The following bug report has been submitted:
Platform: macOS-15.1-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 0x00007ff859859b40 (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.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.segment._segment, chimerax.graphics._graphics, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, scipy._lib._ccallback_c, 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.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.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._webp (total: 123)
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{
"uptime" : 80000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,3",
"coalitionID" : 1511,
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"releaseType" : "User"
},
"captureTime" : "2024-11-07 10:01:30.2176 -0800",
"codeSigningMonitor" : 0,
"incident" : "6604A8B8-5785-41CF-A67F-89BD9C0B202E",
"pid" : 2244,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-11-05 08:37:43.3735 -0800",
"procStartAbsTime" : 11191499594825,
"procExitAbsTime" : 80168348794230,
"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"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "586409D4-F6D0-0B06-6CD4-3641E818D7B4",
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "313C2918-80F6-4EBB-8867-B5ADFF6E446C",
"wakeTime" : 44,
"bridgeVersion" : {"build":"22P1072","train":"9.1"},
"sleepWakeUUID" : "DC0D9BE5-35FF-479E-8A3D-744E49EC8035",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4485771264\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b5f7000-10b5fb000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":2244},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4485771264\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b5f7000-10b5fb000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> graphics silhouettes true width 1
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/petra/Desktop/Model/2A/2A_Map.mrc
Opened 2A_Map.mrc as #1, grid size 460,460,460, pixel 0.65, shown at level
0.0187, step 2, values float32
> surface dust #1 size 6.5
> ui tool show "Fit to Segments"
> ui tool show "Map Statistics"
> measure mapstats
Map 2A_Map.mrc #1, step 2, minimum -0.4596, maximum 1.021, mean -2.923e-05, SD
0.01225, RMS 0.01225
> ui tool show "Volume Viewer"
> volume #1 step 1
> volume #1 level 0.08244
> volume #1 level 0.2017
> volume #1 level 0.1074
> volume #1 level 0.05194
> volume gaussian #1 sDev 2
Opened 2A_Map.mrc gaussian as #2, grid size 460,460,460, pixel 0.65, shown at
step 1, values float32
> ui tool show "Segment Map"
Segmenting 2A_Map.mrc gaussian, density threshold 0.011730
Only showing 60 of 71 regions.
Showing 60 of 71 region surfaces
256 watershed regions, grouped to 71 regions
Showing 2A_Map gaussian.seg - 71 regions, 60 surfaces
> ui mousemode right select
> select #3.34
1 model selected
> select add #3.38
2 models selected
> select add #3.12
3 models selected
> select add #3.40
4 models selected
> select add #3.8
5 models selected
> select add #3.50
6 models selected
> select add #3.10
7 models selected
> select add #3.22
8 models selected
> select add #3.42
9 models selected
> select subtract #3.10
8 models selected
> select add #3.21
9 models selected
> select add #3.10
10 models selected
> select add #3.16
11 models selected
> select add #3.48
12 models selected
> select add #3.60
13 models selected
> select add #3.15
14 models selected
> select add #3.1
15 models selected
> select add #3.2
16 models selected
> select add #3.31
17 models selected
> select add #3.25
18 models selected
> select subtract #3.31
17 models selected
> select add #3.31
18 models selected
> select add #3.24
19 models selected
> select add #3.5
20 models selected
> select subtract #3.5
19 models selected
> select add #3.5
20 models selected
> select add #3.47
21 models selected
Grouped 21 regions
> select add #3.20
4 models selected
Grouped 2 regions
> select add #3
42 models selected
> select subtract #3
2 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> close #3
> show #!2 models
> ui tool show "Segment Map"
Segmenting 2A_Map.mrc gaussian, density threshold 0.011730
Showing 71 region surfaces
256 watershed regions, grouped to 71 regions
Showing 2A_Map gaussian.seg - 71 regions, 71 surfaces
> select add #3.38
1 model selected
> select add #3.34
2 models selected
> select add #3.12
3 models selected
> select add #3.40
4 models selected
> select add #3.50
5 models selected
> select add #3.8
6 models selected
> select add #3.22
7 models selected
> select add #3.10
8 models selected
> select add #3.42
9 models selected
> select add #3.61
10 models selected
> select add #3.20
11 models selected
> select add #3.21
12 models selected
> select add #3.16
13 models selected
> select add #3.48
14 models selected
> select add #3.15
15 models selected
> select add #3.60
16 models selected
> select add #3.5
17 models selected
> select add #3.24
18 models selected
> select add #3.2
19 models selected
> select add #3.1
20 models selected
> select add #3.47
21 models selected
> select add #3.25
22 models selected
> select add #3.31
23 models selected
> select subtract #3.2
22 models selected
> select add #3.62
23 models selected
> select subtract #3.24
22 models selected
> select subtract #3.5
21 models selected
> select subtract #3.47
20 models selected
> select subtract #3.25
19 models selected
> select subtract #3.31
18 models selected
> select add #3.2
19 models selected
> select subtract #3.2
18 models selected
> select subtract #3.1
17 models selected
> select add #3.5
18 models selected
> select subtract #3.5
17 models selected
Grouped 17 regions
> select add #3.45
2 models selected
> select add #3.67
3 models selected
Ungrouped to 20 regions
> select #3.73
1 model selected
Grouped 1 regions
Ungrouped to 1 regions
> select #3.67
1 model selected
Ungrouped to 0 regions
> select add #3.45
1 model selected
Ungrouped to 3 regions
> select #3.8
1 model selected
Ungrouped to 0 regions
> select #3.61
1 model selected
> select add #3.12
2 models selected
> select add #3.72
3 models selected
> select add #3.20
4 models selected
> select add #3.16
5 models selected
> select add #3.21
6 models selected
> select add #3.10
7 models selected
> select add #3.15
8 models selected
> select add #3.50
9 models selected
> select add #3.62
10 models selected
> select add #3.60
11 models selected
> select add #3.22
12 models selected
> select add #3.38
13 models selected
> select add #3.42
14 models selected
> select add #3.48
15 models selected
> select add #3.40
16 models selected
Grouped 16 regions
> select add #3.5
2 models selected
> select add #3.24
3 models selected
> select add #3.2
4 models selected
> select add #3.1
5 models selected
> select add #3.47
6 models selected
> select add #3.25
7 models selected
> select add #3.31
8 models selected
> select subtract #3.47
7 models selected
> select subtract #3.10
6 models selected
> select add #3.47
7 models selected
Grouped 7 regions
> select add #3.10
2 models selected
> hide #!2 models
> select add #3
55 models selected
> select subtract #3
Nothing selected
Drag select of 364, 337, 316, 310, 383, 376, 375, 377, 291, 305, 381, 372,
344, 380, 382, 278, 369, 365, 366, 297, 355, 347, 370, 345, 317, 293, 336,
360, 304, 52, 167, 265, 320, 324, 309, 295, 69, 325, 287, 328, 123, 125, 264,
269, 140, 170, 350, 188, 183, 156, 194, 193
Grouped 52 regions
> show #!2 models
> select add #3
4 models selected
> select subtract #3
Nothing selected
> hide #!2 models
> hide #!3 models
> show #!1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 level 0.1747
> volume #1 level 0.109
> show #!3 models
> hide #!1 models
> show #!1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!1 models
> select #3.2
1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!3 models
> show #!1 models
> select add #3
4 models selected
> open /Users/petra/Desktop/Model/3A/3A_Map.mrc
Opened 3A_Map.mrc as #4, grid size 380,380,380, pixel 0.832, shown at level
0.00946, step 2, values float32
> hide #!1 models
> select subtract #3
Nothing selected
> surface dust #4 size 8.32
> lighting soft
> volume #4 step 1
> volume #4 level 0.04219
> volume #4 level 0.07492
> volume #4 level 0.04963
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> volume #1 level 0.06621
> open /Users/petra/Downloads/cryosparc_P14_J305_010_volume_map_sharp.mrc
Opened cryosparc_P14_J305_010_volume_map_sharp.mrc as #5, grid size
420,420,420, pixel 0.65, shown at level 0.0104, step 2, values float32
> show #!4 models
> hide #!4 models
> show #!3 models
> close #3
> close #2
> show #!4 models
> surface dust #1 size 6.5
> surface dust #4 size 8.32
> surface dust #5 size 6.5
> volume #5 step 1
> volume #5 level 0.06384
> hide #!4 models
> hide #!1 models
> show #!4 models
> hide #!5 models
> show #!1 models
> hide #!4 models
Drag select of 1 2A_Map.mrc
> ui mousemode right select
> ui mousemode right translate
> select add #1
2 models selected
> select subtract #1
Nothing selected
> ui tool show "Segment Map"
Segmenting 2A_Map.mrc, density threshold 0.066213
Only showing 90 of 114 regions.
