![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15740 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.8 (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 0x00000001f4860c00 (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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, chimerax.surface._surface, chimerax.core._mac_util, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 124)
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{
"uptime" : 770000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 64210,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-08-07 10:53:50.0044 -0700",
"codeSigningMonitor" : 1,
"incident" : "D651FC01-2762-4B65-BB3D-0A02B10FF6A7",
"pid" : 94338,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-05 11:38:12.2526 -0700",
"procStartAbsTime" : 17041444692540,
"procExitAbsTime" : 18535285013637,
"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":"75A6AF2F-20C3-5360-BD3A-381717AEC7EF","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "01DCA152-1CDB-B331-3941-F49EA5A3C7E2",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 6488,
"sleepWakeUUID" : "674010D8-BA38-483E-B1F2-1AD2544B2453",
"sip" : "enabled",
"vmRegionInfo" : "0x7e4577e870d8 is not in any region. Bytes after previous region: 33282102685913 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600040000000-600060000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x00007e4577e870d8","rawCodes":[1,138836829565144],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00007e4577e870d8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":94338},
"vmregioninfo" : "0x7e4577e870d8 is not in any region. Bytes after previous region: 33282102685913 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600040000000-600060000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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===== Log before crash start =====
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
ra rd; rt
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color {arguments} bychain; color {arguments} byhet
cs clipper set contourSensitivity {arguments}
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/udalwadi/Library/CloudStorage/Box-
> Box/Dp71_Project/maps_models/240711_J18_Dp71-PP1-eIF2a-Gactin-DNAseI_v2.cif
> /Users/udalwadi/Library/CloudStorage/Box-
> Box/Dp71_Project/maps_models/Dp71-PP1-Gactin-DNAseI-J147-isolde_032124.pdb
> /Users/udalwadi/Library/CloudStorage/Box-
> Box/Dp71_Project/maps_models/Dp71-PP1-Gactin-DNAseI-P327_J147.mrc
Summary of feedback from opening /Users/udalwadi/Library/CloudStorage/Box-
Box/Dp71_Project/maps_models/240711_J18_Dp71-PP1-eIF2a-Gactin-DNAseI_v2.cif
---
warnings | Unknown polymer entity '2' on line 3012
Atom H is not in the residue template for LYS /C:6
Atom H is not in the residue template for MET /D:1
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 240711_J18_Dp71-PP1-eIF2a-Gactin-DNAseI_v2.cif #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for Dp71-PP1-Gactin-DNAseI-J147-isolde_032124.pdb #2
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
Opened Dp71-PP1-Gactin-DNAseI-P327_J147.mrc as #3, grid size 256,256,256,
pixel 1.12, shown at level 0.0394, step 1, values float32
> open "/Users/udalwadi/Downloads/cryosparc_P512_J18_009_volume_map (1).mrc"
Opened cryosparc_P512_J18_009_volume_map (1).mrc as #4, grid size 320,320,320,
pixel 0.929, shown at level 0.00378, step 2, values float32
> set bgColor white
> style stick
Changed 34243 atom styles
> show cartoons
> volume #4 step 1
> volume #4 level 0.008253
> hide #2 models
> volume #4 color #ffffb257
> color #1 byhetero
> volume #4 level 0.01397
> hide #1 models
> volume #3 level 0.3662
> select add #3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.94813,0.030771,0.31639,238.18,-0.24996,-0.68708,-0.68223,366.68,0.19639,-0.72593,0.65914,119.66
> view matrix models
> #3,0.064349,-0.99642,0.054836,269.42,0.5919,-0.0061304,-0.80599,164.68,0.80344,0.084322,0.58939,-73.404
> view matrix models
