60.392,-0.61132,-0.16949,-0.77302,198.24
> view matrix models
> #6,0.29464,0.85783,-0.42109,325.35,0.73449,-0.48519,-0.47447,-53.093,-0.61132,-0.16949,-0.77302,212.41
> select add #6
6914 atoms, 7029 bonds, 877 residues, 1 model selected
> select subtract #6
Nothing selected
> hide #6 models
> show #6 models
> select add #6
6914 atoms, 7029 bonds, 877 residues, 1 model selected
> view matrix models
> #6,0.29464,0.85783,-0.42109,334.89,0.73449,-0.48519,-0.47447,-55.658,-0.61132,-0.16949,-0.77302,221.34
> view matrix models
> #6,0.29464,0.85783,-0.42109,335.52,0.73449,-0.48519,-0.47447,-56.823,-0.61132,-0.16949,-0.77302,216.56
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.70196,0.70911,-0.066345,342.35,0.30485,-0.38335,-0.87184,-64.248,-0.64367,0.59178,-0.48527,219.06
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.70196,0.70911,-0.066345,336.48,0.30485,-0.38335,-0.87184,-56.596,-0.64367,0.59178,-0.48527,213.41
> view matrix models
> #6,0.70196,0.70911,-0.066345,333.44,0.30485,-0.38335,-0.87184,-59.364,-0.64367,0.59178,-0.48527,213.76
> select #6:1-270
2168 atoms, 2205 bonds, 270 residues, 1 model selected
> fitmap sel inMap #3
Fit molecule scSnd1 exit .pdb (#6) to map cryosparc_P1_J49_001_volume_map.mrc
(#3) using 2168 atoms
average map value = 0.3329, steps = 120
shifted from previous position = 27.3
rotated from previous position = 40 degrees
atoms outside contour = 1364, contour level = 0.34937
Position of scSnd1 exit .pdb (#6) relative to
cryosparc_P1_J49_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.80292394 -0.17898668 0.56857444 168.17699942
-0.12672895 -0.88078934 -0.45623447 121.30672228
0.58245420 -0.43837643 0.68452406 229.41672846
Axis 0.31361631 -0.24375135 0.91773095
Axis point 43.50623610 91.85617503 0.00000000
Rotation angle (degrees) 178.36850223
Shift along axis 233.71720335
> view matrix models
> #6,0.79571,0.26493,-0.54466,386.38,-0.099914,-0.82952,-0.54946,-60.269,-0.59738,0.49163,-0.63359,218.79
> volume #3 level 0.2864
> view matrix models
> #6,0.79571,0.26493,-0.54466,340.87,-0.099914,-0.82952,-0.54946,-76.754,-0.59738,0.49163,-0.63359,217.7
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.79115,0.52227,-0.3183,344.01,0.059666,-0.58384,-0.80967,-82.229,-0.6087,0.62158,-0.49307,219.75
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.79115,0.52227,-0.3183,335.33,0.059666,-0.58384,-0.80967,-70.146,-0.6087,0.62158,-0.49307,232.26
> view matrix models
> #6,0.79115,0.52227,-0.3183,336.36,0.059666,-0.58384,-0.80967,-58.564,-0.6087,0.62158,-0.49307,226.07
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.69428,0.27945,-0.66324,331.06,-0.23454,-0.78338,-0.57559,-53.713,-0.68042,0.55518,-0.47834,226.56
> view matrix models
> #6,0.68376,0.45209,-0.57279,332.07,0.11724,-0.84282,-0.52526,-52.61,-0.72023,0.292,-0.62929,224.78
> hide #6 models
> hide #5 models
> select add #6
6914 atoms, 7029 bonds, 877 residues, 1 model selected
> select up
219303 atoms, 228626 bonds, 19941 residues, 8 models selected
> select up
219303 atoms, 228626 bonds, 19941 residues, 8 models selected
> show #!1.2 models
> select subtract #6
212389 atoms, 221597 bonds, 19064 residues, 7 models selected
> select subtract #5
205475 atoms, 214568 bonds, 18187 residues, 6 models selected
> select add #4
205475 atoms, 214568 bonds, 3951 pseudobonds, 18187 residues, 8 models
selected
> select subtract #2
205475 atoms, 214568 bonds, 3951 pseudobonds, 18187 residues, 6 models
selected
> select subtract #3
205475 atoms, 214568 bonds, 3951 pseudobonds, 18187 residues, 4 models
selected
> select subtract #4
1 model selected
> hide #!3 models
> color zone #1.2 near #4 distance 7
> color zone #1.2 near #4 distance 15
> show #!3 models
> color zone #3 near #4 distance 15
> volume #3 level 0.148
> volume #3 level 0.2675
> hide #!3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!2 models
> color #2 #33ff00ff models
> color #2 #339900ff models
> color zone #2 near #4 distance 15
> color #2 #3300ffff models
> color zone #2 near #4 distance 15
> save /Users/haandrew/Documents/fit.cxs
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
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: MacBookPro17,1
Model Number: Z11D000L9D/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8419.41.10
OS Loader Version: 8419.41.10
Software:
System Software Overview:
System Version: macOS 13.0.1 (22A400)
Kernel Version: Darwin 22.1.0
Time since boot: 2 days, 21 hours, 11 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
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
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: 1.6.4
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: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
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: 1.8
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: 1.5.17
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: 1.13.5
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: 3.0.47
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: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
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 , 6 weeks ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Input/Output |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash during/after session save |
comment:2 by , 6 weeks ago
| Status: | accepted → feedback |
|---|
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Hi Halle,
--Eric