Showing 90 of 114 region surfaces
2686 watershed regions, grouped to 114 regions
Showing 2A_Map.seg - 114 regions, 90 surfaces
Segmenting 2A_Map.mrc, density threshold 0.066213
Only showing 90 of 114 regions.
Showing 90 of 114 region surfaces
2686 watershed regions, grouped to 114 regions
Showing 2A_Map.seg - 114 regions, 90 surfaces
> ui mousemode right select
Smoothing and grouping, standard deviation 5 voxels
Showing 73 region surfaces
Got 73 regions after smoothing 5 voxels.
> ui mousemode right rotate
> ui mousemode right select
Drag select of 3803, 3794, 20206 of 21268 triangles, 3801, 16349 of 18148
triangles, 3818, 3640, 3814, 3062, 3743, 3830, 3843, 19627 of 36532 triangles,
3834, 915 of 34632 triangles, 3831, 9559 of 28488 triangles, 3825, 3835, 12527
of 17788 triangles, 3826, 3740, 3912 of 3920 triangles, 1 2A_Map.mrc
> hide #!1 models
Drag select of 3762, 16082 of 16168 triangles, 3810, 5962 of 13524 triangles,
3813, 939 of 11988 triangles, 3838, 17320 of 24328 triangles, 3820, 16277 of
21612 triangles, 3832, 4823 of 21148 triangles, 3828, 27070 of 27848
triangles, 3837, 3771
Drag select of 3779, 3756, 3766, 3792, 3785, 3806, 3773, 3784, 3815, 3572,
3783, 3770, 3778, 3786, 3805, 3780, 3808, 3812, 3798, 3667, 3763, 3781, 3811,
3787, 3791, 3774, 3761, 3646, 3647, 3608, 3797, 3590, 3840, 3822, 3836, 3833,
3841, 3829, 3824, 3844, 3827, 3842, 3839, 3819, 3821, 3823, 3620, 3563
Grouped 73 regions
Ungrouped to 73 regions
> undo
> select add #2
76 models selected
> select subtract #2
2 models selected
Drag select of 3801, 3826, 3803, 3831, 27466 of 28488 triangles, 3640, 3834,
22047 of 34632 triangles, 3835, 17278 of 17788 triangles, 3836, 82 of 44804
triangles, 3780, 103 of 18340 triangles, 3743, 3830, 3814, 3839, 339 of 27592
triangles, 3785, 1340 of 29892 triangles, 3062, 3818, 3825, 3740, 3843, 29622
of 36532 triangles, 3794
> select subtract #2.38
19 models selected
> select subtract #2.48
18 models selected
> select subtract #2.28
17 models selected
> select subtract #2.29
16 models selected
Drag select of 3771, 3832, 7064 of 21148 triangles, 3810, 7483 of 13524
triangles, 3838, 20293 of 24328 triangles, 3813, 2318 of 11988 triangles,
3837, 3820, 19117 of 21612 triangles, 3828, 3762, 3766, 65 of 35680 triangles
> select subtract #2.71
25 models selected
> ui mousemode right translate
> ui mousemode right select
Drag select of 3572, 3822, 3620, 3819, 3770, 3827, 3773, 3805, 3774, 3806,
3808, 3833, 3778, 3779, 3811, 3590, 3836, 3780, 3812, 3781, 3563, 3839, 3821,
3783, 3815, 3823, 3784, 3608, 3841, 3785, 3840, 3786, 3787, 3842, 3844, 3756,
3791, 3829, 3792, 3824, 3761, 3763, 3667, 3797, 3766, 3798, 3647, 3646
Deleted 25 regions
Grouped 48 regions
> show #!1 models
Volume of 1 region: 4.04e+04 Angstroms^3, 147002 points
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
Volume of 1 region: 4.04e+04 Angstroms^3, 147002 points
> open /Users/petra/Downloads/cryosparc_P705_J166_class_04_final_volume.mrc
Opened cryosparc_P705_J166_class_04_final_volume.mrc as #3, grid size
380,380,380, pixel 0.832, shown at level 0.0586, step 2, values float32
> open /Users/petra/Downloads/cryosparc_P705_J166_class_03_final_volume.mrc
Opened cryosparc_P705_J166_class_03_final_volume.mrc as #6, grid size
380,380,380, pixel 0.832, shown at level 0.0581, step 2, values float32
> open /Users/petra/Downloads/cryosparc_P705_J166_class_02_final_volume.mrc
Opened cryosparc_P705_J166_class_02_final_volume.mrc as #7, grid size
380,380,380, pixel 0.832, shown at level 0.0579, step 2, values float32
> open /Users/petra/Downloads/cryosparc_P705_J166_class_01_final_volume.mrc
Opened cryosparc_P705_J166_class_01_final_volume.mrc as #8, grid size
380,380,380, pixel 0.832, shown at level 0.0577, step 2, values float32
> open /Users/petra/Downloads/cryosparc_P705_J166_class_00_final_volume.mrc
Opened cryosparc_P705_J166_class_00_final_volume.mrc as #9, grid size
380,380,380, pixel 0.832, shown at level 0.0581, step 2, values float32
> hide #!2 models
> select add #2
2 models selected
> hide #!1 models
> select subtract #2
Nothing selected
> hide #!3 models
> surface dust #6 size 8.32
> surface dust #7 size 8.32
> surface dust #8 size 8.32
> surface dust #9 size 8.32
> close #2
> close #1
> show #!3 models
> hide #!3 models
> close #4
> show #!5 models
> show #!3 models
> hide #!3 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> volume #9 step 1
> volume #8 step 1
> volume #7 step 1
> volume #6 step 1
> volume #3 step 1
> volume #9 level 0.09173
> volume #8 level 0.1084
> volume #7 level 0.115
> volume #6 level 0.118
> volume #6 level 0.1046
> volume #3 level 0.1164
> volume #3 level 0.1457
> volume #5 level 0.09275
Drag select of 5 cryosparc_P14_J305_010_volume_map_sharp.mrc
> show #!5 models
> select subtract #5
Nothing selected
> show #!3 models
> hide #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> close #5-9
> hide #!3 models
> close #3
> open /Users/petra/Desktop/Model/3A/3A_Map.mrc format mrc
Opened 3A_Map.mrc as #1, grid size 380,380,380, pixel 0.832, shown at level
0.00946, step 2, values float32
> volume #1 level 0.05464
> surface dust #1 size 8.32
> volume #1 step 1
> volume #1 level 0.08498
> volume #1 level 0.0373
> volume #1 level 0.06331
> volume gaussian #1 sDev 2
Opened 3A_Map.mrc gaussian as #2, grid size 380,380,380, pixel 0.832, shown at
step 1, values float32
> ui tool show "Segment Map"
Segmenting 3A_Map.mrc gaussian, density threshold 0.005243
Showing 51 region surfaces
262 watershed regions, grouped to 51 regions
Showing 3A_Map gaussian.seg - 51 regions, 51 surfaces
Drag select of 396, 402, 31614 of 31828 triangles, 389, 388, 2453 of 26316
triangles, 366, 394, 11299 of 19624 triangles, 374, 44 of 22808 triangles, 4,
373, 13554 of 16340 triangles, 363, 6707 of 13836 triangles, 312, 5, 2
3A_Map.mrc gaussian
> select subtract #3.15
13 models selected
> select subtract #3.10
12 models selected
Grouped 10 regions
Drag select of 406, 55336 of 59040 triangles, 400, 23159 of 35148 triangles,
392, 16197 of 29972 triangles, 255, 2 3A_Map.mrc gaussian
> select subtract #3.2
4 models selected
Grouped 4 regions
> select add #3.2
2 models selected
> hide #!2 models
> select add #3
40 models selected
> select subtract #3
Nothing selected
Drag select of 399, 401, 407, 388, 393, 390, 374, 377, 397, 370, 395, 405,
367, 391, 403, 54, 398, 385, 57, 310, 331, 404, 408, 317, 318, 350, 269, 303,
335, 290, 339, 332, 348, 289, 135, 330, 134
Grouped 37 regions
Saving 1 regions to mrc file...