> #3,0.82147,-0.47161,0.32056,48.322,0.55783,0.5479,-0.62341,67,0.11837,0.69093,0.71316,-74.855
> view matrix models
> #3,0.81682,0.18647,-0.54593,75.63,-0.45541,0.78934,-0.41177,152.83,0.35414,0.58496,0.72966,-96.867
> hide #!3 models
> show #!3 models
> hide #!4 models
> view matrix models
> #3,0.89206,-0.4107,-0.18854,99.256,0.25431,0.8011,-0.54181,64.867,0.37357,0.43538,0.81908,-91.021
> show #!4 models
> view matrix models
> #3,0.93522,-0.041663,0.35162,-32.882,0.23104,0.82431,-0.51685,61.605,-0.26831,0.5646,0.78053,-9.6461
> view matrix models
> #3,0.93522,-0.041663,0.35162,-35.435,0.23104,0.82431,-0.51685,64.488,-0.26831,0.5646,0.78053,-12.919
> view matrix models
> #3,0.93522,-0.041663,0.35162,-38.082,0.23104,0.82431,-0.51685,74.106,-0.26831,0.5646,0.78053,-10.632
> fitmap #3 inMap #4
Fit map Dp71-PP1-Gactin-DNAseI-P327_J147.mrc in map
cryosparc_P512_J18_009_volume_map (1).mrc using 25008 points
correlation = 0.6302, correlation about mean = 0.02715, overlap = 241.5
steps = 132, shift = 13.4, angle = 14.2 degrees
Position of Dp71-PP1-Gactin-DNAseI-P327_J147.mrc (#3) relative to
cryosparc_P512_J18_009_volume_map (1).mrc (#4) coordinates:
Matrix rotation and translation
0.98192586 0.09223263 0.16527177 -28.42276321
0.00426871 0.86221043 -0.50653229 96.96371768
-0.18921784 0.49808265 0.84623300 -11.55752584
Axis 0.93981570 0.33162447 -0.08229011
Axis point 0.00000000 73.75783161 167.17611647
Rotation angle (degrees) 32.30827604
Shift along axis 6.39445271
> volume flip #3
Opened Dp71-PP1-Gactin-DNAseI-P327_J147.mrc z flip as #5, grid size
256,256,256, pixel 1.12, shown at step 1, values float32
> select subtract #3
Nothing selected
> select add #5
2 models selected
> view matrix models
> #5,0.73016,-0.6397,0.24013,100.04,0.51122,0.74462,0.42918,-99.136,-0.45335,-0.19061,0.87072,120.1
> view matrix models
> #5,-0.5652,-0.78934,0.23978,311.16,-0.69975,0.61266,0.36742,106.19,-0.43692,0.039878,-0.89861,346.68
> view matrix models
> #5,-0.98834,-0.063955,0.13821,286.6,0.024914,0.82742,0.56103,-58.844,-0.15024,0.55793,-0.81618,219.83
> view matrix models
> #5,-0.98834,-0.063955,0.13821,285.49,0.024914,0.82742,0.56103,-47.881,-0.15024,0.55793,-0.81618,207.68
> select up
34243 atoms, 34609 bonds, 2169 residues, 8 models selected
> fitmap #5 inMap #4
Fit map Dp71-PP1-Gactin-DNAseI-P327_J147.mrc z flip in map
cryosparc_P512_J18_009_volume_map (1).mrc using 25008 points
correlation = 0.6087, correlation about mean = -0.02619, overlap = 229.7
steps = 144, shift = 8.16, angle = 10.1 degrees
Position of Dp71-PP1-Gactin-DNAseI-P327_J147.mrc z flip (#5) relative to
cryosparc_P512_J18_009_volume_map (1).mrc (#4) coordinates:
Matrix rotation and translation
-0.98969135 -0.01526712 0.14240070 270.32468109
0.04468843 0.91173711 0.40833612 -41.78917257
-0.13606612 0.41049039 -0.90165606 240.11893632
Axis 0.00756264 0.97756966 0.21047651
Axis point 144.02449318 0.00000000 114.66468077
Rotation angle (degrees) 171.81162441
Shift along axis 11.73193778
> volume #3 level 0.2389
> volume #5 level 0.248
> volume #4 level 0.01806
> select subtract #5
34243 atoms, 34609 bonds, 2169 residues, 6 models selected
> select subtract #4
34243 atoms, 34609 bonds, 2169 residues, 4 models selected
> select subtract #3
34243 atoms, 34609 bonds, 2169 residues, 2 models selected
> select subtract #1
15586 atoms, 15757 bonds, 991 residues, 1 model selected
> show #1 models
> show #!3 models
> show #2 models
> select subtract #2
Nothing selected
> hide #!3 models
> hide #!5 models
> mmaker #2/C to #1/C
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 240711_J18_Dp71-PP1-eIF2a-Gactin-DNAseI_v2.cif, chain C (#1) with
Dp71-PP1-Gactin-DNAseI-J147-isolde_032124.pdb, chain C (#2), sequence
alignment score = 1509.1
RMSD between 293 pruned atom pairs is 0.437 angstroms; (across all 295 pairs:
0.472)
> select clear
> color bychain
> hide atoms
> show atoms
> color byhetero
> hide H
> select add #2
15586 atoms, 15757 bonds, 991 residues, 1 model selected
> color sel orange red
> select clear
> color byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> view sel
> select clear
> ui tool show "Side View"
> hide #1 models
> show #!3 models
> view
> hide #2 models
> show #!4 models
> select add #3
2 models selected
> view matrix models
> #3,0.99332,-0.10567,-0.046284,26.788,-0.11517,-0.93136,-0.3454,343.76,-0.0066091,0.34842,-0.93731,228.27
> view matrix models
> #3,-0.81413,0.36767,0.44946,156.72,-0.56072,-0.29651,-0.7731,378.84,-0.15098,-0.88142,0.44756,231.17
> volume #3 level 0.1752
> view matrix models
> #3,-0.89686,0.08219,0.4346,211.26,-0.36665,-0.68774,-0.62657,385.51,0.2474,-0.72129,0.64694,122.64
> volume #3 level 0.73
> view matrix models
> #3,0.93779,0.3234,-0.12636,-8.3023,0.2337,-0.85708,-0.45912,299.35,-0.25679,0.40103,-0.87934,251.49
> select subtract #3
Nothing selected
> hide #!3 models
> show #!5 models
> select add #5
2 models selected
> volume #5 level 0.4481
> view matrix models
> #5,0.51134,-0.5194,0.68466,43.405,-0.58537,-0.79379,-0.16501,373.3,0.62918,-0.3164,-0.70994,202.82
> view matrix models
> #5,-0.93288,-0.13532,0.3338,250.55,-0.30562,-0.19305,-0.93238,362.46,0.19061,-0.97181,0.13873,232.25
> view matrix models
> #5,0.25333,-0.66957,-0.69822,306.81,-0.089851,0.70235,-0.70613,172.26,0.9632,0.24162,0.11777,-46.401
> view matrix models
> #5,0.92784,0.31699,0.19653,-61.644,-0.33317,0.94128,0.054732,61.165,-0.16764,-0.11626,0.97897,39.631
> view matrix models
> #5,0.92708,0.31874,0.19728,-64.337,-0.33493,0.94069,0.054046,59.059,-0.16836,-0.11618,0.97886,51.697
> view matrix models
> #5,0.96647,0.20454,0.15521,-47.798,-0.24357,0.92161,0.30218,11.725,-0.081239,-0.32985,0.94053,74.711
> fitmap #5 inMap #4
Fit map Dp71-PP1-Gactin-DNAseI-P327_J147.mrc z flip in map
cryosparc_P512_J18_009_volume_map (1).mrc using 18939 points
correlation = 0.6918, correlation about mean = 0.1145, overlap = 238.1
steps = 260, shift = 8.05, angle = 11.4 degrees
Position of Dp71-PP1-Gactin-DNAseI-P327_J147.mrc z flip (#5) relative to
cryosparc_P512_J18_009_volume_map (1).mrc (#4) coordinates:
Matrix rotation and translation
0.95367170 0.29783796 0.04246017 -40.29656884
-0.30068176 0.93889022 0.16755793 35.70545579
0.01003968 -0.17256225 0.98494746 41.02815914
Axis -0.49351969 0.04704264 -0.86846146
Axis point 85.99627722 171.97862521 0.00000000
Rotation angle (degrees) 20.15653924
Shift along axis -14.06454590
> show #!3 models
> select subtract #5
Nothing selected
> hide #!5 models
> select add #3
2 models selected
> view matrix models
> #3,0.51374,0.75559,-0.40639,31.466,0.31119,-0.60553,-0.73246,291.2,-0.79952,0.24983,-0.54621,304.27
> hide #!4 models
> volume #3 level 0.3298
> hide #!3 models
> select subtract #3
Nothing selected
> show #!5 models
> volume #5 level 0.1934
> volume #5 level 0.2571
> volume #5 level 0.3662
> show #!4 models
> select add #5
2 models selected
> view matrix models
> #5,0.74899,0.58201,-0.31665,2.9486,-0.50751,0.81119,0.29053,65.794,0.42596,-0.056902,0.90295,-24.108
> view matrix models
> #5,0.74899,0.58201,-0.31665,1.5401,-0.50751,0.81119,0.29053,68.894,0.42596,-0.056902,0.90295,-36.883
> view matrix models
> #5,0.99341,-0.069767,-0.090947,23.68,0.08629,0.97745,0.19271,-27.103,0.075452,-0.19929,0.97703,23.568
> fitmap #5 inMap #4
Fit map Dp71-PP1-Gactin-DNAseI-P327_J147.mrc z flip in map
cryosparc_P512_J18_009_volume_map (1).mrc using 25008 points
correlation = 0.6481, correlation about mean = 0.05095, overlap = 246.7
steps = 124, shift = 8.62, angle = 13.5 degrees
Position of Dp71-PP1-Gactin-DNAseI-P327_J147.mrc z flip (#5) relative to
cryosparc_P512_J18_009_volume_map (1).mrc (#4) coordinates:
Matrix rotation and translation
0.98807493 0.15305448 -0.01680063 -14.48771814
-0.14639119 0.96762648 0.20559332 0.83983312
0.04772371 -0.20068215 0.97849329 34.17844025
Axis -0.79847669 -0.12681341 -0.58851791
Axis point 0.00000000 142.39837389 23.67500357
Rotation angle (degrees) 14.73842576
Shift along axis -8.65302099
> view matrix models
> #5,0.98354,0.18067,0.0022635,-20.508,-0.17766,0.96471,0.19433,7.5003,0.032926,-0.19153,0.98093,34.707
> view matrix models