Opened 3A_Get3only.mrc as #4, grid size 91,114,84, pixel 0.832, shown at step
1, values float32
Wrote 3A_Get3only.mrc
> select add #3
4 models selected
> select subtract #3
Nothing selected
> hide #!3 models
> volume #4 level 0.006103
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> volume #4 level 0.005966
> volume resample #4 onGrid #1
Opened 3A_Get3only.mrc resampled as #5, grid size 380,380,380, pixel 0.832,
shown at step 1, values float32
> save /Users/petra/Downloads/3A_Get3only.mrc models #5
> hide #!5 models
Showing 3 region surfaces
> show #!2 models
> hide #!2 models
> show #!3 models
> select #3.3
1 model selected
> select #3.3
1 model selected
> select #3.1
1 model selected
> select #3.2
1 model selected
> select #3.3
1 model selected
> select #3.1
1 model selected
> select #3.2
1 model selected
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
Saving 1 regions to mrc file...
Opened 3A_Get4Only.mrc as #6, grid size 74,87,108, pixel 0.832, shown at step
1, values float32
Wrote 3A_Get4Only.mrc
> select add #3
4 models selected
> select subtract #3
Nothing selected
> hide #!3 models
> volume #6 level 0.005709
> volume resample #6 onGrid #1
Opened 3A_Get4Only.mrc resampled as #7, grid size 380,380,380, pixel 0.832,
shown at step 1, values float32
> save /Users/petra/Downloads/3A_Get4Only.mrc models #7
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!1 models
> ui mousemode right translate
> volume #1 style image colorMode opaque8 showOutlineBox true orthoplanes xyz
> positionPlanes 189,189,189 imageMode orthoplanes
> volume #1 orthoplanes xyz positionPlanes 189,213,189
> volume #1 orthoplanes xyz positionPlanes 189,213,198
> volume #1 style surface
> volume #1 style image positionPlanes 189,189,189
> volume #1 orthoplanes xyz positionPlanes 189,189,146
> volume #1 orthoplanes xyz positionPlanes 189,189,139
> volume #1 orthoplanes xyz positionPlanes 189,186,139
> volume #1 orthoplanes xyz positionPlanes 189,181,139
> volume #1 orthoplanes xyz positionPlanes 198,181,139
> volume #1 orthoplanes xyz positionPlanes 198,177,139
> volume #1 orthoplanes xyz positionPlanes 198,177,146
> volume #1 orthoplanes xyz positionPlanes 198,177,150
> volume #1 style surface
> volume #1 style image positionPlanes 189,189,189
> volume #1 orthoplanes xyz positionPlanes 189,189,139
> volume #1 orthoplanes xyz positionPlanes 193,189,139
> volume #1 style surface
> ui mousemode right translate
> volume #1 style image positionPlanes 189,189,189
> volume #1 orthoplanes xyz positionPlanes 189,189,144
> volume #1 orthoplanes xyz positionPlanes 198,189,144
> volume #1 style surface
> volume #1 style image positionPlanes 189,189,189
> volume #1 orthoplanes xyz positionPlanes 189,189,142
> volume #1 orthoplanes xyz positionPlanes 200,189,142
> volume #1 style surface
> volume #1 region 0,0,0,379,379,379
> ui mousemode right translate
> volume #1 style image positionPlanes 189,189,189
> volume #1 orthoplanes xyz positionPlanes 189,189,147
> volume #1 orthoplanes xyz positionPlanes 189,189,136
> volume #1 orthoplanes xyz positionPlanes 194,189,136
> volume #1 style surface
> ui mousemode right translate
> volume #1 style image positionPlanes 189,189,189
> volume #1 orthoplanes xyz positionPlanes 189,211,189
> volume #1 orthoplanes xyz positionPlanes 194,211,189
> volume #1 orthoplanes xyz positionPlanes 185,211,189
> volume #1 orthoplanes xyz positionPlanes 185,208,189
> volume #1 orthoplanes xyz positionPlanes 185,208,193
> open /Users/petra/Downloads/cryosparc_P14_J282_003_volume_map.mrc
Opened cryosparc_P14_J282_003_volume_map.mrc as #8, grid size 420,420,420,
pixel 0.65, shown at level 0.0079, step 2, values float32
> volume #1 style surface
> hide #!1 models
> volume #8 step 1
> volume #8 level 0.02167
> volume #8 level 0.01774
> volume #8 level 0.03839
> volume #8 level 0.02266
> volume #8 level 0.02905
> show #!2 models
> close #2-8
> volume #1 change image level -0.002372,0 level 0.00946,0.8 level 0.4891,1
> close #1
> open /Users/petra/Downloads/cryosparc_P705_J160_011_volume_map_sharp(1).mrc
Opened cryosparc_P705_J160_011_volume_map_sharp(1).mrc as #1, grid size
380,380,380, pixel 0.832, shown at level 0.0095, step 2, values float32
> surface dust #1 size 8.32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 step 1
> volume #1 level 0.0225
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 level 0.07886
> volume #1 level 0.04562
> volume gaussian #1 sDev 2
Opened cryosparc_P705_J160_011_volume_map_sharp(1).mrc gaussian as #2, grid
size 380,380,380, pixel 0.832, shown at step 1, values float32
> ui tool show "Segment Map"
Segmenting cryosparc_P705_J160_011_volume_map_sharp(1).mrc gaussian, density
threshold 0.005243
Showing 51 region surfaces
262 watershed regions, grouped to 51 regions
Showing cryosparc_P705_J160_011_volume_map_sharp(1) gaussian.seg - 51 regions,
51 surfaces
> ui mousemode right select
Drag select of 400, 392, 29241 of 31804 triangles, 403, 25733 of 27272
triangles, 383, 401, 7811 of 19616 triangles, 4, 359, 8973 of 16336 triangles,
386, 2381 of 13848 triangles, 339, 10467 of 11136 triangles, 5, 2
cryosparc_P705_J160_011_volume_map_sharp(1).mrc gaussian
Grouped 10 regions
> select add #3
45 models selected
> select subtract #3
2 models selected
> select subtract #2
Nothing selected
Drag select of 394, 54623 of 58972 triangles, 406, 22526 of 35056 triangles,
404, 16738 of 29972 triangles, 253, 2
cryosparc_P705_J160_011_volume_map_sharp(1).mrc gaussian
> hide #!2 models
Grouped 4 regions
Drag select of 393, 399, 396, 398, 391, 407, 363, 387, 388, 380, 402, 405,
375, 408, 395, 50, 389, 371, 55, 341, 313, 397, 390, 343, 353, 335, 275, 268,
358, 265, 315, 329, 319, 301, 137, 352, 138
Grouped 37 regions
Saving 1 regions to mrc file...