> #5,0.98354,0.18067,0.0022635,-18.587,-0.17766,0.96471,0.19433,13.435,0.032926,-0.19153,0.98093,29.93
> fitmap #5 inMap #4
Fit map Dp71-PP1-Gactin-DNAseI-P327_J147.mrc z flip in map
cryosparc_P512_J18_009_volume_map (1).mrc using 25008 points
correlation = 0.6733, correlation about mean = 0.07698, overlap = 267
steps = 104, shift = 9.39, angle = 10.5 degrees
Position of Dp71-PP1-Gactin-DNAseI-P327_J147.mrc z flip (#5) relative to
cryosparc_P512_J18_009_volume_map (1).mrc (#4) coordinates:
Matrix rotation and translation
0.95096915 0.26880986 0.15296714 -51.25028321
-0.29862852 0.92674986 0.22793794 29.04205617
-0.08049031 -0.26244230 0.96158481 66.85137173
Axis -0.62431525 0.29722046 -0.72241987
Axis point 51.44676672 217.84579107 -0.00000000
Rotation angle (degrees) 23.12475366
Shift along axis -7.66653271
> volume #4 level 0.01166
> volume #4 level 0.02189
> view matrix models
> #5,0.91758,-0.39268,-0.062011,78.096,0.39123,0.86427,0.31618,-76.473,-0.070564,-0.31439,0.94667,74.877
> view matrix models
> #5,0.84085,-0.53735,-0.064978,110.07,0.53582,0.8094,0.24036,-78.804,-0.076564,-0.23693,0.96851,61.677
> select subtract #5
Nothing selected
> hide #!5 models
> show #!3 models
> select add #3
2 models selected
> view matrix models
> #3,-0.60572,0.7569,-0.24537,173.61,-0.45757,-0.58364,-0.67081,392.58,-0.65095,-0.29405,0.69986,187.82
> view matrix models
> #3,0.8255,-0.37977,-0.41752,146.37,0.34982,0.92481,-0.14954,-8.9379,0.44291,-0.022614,0.89628,-37.809
> view matrix models
> #3,-0.5868,-0.64803,-0.4855,400.71,0.49824,0.18368,-0.84736,168.85,0.63829,-0.73913,0.21509,127.35
> view matrix models
> #3,0.97972,-0.19818,0.029431,36.975,0.19438,0.90463,-0.37929,48.223,0.048541,0.37732,0.92481,-39.868
> view matrix models
> #3,0.97972,-0.19818,0.029431,35.491,0.19438,0.90463,-0.37929,49.762,0.048541,0.37732,0.92481,-37.895
> view matrix models
> #3,0.97972,-0.19818,0.029431,26.452,0.19438,0.90463,-0.37929,42.992,0.048541,0.37732,0.92481,-37.901
> fitmap #3 inMap #4
Fit map Dp71-PP1-Gactin-DNAseI-P327_J147.mrc in map
cryosparc_P512_J18_009_volume_map (1).mrc using 28496 points
correlation = 0.901, correlation about mean = 0.4869, overlap = 577.8
steps = 200, shift = 6.37, angle = 30.3 degrees
Position of Dp71-PP1-Gactin-DNAseI-P327_J147.mrc (#3) relative to
cryosparc_P512_J18_009_volume_map (1).mrc (#4) coordinates:
Matrix rotation and translation
0.94130932 0.31414577 0.12348762 -52.93819478
-0.24237150 0.88366925 -0.40048060 117.54448819
-0.23493150 0.34704624 0.90794609 8.87256065
Axis 0.74866113 0.35896298 -0.55736172
Axis point 0.00000000 52.62753159 280.35817464
Rotation angle (degrees) 29.94989403
Shift along axis -2.38387462
> select clear
> show #2 models
> show #1 models
> volume #3 color #b2b2b24a
> select #1/C:74@NH1
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> view sel
> select #3
4 models selected
> select clear
> hide #!4 models
> volume #3 level 0.2662
> volume #3 level 0.2207
> hide #2 models
> hide #1 models
> show #1 models
> show #!4 models
> hide #1 models
> show #2 models
> volume #3 level 0.1934
> fitmap #2 inMap #3
Fit molecule Dp71-PP1-Gactin-DNAseI-J147-isolde_032124.pdb (#2) to map
Dp71-PP1-Gactin-DNAseI-P327_J147.mrc (#3) using 15586 atoms
average map value = 0.322, steps = 60
shifted from previous position = 2.31
rotated from previous position = 5.55 degrees
atoms outside contour = 6145, contour level = 0.19344
Position of Dp71-PP1-Gactin-DNAseI-J147-isolde_032124.pdb (#2) relative to
Dp71-PP1-Gactin-DNAseI-P327_J147.mrc (#3) coordinates:
Matrix rotation and translation
0.99999932 0.00043781 -0.00108226 0.08860274
-0.00043845 0.99999973 -0.00059039 0.16519389
0.00108201 0.00059086 0.99999924 -0.22842414
Axis 0.45142299 -0.82709254 -0.33486596
Axis point 217.40865071 0.00000000 90.13236437
Rotation angle (degrees) 0.07496356
Shift along axis -0.02014185
> show #1 models
> fitmap #1 inMap #4
Fit molecule 240711_J18_Dp71-PP1-eIF2a-Gactin-DNAseI_v2.cif (#1) to map
cryosparc_P512_J18_009_volume_map (1).mrc (#4) using 18657 atoms
average map value = 0.02389, steps = 44
shifted from previous position = 0.0244