Opened Get3Monly.mrc as #4, grid size 91,114,84, pixel 0.832, shown at step 1,
values float32
Wrote Get3Monly.mrc
> select #3.2
1 model selected
> select #3.3
1 model selected
> volume #4 level 0.009455
> volume #4 color #b2ffff81
> show #!1 models
> volume #4 level 0.01107
> volume #4 level 0.008689
> volume #4 level 0.009284
> select #3.2
1 model selected
> select #4
2 models selected
> select #4
2 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #4
2 models selected
> select add #3
6 models selected
> select subtract #3
2 models selected
> hide #!3 models
> show #!3 models
> select #3.2
1 model selected
> volume resample #4 onGrid #1
Opened Get3Monly.mrc resampled as #5, grid size 380,380,380, pixel 0.832,
shown at step 1, values float32
> volume #5 level 0.009
> volume #4 level 0.009
> volume #2 level 0.001333
> select add #3
4 models selected
> select subtract #3
Nothing selected
> volume #2 level 0.007265
> volume #1 level 0.06765
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/petra/Desktop/Mask/2024:11:05/Get3Monly.mrc models #5
> show #!4 models
> close #4
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!5 models
> show #!3 models
> show #!2 models
> hide #!2 models
> select #3.2
1 model selected
> select #3.1
1 model selected
> select #5
2 models selected
> select add #3.1
3 models selected
> select #5
2 models selected
> select #3.3
1 model selected
> select add #3.1
2 models selected
> select add #3.2
3 models selected
> select #3.1
1 model selected
> select #3.1
1 model selected
> select #3.2
1 model selected
> select #3.1
1 model selected
> select #3.2
1 model selected
Saving 1 regions to mrc file...
Opened Get4Monly.mrc as #4, grid size 74,87,108, pixel 0.832, shown at step 1,
values float32
Wrote Get4Monly.mrc
> volume #4 level 0.007041
> select add #3
4 models selected
> select subtract #3
Nothing selected
> hide #!3 models
> volume #4 level 0.006464
> volume #4 level 0.0522
> volume #4 level 0.007387
> volume resample #4 onGrid #1
Opened Get4Monly.mrc resampled as #6, grid size 380,380,380, pixel 0.832,
shown at step 1, values float32
> volume #6 level 0.009004
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/petra/Desktop/Mask/2024:11:05/Get4Monly.mrc models #6
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> show #!4 models
> show #!6 models
> hide #!4 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 style image colorMode opaque8 showOutlineBox true orthoplanes xyz
> positionPlanes 189,189,189 imageMode orthoplanes
> volume #1 orthoplanes xyz positionPlanes 189,168,189
> volume #1 style surface
> volume #1 style image positionPlanes 189,189,189
> volume #1 orthoplanes xyz positionPlanes 189,189,136
> volume #1 orthoplanes xyz positionPlanes 189,198,136
> volume #1 orthoplanes xyz positionPlanes 193,198,136
> volume #1 orthoplanes xyz positionPlanes 193,198,142
> volume #1 orthoplanes xyz positionPlanes 199,198,142
> volume #1 style surface
> volume #1 style image positionPlanes 189,189,189
> volume #1 orthoplanes xyz positionPlanes 189,189,197
> volume #1 orthoplanes xyz positionPlanes 189,172,197
> volume #1 style surface
> close #1-6
> open /Users/petra/Downloads/cryosparc_P705_J160_011_volume_map_sharp(2).mrc
Opened cryosparc_P705_J160_011_volume_map_sharp(2).mrc as #1, grid size
380,380,380, pixel 0.832, shown at level 0.0095, step 2, values float32
> open /Users/petra/Downloads/cryosparc_P705_J160_011_volume_map.mrc
Opened cryosparc_P705_J160_011_volume_map.mrc as #2, grid size 380,380,380,
pixel 0.832, shown at level 0.00433, step 2, values float32
> open /Users/petra/Downloads/cryosparc_P14_J268_011_volume_map(1).mrc
Opened cryosparc_P14_J268_011_volume_map(1).mrc as #3, grid size 420,420,420,
pixel 0.65, shown at level 0.0079, step 2, values float32
> open /Users/petra/Downloads/cryosparc_P14_J268_011_volume_map_sharp.mrc
Opened cryosparc_P14_J268_011_volume_map_sharp.mrc as #4, grid size
420,420,420, pixel 0.65, shown at level 0.0111, step 2, values float32
> open /Users/petra/Downloads/cryosparc_P14_J305_010_volume_map(1).mrc
Opened cryosparc_P14_J305_010_volume_map(1).mrc as #5, grid size 420,420,420,
pixel 0.65, shown at level 0.00465, step 2, values float32
> open /Users/petra/Downloads/cryosparc_P14_J305_010_volume_map_sharp(1).mrc
Opened cryosparc_P14_J305_010_volume_map_sharp(1).mrc as #6, grid size
420,420,420, pixel 0.65, shown at level 0.0104, step 2, values float32
> surface dust #1 size 8.32
> surface dust #2 size 8.32
> surface dust #3 size 6.5
> surface dust #4 size 6.5
> surface dust #5 size 6.5
> surface dust #6 size 6.5
> hide #!6 models
> hide #!5 models
> hide #!3 models
> hide #!4 models
> hide #!2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 step 1
> volume #2 step 1
> volume #1 level 0.07948
> volume #1 region 0,0,0,379,379,379
> ui mousemode right translate
> show #!2 models
> hide #!1 models
> volume #2 level 0.02716
> volume #2 level 0.03296
> volume #2 level 0.03875
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.02894
> volume #1 level 0.05616
> volume #1 level 0.07689
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!5 models
> hide #!1 models
> show #!6 models
> volume #5 step 1
> volume #6 step 1
> volume #6 level 0.06193
> show #!1 models
> hide #!1 models
> volume #5 level 0.02185
> volume #5 level 0.03086
> volume #5 level 0.01939
> hide #!5 models
> show #!4 models
> show #!3 models
> volume #3 step 1
> volume #4 step 1
> volume #3 level 0.02277
> volume #3 level 0.03256
> volume #4 level 0.04578
> open /Users/petra/Downloads/cryosparc_P14_J268_011_volume_map_half_A.mrc
Opened cryosparc_P14_J268_011_volume_map_half_A.mrc as #7, grid size
420,420,420, pixel 0.65, shown at level 0.00634, step 2, values float32
> volume #7 step 1
> volume #7 level 0.03547
> hide #!4 models
> volume #7 level 0.05705
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> volume #7 level 0.02792
> hide #!7 models
> hide #!4 models
> show #!4 models
> show #!7 models
> surface dust #4 size 6.5
> surface dust #7 size 6.5
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> volume #7 level 0.06245
> hide #!4 models
> open /Users/petra/Downloads/Get3_Trial3.mrc
Opened Get3_Trial3.mrc as #8, grid size 460,460,460, pixel 0.65, shown at
level 0.000546, step 2, values float32
> hide #!7 models
> open /Users/petra/Downloads/Get3_Trial4.mrc
Opened Get3_Trial4.mrc as #9, grid size 460,460,460, pixel 0.65, shown at
level 5.93e-06, step 2, values float32
> hide #!8 models
> volume #8 level 0.002521