rotated from previous position = 0.0418 degrees
atoms outside contour = 9070, contour level = 0.021895
Position of 240711_J18_Dp71-PP1-eIF2a-Gactin-DNAseI_v2.cif (#1) relative to
cryosparc_P512_J18_009_volume_map (1).mrc (#4) coordinates:
Matrix rotation and translation
0.99999973 0.00039227 -0.00061469 0.02424739
-0.00039228 0.99999992 -0.00002516 0.06059358
0.00061468 0.00002540 0.99999981 -0.07170435
Axis 0.03464207 -0.84246352 -0.53763849
Axis point 126.86198088 0.00000000 40.04883177
Rotation angle (degrees) 0.04180439
Shift along axis -0.01165688
> hide #2 models
> hide #!3 models
> view
> hide #!4 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> view sel
> show #!4 models
> select add #1
18657 atoms, 18852 bonds, 1178 residues, 1 model selected
> select clear
> volume #4 level 0.02317
> open 7nzm
7nzm title:
Cryo-EM structure of pre-dephosphorylation complex of phosphorylated eIF2alpha
with trapped holophosphatase (PP1A_D64A/PPP1R15A/G-actin/DNase I) [more
info...]
Chain information for 7nzm #6
---
Chain | Description | UniProt
A | Actin, alpha skeletal muscle, intermediate form | ACTS_RABIT 1-375
B | Serine/threonine-protein phosphatase PP1-alpha catalytic subunit | PP1A_RABIT 7-300
C | Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein | PR15A_HUMAN 553-624, MALE_ECOLI 626-996
D | Deoxyribonuclease-1 | DNAS1_BOVIN 1-260
E | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 1-186
Non-standard residues in 7nzm #6
---
ATP — adenosine-5'-triphosphate
MN — manganese (II) ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> mmaker #6/C to #1/C
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 240711_J18_Dp71-PP1-eIF2a-Gactin-DNAseI_v2.cif, chain C (#1) with
7nzm, chain C (#6), sequence alignment score = 14.7
RMSD between 11 pruned atom pairs is 1.225 angstroms; (across all 49 pairs:
32.999)
> select add #6
9109 atoms, 9309 bonds, 4 pseudobonds, 1161 residues, 2 models selected
> style sel stick
Changed 9109 atom styles
> show sel atoms
> show sel cartoons
> hide sel atoms
> select clear
> open 6o9z
6o9z title:
Electron cryo-microscopy of the eukaryotic translation initiation factor 2B
bound to eukaryotic translation initiation factor 2 from Homo sapiens [more
info...]
Chain information for 6o9z #7
---
Chain | Description | UniProt
A B | Translation initiation factor eIF-2B subunit epsilon | EI2BE_HUMAN 1-721
C D | Translation initiation factor eIF-2B subunit beta | EI2BB_HUMAN 2-351
E F | Translation initiation factor eIF-2B subunit delta | EI2BD_HUMAN 1-523
G H | Translation initiation factor eIF-2B subunit alpha | EI2BA_HUMAN 1-305
I J | Translation initiation factor eIF-2B subunit gamma | EI2BG_HUMAN 1-452
L M | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 1-314
> select add #7
25788 atoms, 26213 bonds, 10 pseudobonds, 3605 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 25788 atom styles
> view
> hide #!6 models
> hide #!4 models
> hide #1 models
> show sel cartoons
> select clear
> hide #!7 models
> show #1 models
> mmaker #7/M to #1/A
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 240711_J18_Dp71-PP1-eIF2a-Gactin-DNAseI_v2.cif, chain A (#1) with
6o9z, chain M (#7), sequence alignment score = 915.9
RMSD between 139 pruned atom pairs is 0.992 angstroms; (across all 176 pairs:
2.482)
> show #!7 models
> select #7/M
930 atoms, 929 bonds, 176 residues, 1 model selected
> select ~sel & ##selected
24858 atoms, 25284 bonds, 10 pseudobonds, 3429 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select add #7
25788 atoms, 26213 bonds, 10 pseudobonds, 3605 residues, 2 models selected
> select subtract #7
Nothing selected
> hide #!7 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> view sel
> show #!7 models
> select add #1
18657 atoms, 18852 bonds, 1178 residues, 1 model selected
> color sel byhetero
> select clear
> color #1#!7 byhetero
> open 6o85
6o85 title:
Electron cryo-microscopy of the eukaryotic translation initiation factor 2B
bound to eukaryotic translation initiation factor 2 from Homo sapiens [more
info...]