> volume #9 level 0.0005733
> hide #!8 models
> volume #9 level 7.264e-17
> volume #9 level 0.0003822
> volume #8 level 0.0003747
> show #!8 models
> show #!9 models
> close #8-9
> show #!7 models
> show #!6 models
> hide #!6 models
> volume #7 level 0.01281
> volume #7 level 0.02037
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> surface dust #7 size 6.5
> volume #7 level 0.03871
> open /Users/petra/Downloads/cryosparc_P705_J172_004_volume_map.mrc
Opened cryosparc_P705_J172_004_volume_map.mrc as #8, grid size 380,380,380,
pixel 0.832, shown at level 0.00438, step 2, values float32
> lighting soft
> hide #!7 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #8 step 1
> volume #8 level 0.002419
> volume #8 level 0.002811
> volume #8 level 0.003596
> volume #8 level 0.005165
> volume #8 level 0.02831
> volume #8 level 0.03616
> open /Users/petra/Downloads/cryosparc_P705_J176_004_volume_map.mrc
Opened cryosparc_P705_J176_004_volume_map.mrc as #9, grid size 380,380,380,
pixel 0.832, shown at level 0.00448, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #9 step 1
> volume #9 level 0.01986
> volume #9 level 0.0308
> volume #9 level 0.03565
> volume #8 level 0.0357
> open /Users/petra/Downloads/cryosparc_P705_J173_004_volume_map_sharp.mrc
Opened cryosparc_P705_J173_004_volume_map_sharp.mrc as #10, grid size
380,380,380, pixel 0.832, shown at level 0.00842, step 2, values float32
> hide #!8 models
> hide #!9 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #10 step 1
> volume #10 level 0.1111
> open /Users/petra/Downloads/cryosparc_P705_J177_003_volume_map.mrc
Opened cryosparc_P705_J177_003_volume_map.mrc as #11, grid size 380,380,380,
pixel 0.832, shown at level 0.00591, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #11 step 1
> volume #11 level 0.04212
> hide #!10 models
> hide #!11 models
> open /Users/petra/Downloads/cryosparc_P14_J302_012_volume_map(1).mrc
Opened cryosparc_P14_J302_012_volume_map(1).mrc as #12, grid size 460,460,460,
pixel 0.65, shown at level 0.00801, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #12 step 1
> volume #12 level 0.04119
> surface dust #12 size 6.5
> hide #!12 models
> show #!11 models
> show #!10 models
> show #!9 models
> hide #!10 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!12 models
> volume gaussian #12 sDev 2
Opened cryosparc_P14_J302_012_volume_map(1).mrc gaussian as #13, grid size
460,460,460, pixel 0.65, shown at step 1, values float32
> ui tool show "Segment Map"
Segmenting cryosparc_P14_J302_012_volume_map(1).mrc gaussian, density
threshold 0.012095
Showing 68 region surfaces
192 watershed regions, grouped to 68 regions
Showing cryosparc_P14_J302_012_volume_map(1) gaussian.seg - 68 regions, 68
surfaces
> ui mousemode right select
> select add #14.35
1 model selected
> select #14.38
1 model selected
> select add #14.35
2 models selected
> select add #14.16
3 models selected
> select add #14.39
4 models selected
> select add #14.10
5 models selected
> select add #14.21
6 models selected
> select add #14.11
7 models selected
> select add #14.58
8 models selected
> select add #14.23
9 models selected
> select add #14.5
10 models selected
> select add #14.42
11 models selected
> select add #14.19
12 models selected
> select add #14.17
13 models selected
> select add #14.57
14 models selected
> select add #14.51
15 models selected
Drag select of 244, 45905 of 55124 triangles, 275, 30010 of 45456 triangles,
256, 8494 of 21972 triangles, 253, 9386 of 24044 triangles, 13, 395 of 15052
triangles, 13 cryosparc_P14_J302_012_volume_map(1).mrc gaussian
> select add #14.6
23 models selected
> select add #14.47
24 models selected
> select add #14.48
25 models selected
> hide #!13 models
> select add #14.68
26 models selected
Drag select of 263, 227, 241, 222, 282, 270, 283, 272, 285, 239, 284, 243,
274, 259, 279, 237, 266, 281, 109, 286, 255, 232, 260, 268, 251, 208, 212,
122, 242, 224, 125, 44, 39, 29, 195, 48, 72, 84, 62, 91, 233, 133, 53, 127
Grouped 44 regions
Saving 1 regions to mrc file...
Opened P14J302_2Arms.mrc as #15, grid size 115,140,94, pixel 0.65, shown at
step 1, values float32
Wrote P14J302_2Arms.mrc
> select add #14
26 models selected
> select subtract #14
Nothing selected
> hide #!14 models
> hide #!15 models
> show #!15 models
> volume #15 level 0.04366
> volume #15 level 0.03692
> volume #15 level 0.01422
> hide #!15 models
> show #!15 models
> show #!14 models
> hide #!15 models
> show #!15 models
> hide #!14 models
> show #!13 models
> hide #!15 models
> show #!12 models
> hide #!13 models
> show #!15 models
> volume resample #12 onGrid #1
Opened cryosparc_P14_J302_012_volume_map(1).mrc resampled as #16, grid size
380,380,380, pixel 0.832, shown at step 1, values float32
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!1 models
> hide #!1 models
> close #16
> close #15
> close #14
> show #!13 models
> close #13
> show #!12 models
> close #12
> open /Users/petra/Downloads/cryosparc_P14_J302_012_volume_map(1).mrc
Opened cryosparc_P14_J302_012_volume_map(1).mrc as #12, grid size 460,460,460,
pixel 0.65, shown at level 0.00801, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #12 step 1
> volume #12 level 0.0377
> surface dust #12 size 6.5
> volume #12 level 0.03857
> volume gaussian #12 sDev 2
Opened cryosparc_P14_J302_012_volume_map(1).mrc gaussian as #13, grid size
460,460,460, pixel 0.65, shown at step 1, values float32
Segmenting cryosparc_P14_J302_012_volume_map(1).mrc gaussian, density
threshold 0.012095
Showing 68 region surfaces
192 watershed regions, grouped to 68 regions
Showing cryosparc_P14_J302_012_volume_map(1) gaussian.seg - 68 regions, 68
surfaces
Drag select of 236, 282, 38427 of 45456 triangles, 276, 12157 of 31624
triangles, 254, 18266 of 21972 triangles, 269, 22702 of 24044 triangles, 19,
7903 of 14820 triangles, 284, 5845 of 17696 triangles, 13, 14138 of 15052
triangles, 23, 2621 of 8604 triangles, 13
cryosparc_P14_J302_012_volume_map(1).mrc gaussian
Drag select of 277, 17333 of 32448 triangles, 268, 29055 of 33624 triangles,
274, 260, 20055 of 26816 triangles, 286, 9901 of 22800 triangles, 283, 18099
of 23800 triangles, 256, 13632 of 24184 triangles, 166, 21503 of 22712
triangles, 187, 13652 of 21896 triangles, 192, 6876 of 17260 triangles, 217,
21390 of 21412 triangles, 167, 19089 of 19148 triangles, 171, 174, 244, 13
cryosparc_P14_J302_012_volume_map(1).mrc gaussian
Drag select of 236, 282, 42451 of 45456 triangles, 276, 19964 of 31624