Chain information for 6o85 #8
---
Chain | Description | UniProt
A B | Translation initiation factor eIF-2B subunit epsilon | EI2BE_HUMAN 1-721
C D | Translation initiation factor eIF-2B subunit beta | EI2BB_HUMAN 2-351
E F | Translation initiation factor eIF-2B subunit delta | EI2BD_HUMAN 1-523
G H | Translation initiation factor eIF-2B subunit alpha | EI2BA_HUMAN 1-305
I J | Translation initiation factor eIF-2B subunit gamma | EI2BG_HUMAN 1-452
L | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 1-314
S | Eukaryotic translation initiation factor 2 subunit 3 | IF2G_HUMAN 1-472
d | Eukaryotic translation initiation factor 2 subunit beta |
Non-standard residues in 6o85 #8
---
C7B —
2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide
(ISRIB)
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> mmaker #8/M to #1/A
No molecules/chains to match specified
> show #!4 models
> hide #!4 models
> hide #1 models
> hide #!7 models
> view
> mmaker #8/L to #1/A
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 240711_J18_Dp71-PP1-eIF2a-Gactin-DNAseI_v2.cif, chain A (#1) with
6o85, chain L (#8), sequence alignment score = 894.9
RMSD between 165 pruned atom pairs is 0.756 angstroms; (across all 184 pairs:
2.224)
> show #1 models
> select add #8
28546 atoms, 29000 bonds, 15 pseudobonds, 4115 residues, 2 models selected
> style sel stick
Changed 28546 atom styles
> show sel cartoons
> color sel byhetero
> select #8/L
1651 atoms, 1670 bonds, 275 residues, 1 model selected
> select ~sel & ##selected
26895 atoms, 27330 bonds, 15 pseudobonds, 3840 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select clear
> show #!7 models
> select clear
> select #1/A:51
14 atoms, 13 bonds, 1 residue, 1 model selected
> view sel
> select clear
> show #!4 models
> hide #!4 models
> show #!6 models
> mmaker #6/A to #1/A
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 240711_J18_Dp71-PP1-eIF2a-Gactin-DNAseI_v2.cif, chain A (#1) with
7nzm, chain A (#6), sequence alignment score = 24.4
RMSD between 4 pruned atom pairs is 1.142 angstroms; (across all 143 pairs:
28.696)
> hide #!7 models
> hide #!8 models
> hide #1 models
> view
> mmaker #6/E to #1/A
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 240711_J18_Dp71-PP1-eIF2a-Gactin-DNAseI_v2.cif, chain A (#1) with
7nzm, chain E (#6), sequence alignment score = 879.3
RMSD between 150 pruned atom pairs is 0.911 angstroms; (across all 178 pairs:
1.588)
> show #!7 models
> show #1 models
> hide #!7 models
> select #6/E:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
76 atoms, 75 bonds, 9 residues, 1 model selected
> select up
1392 atoms, 1416 bonds, 178 residues, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> select clear
> select #6/B:127
6 atoms, 5 bonds, 1 residue, 1 model selected
> view sel
> select clear
> show #!4 models
> select #1/C:64
10 atoms, 9 bonds, 1 residue, 1 model selected
> view sel
> select clear
> color #1#!6 byhetero
> select clear
> select #1/A:40-60
369 atoms, 368 bonds, 21 residues, 1 model selected
> view sel
> select clear
> hide #1#!6 atoms
> select #1/A:40-60
369 atoms, 368 bonds, 21 residues, 1 model selected
> show sel atoms
> select sel : show sel & #1#!6 atoms
> hide H
> select clear
> hide #!4 models
> show #!4 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!4 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #!7 models
> show #!8 models
> hide #!6 models
> hide #!8 models
> hide #!7 models
> show #!4 models
> hide #1 models
> view
> ui mousemode right "map eraser"
> volume erase #4 center 142.65,109.71,156.94 radius 21.08
Opened cryosparc_P512_J18_009_volume_map (1).mrc copy as #10, grid size
320,320,320, pixel 0.929, shown at step 1, values float32
> volume erase #10 center 159.63,116.92,167.33 radius 20.949
> volume erase #10 center 152.96,175.69,181.6 radius 20.949
> volume erase #10 center 144.01,166.78,190.48 radius 20.949
> volume erase #10 center 154.22,172.13,173.47 radius 20.949
> volume erase #10 center 156.51,150.45,187.54 radius 20.949
> volume erase #10 center 143.47,167.94,125.63 radius 31.498 outside true
> volume resample #10 onGrid #4
Opened cryosparc_P512_J18_009_volume_map (1).mrc copy resampled as #11, grid
size 320,320,320, pixel 0.929, shown at step 1, values float32
> save /Users/udalwadi/Downloads/J18_PP1_mask.mrc models #11
> volume #11 level 0.01407
> hide #!11 models
> hide #9 models
> close #9
> ui mousemode right "translate selected models"
> open /Users/udalwadi/Downloads/cryosparc_P512_J22_mask.mrc
> /Users/udalwadi/Downloads/cryosparc_P512_J18_009_volume_map.mrc
Opened cryosparc_P512_J22_mask.mrc as #9.1, grid size 320,320,320, pixel
0.929, shown at level 5e-05, step 2, values float32
Opened cryosparc_P512_J18_009_volume_map.mrc as #9.2, grid size 320,320,320,
pixel 0.929, shown at level 0.00378, step 2, values float32
> close #9-11#9.1-2
> open /Users/udalwadi/Downloads/cryosparc_P512_J23_005_volume_map.mrc
Opened cryosparc_P512_J23_005_volume_map.mrc as #9, grid size 320,320,320,
pixel 0.929, shown at level 0.00435, step 2, values float32
> volume #9 step 1
> volume #9 level 0.01691
> show #!4 models
> open /Users/udalwadi/Downloads/cryosparc_P512_J24_006_volume_map.mrc
Opened cryosparc_P512_J24_006_volume_map.mrc as #10, grid size 320,320,320,
pixel 0.929, shown at level 0.0042, step 2, values float32
> volume #10 level 0.01669
> volume #10 step 1
> close #9
> volume #10 level 0.01603
> hide #!10 models
> show #!3 models
> open /Users/udalwadi/Library/CloudStorage/Box-
> Box/Dp71_Project/maps_models/Dp71-PP1-Gactin-DNAseI-P327-J104-local.mrc
Opened Dp71-PP1-Gactin-DNAseI-P327-J104-local.mrc as #9, grid size
256,256,256, pixel 1.12, shown at level 0.00451, step 1, values float32
> volume #9 level 0.03008
> volume #!3-4,9 style surface
> transparency #3.1#4.1#9.1 0
> hide #!4 models
> hide #!3 models
> volume #9 level 0.1068
> volume #9 level 0.1725
> show #!3 models
> volume #3 level 0.3298
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #9
2 models selected
> view matrix models #9,1,0,0,-3.417,0,1,0,6.2971,0,0,1,10.328
> view matrix models #9,1,0,0,-1.525,0,1,0,8.1401,0,0,1,8.9792
> view matrix models
> #9,0.70377,0.64285,0.30241,-80.462,-0.51969,0.75609,-0.39781,163.93,-0.48438,0.12281,0.86619,79.068
> view matrix models
> #9,0.70377,0.64285,0.30241,-84.192,-0.51969,0.75609,-0.39781,163.4,-0.48438,0.12281,0.86619,79.248
> view matrix models
> #9,0.70377,0.64285,0.30241,-88.134,-0.51969,0.75609,-0.39781,172.63,-0.48438,0.12281,0.86619,88.751
> view matrix models
> #9,0.54956,0.74646,0.3752,-87.766,-0.43131,0.63812,-0.63779,203.2,-0.71551,0.18867,0.67264,136.13
> fitmap #9 inMap #3
Fit map Dp71-PP1-Gactin-DNAseI-P327-J104-local.mrc in map Dp71-PP1-Gactin-
DNAseI-P327_J147.mrc using 14216 points
correlation = 0.3433, correlation about mean = 0.05761, overlap = 435.3
steps = 100, shift = 3.19, angle = 5.52 degrees
Position of Dp71-PP1-Gactin-DNAseI-P327-J104-local.mrc (#9) relative to
Dp71-PP1-Gactin-DNAseI-P327_J147.mrc (#3) coordinates:
Matrix rotation and translation
0.83884477 0.46633287 0.28084358 -77.41735076
-0.41479053 0.88165189 -0.22503058 102.89753969
-0.35254543 0.07227447 0.93299953 59.92213387
Axis 0.26423719 0.56294010 -0.78312014
Axis point 195.76609280 228.30693159 0.00000000
Rotation angle (degrees) 34.23387685
Shift along axis -9.45762160
> view matrix models
> #9,0.61577,0.72486,0.30888,-86.261,-0.42866,0.63712,-0.64057,214.9,-0.66111,0.26204,0.70304,82.957
> view matrix models
> #9,0.61577,0.72486,0.30888,-80.846,-0.42866,0.63712,-0.64057,201.63,-0.66111,0.26204,0.70304,108.51
> view matrix models
> #9,0.89196,0.40329,0.20434,-65.628,-0.32926,0.88919,-0.3177,115.36,-0.30983,0.21609,0.92591,37.309
> view matrix models
> #9,0.89196,0.40329,0.20434,-65.705,-0.32926,0.88919,-0.3177,115.99,-0.30983,0.21609,0.92591,37.089