triangles, 242, 99 of 38584 triangles, 281, 269 of 35528 triangles, 229, 2695
of 23776 triangles, 285, 1173 of 23140 triangles, 254, 269, 23568 of 24044
triangles, 19, 10574 of 14820 triangles, 284, 8127 of 17696 triangles, 13, 23,
4232 of 8604 triangles, 13 cryosparc_P14_J302_012_volume_map(1).mrc gaussian
> select subtract #14.9
27 models selected
> select subtract #14.7
26 models selected
> select subtract #14.18
25 models selected
> select subtract #14.20
24 models selected
> select add #14.9
25 models selected
> hide #!13 models
> select clear
Drag select of 277, 10070 of 32448 triangles, 268, 274, 34544 of 34712
triangles, 260, 286, 1563 of 22800 triangles, 283, 9678 of 23800 triangles,
256, 166, 16584 of 22712 triangles, 187, 192, 217, 167, 15721 of 19148
triangles, 171, 174, 244, 11056 of 11104 triangles
Drag select of 236, 26944 of 55124 triangles, 282, 25066 of 45456 triangles,
276, 12131 of 31624 triangles, 254, 17546 of 21972 triangles, 269, 19459 of
24044 triangles, 19, 4211 of 14820 triangles, 284, 947 of 17696 triangles, 13,
11191 of 15052 triangles, 23, 312 of 8604 triangles
> select clear
> select #14.9
1 model selected
> select add #14.7
2 models selected
Ungrouped to 4 regions
Ungrouped to 5 regions
Ungrouped to 3 regions
> select #14.69
1 model selected
> select #14.69
1 model selected
> select #14.73
1 model selected
> select #14.69
1 model selected
Ungrouped to 0 regions
> select #14.69
1 model selected
Ungrouped to 0 regions
> select #14.69
1 model selected
Ungrouped to 0 regions
Drag select of 236, 23944 of 55124 triangles, 282, 38095 of 45456 triangles,
276, 13307 of 31624 triangles, 254, 20335 of 21972 triangles, 269, 245, 240 of
16600 triangles, 19, 6214 of 14820 triangles, 284, 11734 of 17696 triangles,
13, 13832 of 15052 triangles, 44, 95 of 15608 triangles, 29, 2796 of 14852
triangles, 23, 6360 of 8604 triangles, 33, 42 of 37280 triangles, 32, 3064 of
8368 triangles, 30, 4421 of 17420 triangles
> select clear
Drag select of 236, 48979 of 55124 triangles, 282, 37955 of 45456 triangles,
276, 8364 of 31624 triangles, 254, 14624 of 21972 triangles, 269, 22951 of
24044 triangles, 19, 6720 of 14820 triangles, 284, 6098 of 17696 triangles,
13, 13395 of 15052 triangles, 23, 2604 of 8604 triangles
Grouped 9 regions
> select add #14
68 models selected
> select subtract #14
Nothing selected
> select #14.1
1 model selected
Drag select of 258, 216, 237, 271, 280, 275, 279, 229, 285, 238, 272, 264,
273, 240, 257, 278, 109, 270, 262, 223, 263, 255, 247, 211, 209, 122, 245,
224, 125, 44, 39, 29, 194, 48, 72, 84, 62, 91, 231, 133, 53, 127, 33, 73, 54,
46, 45, 81, 31, 32, 30
Grouped 51 regions
Drag select of 288, 18457 of 230196 triangles
> select #14.23
1 model selected
Drag select of 277, 13144 of 32448 triangles, 268, 274, 34708 of 34712
triangles, 260, 286, 2173 of 22800 triangles, 283, 9615 of 23800 triangles,
256, 166, 18456 of 22712 triangles, 187, 192, 217, 167, 15473 of 19148
triangles, 171, 174, 244
Grouped 15 regions
> select #14.1
1 model selected
> select #14.3
1 model selected
Drag select of 287, 2577 of 116852 triangles
Drag select of 289, 28993 of 124424 triangles
> select #14.2
1 model selected
Saving 1 regions to mrc file...
Opened P14J302_2Arms.mrc as #15, grid size 115,140,94, pixel 0.65, shown at
step 1, values float32
Wrote P14J302_2Arms.mrc
> select add #14
4 models selected
> select subtract #14
Nothing selected
> hide #!14 models
> show #!14 models
> volume #15 level 0.01351
> hide #!14 models
> volume #15 level 0.01368
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> show #!12 models
> show #!13 models
> show #!14 models
> hide #!14 models
> hide #!13 models
> volume #15 color #cccc9987
> volume resample #15 onGrid #12
Opened P14J302_2Arms.mrc resampled as #16, grid size 460,460,460, pixel 0.65,
shown at step 1, values float32
> volume #16 color #b2b2b289
> volume #16 level 0.06371
> volume #16 level 0.01635
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/petra/Desktop/Mask/20241106_Mask/P14J302_G3_2Arms.mrc models #16
> hide #!16 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #12 style image colorMode opaque8 showOutlineBox true orthoplanes xyz
> positionPlanes 229,229,229 imageMode orthoplanes
> volume #12 orthoplanes xyz positionPlanes 229,257,229
> volume #12 style surface
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!12 models
> show #!11 models
> show #!10 models
> volume #11 level 0.006924
> hide #!11 models
> hide #!10 models
> show #!9 models
> volume #9 region 0,0,0,379,379,379
> ui mousemode right translate
> volume #9 level 0.02432
> volume #9 level 0.0393
> hide #!9 models
> show #!1 models
> hide #!1 models
> show #!7 models
> show #!6 models
> hide #!6 models
> volume #7 level 0.01821
> volume #7 level 0.029
> volume #7 level 0.04302
> show #!9 models
> hide #!7 models
> open /Users/petra/Downloads/Get3_Trial4.mrc
Opened Get3_Trial4.mrc as #17, grid size 460,460,460, pixel 0.65, shown at
level 5.93e-06, step 2, values float32
> open /Users/petra/Downloads/Get3_Trial3.mrc
Opened Get3_Trial3.mrc as #18, grid size 460,460,460, pixel 0.65, shown at
level 0.000546, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close #17-18
> show #!16 models
> show #!15 models
> show #!14 models
> show #!13 models
> show #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!12 models
> hide #!16 models
> show #!7 models
> volume #7 level 0.02144
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!16 models
> hide #!16 models
> show #!12 models
> show #!13 models
> hide #!13 models
> show #!11 models
> hide #!12 models
> hide #!11 models
> show #!10 models
> show #!9 models
> hide #!10 models
> volume #9 level 0.02351
> show #!7 models
> hide #!9 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> volume #7 level 0.05921
> volume #7 level 0.03655
> hide #!7 models
> show #!6 models
> ui tool show "Side View"
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!7 models
> open /Users/petra/Downloads/cryosparc_P705_J187_004_volume_map.mrc
Opened cryosparc_P705_J187_004_volume_map.mrc as #17, grid size 380,380,380,
pixel 0.832, shown at level 0.00447, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Side View"
> volume #17 level 0.01133
> volume #17 step 1
> ui mousemode right zoom
> view clip false
> hide #!7 models
> volume #17 level 0.03172
> volume #17 level 0.05525
> surface dust #17 size 8.32
> volume #17 level 0.01878
> volume #17 level 0.03212
> volume #17 level 0.06701
> ui mousemode right translate
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> volume flip #17 axis y
Opened cryosparc_P705_J187_004_volume_map.mrc y flip as #18, grid size
380,380,380, pixel 0.832, shown at step 1, values float32
> open /Users/petra/Desktop/GiGet345_Phenix/GiGet3_D53N_ATP_Dimer.pdb format
> pdb
Chain information for GiGet3_D53N_ATP_Dimer.pdb #19
---
Chain | Description
A E | No description available
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #19
5512 atoms, 5260 bonds, 2 pseudobonds, 1010 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #19,1,0,0,119.7,0,1,0,73.174,0,0,1,-36.036
> ui mousemode right "rotate selected models"
> view matrix models
> #19,-0.093746,-0.73596,0.67051,138.1,0.92377,0.18687,0.33427,38.109,-0.3713,0.65073,0.66234,-17.534
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #19,-0.093746,-0.73596,0.67051,193.04,0.92377,0.18687,0.33427,116.21,-0.3713,0.65073,0.66234,142.82
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #19,-0.093746,-0.73596,0.67051,145.51,0.92377,0.18687,0.33427,110.52,-0.3713,0.65073,0.66234,142.39
> view matrix models
> #19,-0.093746,-0.73596,0.67051,148.02,0.92377,0.18687,0.33427,120.71,-0.3713,0.65073,0.66234,165.36
> view matrix models
> #19,-0.093746,-0.73596,0.67051,146.45,0.92377,0.18687,0.33427,118.49,-0.3713,0.65073,0.66234,166.12
> open
> /Users/petra/Desktop/GiGet345_Krios_Phenix/Phenix_Ref/RealSpaceRefine_4/Get345_Krios_real_space_refined_004.pdb
Chain information for Get345_Krios_real_space_refined_004.pdb #20
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> select add #20
13773 atoms, 13695 bonds, 8 pseudobonds, 2054 residues, 5 models selected
> select subtract #19
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 8196 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide #!19 models
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.99533,-0.09429,0.020735,13.988,-0.076154,-0.89881,-0.43167,420.56,0.059339,0.42808,-0.90179,232.09
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.99533,-0.09429,0.020735,6.617,-0.076154,-0.89881,-0.43167,397.37,0.059339,0.42808,-0.90179,238.88
> view matrix models
> #20,0.99533,-0.09429,0.020735,-1.2303,-0.076154,-0.89881,-0.43167,396.21,0.059339,0.42808,-0.90179,236.67
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.98152,0.18991,0.023442,-49.412,0.18817,-0.93566,-0.29855,334.16,-0.034763,0.29744,-0.95411,284.94
> view matrix models
> #20,0.9803,0.19004,-0.053754,-36.313,0.16601,-0.94034,-0.297,338.61,-0.10699,0.28223,-0.95336,300.15
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.9803,0.19004,-0.053754,-37.537,0.16601,-0.94034,-0.297,343.14,-0.10699,0.28223,-0.95336,307.02
> select #20/C,D
3049 atoms, 3112 bonds, 392 residues, 1 model selected
> select #20/C,D,E
3394 atoms, 3463 bonds, 435 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> view matrix models
> #20,0.9803,0.19004,-0.053754,-42.3,0.16601,-0.94034,-0.297,368.16,-0.10699,0.28223,-0.95336,297.16
> undo
> fitmap #20 inMap #18
Fit molecule Get345_Krios_real_space_refined_004.pdb (#20) to map
cryosparc_P705_J187_004_volume_map.mrc y flip (#18) using 8261 atoms
average map value = 0.04984, steps = 76
shifted from previous position = 0.666
rotated from previous position = 5.59 degrees
atoms outside contour = 5832, contour level = 0.067015
Position of Get345_Krios_real_space_refined_004.pdb (#20) relative to
cryosparc_P705_J187_004_volume_map.mrc y flip (#18) coordinates:
Matrix rotation and translation
0.99247097 0.12206031 0.01013208 -38.69186996
0.12021141 -0.95490027 -0.27150449 349.95193205
-0.02346480 0.27067832 -0.96238384 296.27463928
Axis 0.99807984 0.06184697 -0.00340357
Axis point 0.00000000 155.63615018 172.41314331
Rotation angle (degrees) 164.23973096
Shift along axis -17.98249842
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> select add #20
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #20
Nothing selected
> volume #18 level 0.07054
> ui tool show "Side View"
> volume #18 color #b2b2ff82
> show #!19 models
> select add #19
5512 atoms, 5260 bonds, 2 pseudobonds, 1010 residues, 2 models selected
> fitmap #19 inMap #18
Fit molecule GiGet3_D53N_ATP_Dimer.pdb (#19) to map
cryosparc_P705_J187_004_volume_map.mrc y flip (#18) using 5512 atoms
average map value = 0.05345, steps = 124
shifted from previous position = 2.13
rotated from previous position = 12.2 degrees
atoms outside contour = 3668, contour level = 0.070544
Position of GiGet3_D53N_ATP_Dimer.pdb (#19) relative to
cryosparc_P705_J187_004_volume_map.mrc y flip (#18) coordinates:
Matrix rotation and translation
-0.11633137 -0.76255255 0.63638086 148.13777612
0.97734118 0.02619118 0.21004338 120.51499020
-0.17683668 0.64639586 0.74222716 157.08900189
Axis 0.22155421 0.41290419 0.88341602
Axis point 40.54724582 70.59332516 0.00000000
Rotation angle (degrees) 100.01793941
Shift along axis 221.35663255
> select subtract #19
Nothing selected
> hide #!19 models
> show #!19 models
> hide #!20 models
> color #19 #2b652bff
> color #19 #106519ff
> color #19 #096521ff
> color #19 #0b7827ff
> color #19 #14d546ff
> color #19 #12c340ff
> color #19 #12bc3eff
> color #19 #12be3eff
> show #!20 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> show #!19 models
> show #!20 models
> hide #!19 models
> hide #!20 models
> show #!20 models
> show #!19 models
> show #!18 models
> hide #!18 models
> ui tool show Matchmaker
> ui mousemode right select
> select add #20/B:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #19/A:182
17 atoms, 15 bonds, 2 residues, 2 models selected
> select up
282 atoms, 284 bonds, 34 residues, 2 models selected
> select up
3543 atoms, 3613 bonds, 443 residues, 2 models selected
> matchmaker #!20 to #19
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 GiGet3_D53N_ATP_Dimer.pdb, chain A (#19) with
Get345_Krios_real_space_refined_004.pdb, chain A (#20), sequence alignment
score = 1441.9
RMSD between 268 pruned atom pairs is 0.769 angstroms; (across all 303 pairs:
2.366)
> select add #19
7209 atoms, 6991 bonds, 2 pseudobonds, 1221 residues, 3 models selected
> select add #20
13773 atoms, 13695 bonds, 8 pseudobonds, 2054 residues, 5 models selected
> select subtract #19
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #20
Nothing selected
> show #!18 models
> select add #19
5512 atoms, 5260 bonds, 2 pseudobonds, 1010 residues, 2 models selected
> select add #20
13773 atoms, 13695 bonds, 8 pseudobonds, 2054 residues, 5 models selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.