> view matrix models
> #9,0.89196,0.40329,0.20434,-70.659,-0.32926,0.88919,-0.3177,115.64,-0.30983,0.21609,0.92591,36.956
> fitmap #9 inMap #3
Fit map Dp71-PP1-Gactin-DNAseI-P327-J104-local.mrc in map Dp71-PP1-Gactin-
DNAseI-P327_J147.mrc using 14216 points
correlation = 0.8312, correlation about mean = 0.3931, overlap = 1379
steps = 80, shift = 4.48, angle = 8.86 degrees
Position of Dp71-PP1-Gactin-DNAseI-P327-J104-local.mrc (#9) relative to
Dp71-PP1-Gactin-DNAseI-P327_J147.mrc (#3) coordinates:
Matrix rotation and translation
0.99995922 0.00865591 -0.00257508 -1.12092080
-0.00863518 0.99993108 0.00795525 0.22258915
0.00264377 -0.00793269 0.99996504 1.25271127
Axis -0.66048288 -0.21695463 -0.71881364
Axis point 19.37949742 145.49156150 -0.00000000
Rotation angle (degrees) 0.68914249
Shift along axis -0.20840871
> select clear
> show #!4 models
> color #4 #ff807cff models
> fitmap #4 inMap #3
Fit map cryosparc_P512_J18_009_volume_map (1).mrc in map Dp71-PP1-Gactin-
DNAseI-P327_J147.mrc using 69091 points
correlation = 0.7749, correlation about mean = 0.5625, overlap = 916.5
steps = 60, shift = 0.0291, angle = 0.136 degrees
Position of cryosparc_P512_J18_009_volume_map (1).mrc (#4) relative to
Dp71-PP1-Gactin-DNAseI-P327_J147.mrc (#3) coordinates:
Matrix rotation and translation
0.94101303 -0.24145115 -0.23705659 80.66307416
0.31421301 0.88350228 0.34741029 -90.35274341
0.12555743 -0.40140387 0.90725424 45.51140870
Axis -0.74844967 -0.36243752 0.55539368
Axis point 0.00000000 51.94757440 279.94456387
Rotation angle (degrees) 30.01611101
Shift along axis -2.34827859
> select clear
> select add #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99603,-0.047613,-0.075226,18.971,0.048386,0.99879,0.0084914,-8.1733,0.074731,-0.012098,0.99713,-8.6813
> fitmap #4 inMap #3
Fit map cryosparc_P512_J18_009_volume_map (1).mrc in map Dp71-PP1-Gactin-
DNAseI-P327_J147.mrc using 69091 points
correlation = 0.7749, correlation about mean = 0.5625, overlap = 916.5
steps = 84, shift = 0.315, angle = 5.06 degrees
Position of cryosparc_P512_J18_009_volume_map (1).mrc (#4) relative to
Dp71-PP1-Gactin-DNAseI-P327_J147.mrc (#3) coordinates:
Matrix rotation and translation
0.94099603 -0.24150460 -0.23706960 80.67615334
0.31424099 0.88357075 0.34721080 -90.33583312
0.12561476 -0.40122098 0.90732721 45.46177456
Axis -0.74822857 -0.36258589 0.55559470
Axis point -0.00000000 51.88431625 280.02948965
Rotation angle (degrees) 30.00898428
Shift along axis -2.35138343
> hide #!9 models
> select clear
> open /Users/udalwadi/Downloads/cryosparc_P512_J24_007_volume_map.mrc
Opened cryosparc_P512_J24_007_volume_map.mrc as #11, grid size 320,320,320,
pixel 0.929, shown at level 0.00421, step 2, values float32
> hide #!3 models
> hide #!4 models
> close #10
> volume #11 step 1
> volume #11 level 0.01637
===== Log before crash end =====
Log:
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
ra rd; rt
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color {arguments} bychain; color {arguments} byhet
cs clipper set contourSensitivity {arguments}
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 - 88.1
OpenGL renderer: Apple M1 Pro
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: MacBookPro18,3
Model Number: MKGR3LL/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 43 days, 20 hours, 37 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
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
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-Clipper: 0.23.1
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-ISOLDE: 1.8
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 , 15 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 , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Likes Qt 6.6 bug. Have not yet seen it in Qt 6.7. The usual _NSViewHierarchyDidChangeBackingProperties crash, probably waking from sleep.