> select subtract #19
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #20
Nothing selected
> ui mousemode right translate
> color #19 #6dc237ff
> color #19 #a0c23aff
> color #19 #b3c25aff
> color #19 #58aec2ff
> color #19 #4485c2ff
> color #19 #c08645ff
> hide #!20 models
> show #!20 models
> color #20 #f1f2d1ff
> color #20 #ff6800ff
> color #20 #f1f2d1ff
> color #20 #c3d8bdff
> color #20 #4e6fafff
> color #18 #47686dff models
> color #18 #47686d95 models
> color #18 #b1edf995 models
> color #18 #f0b659ff models
> color #18 #ed5452ff models
> color #18 #ed54528e models
> color #18 #ff8340ff models
> color #18 #fe6d7fff models
> color #18 #fe6d7f80 models
> color #19 #4e6fafff
> color #19 #b2a788ff
> color #18 #f089e880 models
> color #18 #c82df080 models
> color #18 #f023eb80 models
> color #18 #f039c580 models
> color #18 #f05e8c80 models
> color #18 #f0c26780 models
> color #18 #aaf06580 models
> color #18 silver models
> color #18 #929292ff models
> color #18 #797979ff models
> color #18 #797979a1 models
> color #18 #79797972 models
> color #18 #79797980 models
> color #18 #7979799e models
> color #18 #7979795c models
> color #18 #7979797d models
> color #18 #919191ff models
> color #18 #5e5e5eff models
> color #18 #424242ff models
> color #18 silver models
> color #18 #ebebebff models
> color #18 #ebebeb8b models
> color #18 darkgrey models
> color #18 #a9a9a99c models
> color #18 #a9a9a981 models
> color #19 #50c7a2ff
> color #19 #30c7a2ff
> color #19 #1fc7a2ff
> color #19 #16c7a2ff
> color #19 #167ca2ff
> color #19 #16fea2ff
> color #19 #16fed7ff
> color #19 #16feddff
> color #19 #16fe93ff
> color #19 #16fe96ff
> color #19 #12cf7aff
> color #20 #329cfdff
> color #20 #5a9cfdff
> color #20 #089cfdff
> color #20 #0a9cfdff
> color #20 #0a6bfdff
> color #20 #0aaefdff
> color #20 #0a86fdff
> color #20 #0a76fdff
> color #20 #0a7efdff
> color #20 #0a7ed0ff
> color #20 #0a7ef9ff
> color #20 #0a7eebff
> color #18 #919191ff models
> color #18 darkgrey models
> color #18 #797979ff models
> color #18 #7979798a models
> color #18 #d6d6d6ff models
> color #18 #d6d6d690 models
> color #18 #d6d6d680 models
> color #18 #919191ff models
> color #18 black models
> color #18 #424242ff models
> color #18 #5e5e5eff models
> color #18 #797979ff models
> color #18 #4f8f00ff models
> color #18 #929000ff models
> color #18 #92900087 models
> color #18 #011993ff models
> color #18 #005493ff models
> color #18 darkgrey models
> color #18 #a9a9a9a6 models
> color #18 #a9a9a987 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> close #17
> show #!16 models
> hide #!16 models
> close #16
> show #!15 models
> hide #!15 models
> close #15
> show #!14 models
> hide #!14 models
> close #14
> show #!13 models
> close #13
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> close #11
> show #!10 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> volume #10 level 0.08731
> volume #10 level 0.04563
> close #10
> show #!9 models
> ui tool show "Side View"
> ui mousemode right zoom
> volume #9 level 0.02715
> ui mousemode right translate
> volume #9 level 0.04254
> show #!12 models
> hide #!9 models
> hide #!12 models
> show #!18 models
> surface dust #18 size 8.32
> volume #18 level 0.05133
> volume #18 color #a9a9a9fb
> volume #18 color #a9a9a985
> volume #18 color silver
> save /Users/petra/Desktop/3.1.png width 768 height 670 supersample 4
> transparentBackground true
> show #!19 models
> show #!20 models
> hide #!20 models
> hide #!19 models
> hide #!18 models
> show #!18 models
> volume #18 color #c0c0c09a
> show #!19 models
> show #!20 models
> hide #!20 models
> hide #!19 models
> color #18 #c0c0c087 models
> color #18 silver models
> color #18 #d6d6d6ff models
> color #18 #ebebebff models
> color #18 #d6d6d6ff models
> color #18 silver models
> color #18 #c0c0c0a2 models
> color #18 #c0c0c087 models
> color #18 #c0c0c0fd models
> color #18 silver models
> lighting soft
> color #18 #d6d6d6ff models
> lighting full
> color #18 #d6d6d6a0 models
> show #!19 models
> show #!20 models
> hide #!20 models
> hide #!19 models
> lighting soft
> lighting simple
> show #!19 models
> show #!20 models
> hide #!20 models
> hide #!19 models
> show #!19 models
> show #!20 models
> hide #!20 models
> hide #!19 models
> open /Users/petra/Downloads/cryosparc_P14_J312_004_volume_map.mrc
Opened cryosparc_P14_J312_004_volume_map.mrc as #10, grid size 460,460,460,
pixel 0.65, shown at level 0.00923, step 2, values float32
> hide #!18 models
> surface dust #10 size 6.5
> volume #10 step 1
> volume #10 level 0.04631
> volume #10 level 0.06485
> show #!12 models
> hide #!10 models
> ui tool show "Side View"
> hide #!12 models
> show #!12 models
> close #12
> show #!10 models
> show #!18 models
> hide #!18 models
> ui mousemode right zoom
> open /Users/petra/Desktop/GiGet345_Phenix/GiGet3_D53N_ATP_Dimer.pdb format
> pdb
Chain information for GiGet3_D53N_ATP_Dimer.pdb #11
---
Chain | Description
A E | No description available
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #11
5512 atoms, 5260 bonds, 2 pseudobonds, 1010 residues, 2 models selected
> select subtract #11
Nothing selected
> select add #11
5512 atoms, 5260 bonds, 2 pseudobonds, 1010 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,86.718,0,1,0,170.59,0,0,1,50.84
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.027362,-0.63384,0.77298,99.25,0.99928,-0.0028565,-0.037715,141.32,0.026113,0.77346,0.63331,58.003
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.027362,-0.63384,0.77298,96.513,0.99928,-0.0028565,-0.037715,121.3,0.026113,0.77346,0.63331,123.77
> view matrix models
> #11,0.027362,-0.63384,0.77298,131.1,0.99928,-0.0028565,-0.037715,119.45,0.026113,0.77346,0.63331,121.44
> view matrix models
> #11,0.027362,-0.63384,0.77298,134.86,0.99928,-0.0028565,-0.037715,119.5,0.026113,0.77346,0.63331,130.34
> view matrix models
> #11,0.027362,-0.63384,0.77298,132.35,0.99928,-0.0028565,-0.037715,120.14,0.026113,0.77346,0.63331,130.71
> ui mousemode right translate
> select subtract #11
Nothing selected
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> hide #!11 models
> show #!11 models
> color #10 darkgrey models
> color #10 #a9a9a98f models
> color #10 darkgrey models
> color #10 white models
> color #10 #00fdffff models
> color #10 #0433ffff models
> color #10 #0433ff8b models
> color #10 white models
> color #10 #ffffff88 models
> color #10 #fffffffd models
> color #11 #ff2600ff
> color #10 #929292ff models
> color #10 #9292928a models
> hide #!11 models
> color #10 #d6d6d6ff models
> color #10 #d6d6d68f models
> show #!11 models
> show #!7 models
> hide #!7 models
> show #!8 models
> close #8
> show #!9 models
> hide #!9 models
> show #!9 models
> close #9
> show #!7 models
> hide #!10 models
> hide #!11 models
> color #7 #ff9300ff models
> color #7 #00fa92ff models
> color #7 #0433ffff models
> lighting soft
> color #7 #531b93ff models
> color #7 darkgrey models
> hide #!7 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!6 models
> close #6
> show #!5 models
> hide #!7 models
> show #!4 models
> hide #!5 models
> close #4
> show #!3 models
> close #3
> show #!2 models
> volume #2 level 0.02571
> close #2
> show #!1 models
> volume #1 level 0.04968
> save /Users/petra/Desktop/11062024.cxs includeMaps true
> ui mousemode right translate
> hide #!1 models
> show #!5 models
> volume #5 color #008f00
> volume #5 color #011993
> volume #5 color #d6d6d6
> volume #5 level 0.03168
> save /Users/petra/Desktop/onearmG3.tif width 768 height 670 supersample 4
> transparentBackground true
> show #!7 models
> hide #!5 models
> save /Users/petra/Desktop/twoArmsG345.tif width 970 height 670 supersample 4
> transparentBackground true
> show #!5 models
> hide #!5 models
> hide #!7 models
> show #!5 models
> color #7 #30b3bf80 models
> color #7 #4e6fafff models
> show #!7 models
> hide #!5 models
> show #!5 models
> hide #!7 models
> hide #!5 models
> show #!7 models
> show #!10 models
> hide #!10 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!5 models
> show #!7 models
> hide #!5 models
> show #!10 models
> hide #!10 models
> hide #!7 models
> show #!10 models
> show #!11 models
> hide #!11 models
> hide #!10 models
> show #!1 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> graphics silhouettes true width 1
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 INTEL-23.0.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
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: MacBookPro16,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.11072.0.0,0)
OS Loader Version: 582~2132
Software:
System Software Overview:
System Version: macOS 15.1 (24B83)
Kernel Version: Darwin 24.1.0
Time since boot: 2 days, 17 hours, 58 minutes
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Mirror: On
Mirror Status: Hardware Mirror
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
BREAKROOM355:
Resolution: 2880 x 1620
UI Looks like: 2880 x 1620 @ 60.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Connection Type: AirPlay
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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
