![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17633 closed defect (duplicate)
Crash moving window between screens
| 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-14.7.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001f07ccf40 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.segment._segment, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, cython.cimports.libc.math, 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._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._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.dssp._dssp, chimerax.mlp._mlp, chimerax.atom_search.ast (total: 122)
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{
"uptime" : 210000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 22464,
"osVersion" : {
"train" : "macOS 14.7.1",
"build" : "23H222",
"releaseType" : "User"
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"captureTime" : "2025-05-12 16:30:09.7909 +0200",
"codeSigningMonitor" : 1,
"incident" : "EA00DD76-F46A-487B-9830-503575663408",
"pid" : 1819,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-12 12:18:08.6985 +0200",
"procStartAbsTime" : 4839990464001,
"procExitAbsTime" : 5202895855379,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"53E5AB7B-442B-5886-989B-1398878D1692","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "AD01A641-B3E6-5B13-BD34-E8A0F9C6DCF5",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 20926,
"sleepWakeUUID" : "AF5185F5-020F-4BFF-AA9A-EFBE17540DEC",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4342365847\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102d34000-102d38000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":1819},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4342365847\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102d34000-102d38000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.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
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/jawh0004/Desktop/SLU/Manuscripts/C3_TiO2/Images/Manuscript_working.cxs
> format session
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened C3_seg_fullres.mrc as #3, grid size 173,177,200, pixel
0.648,0.648,0.648, shown at level 0.0312, step 1, values float32
opened ChimeraX session
Showing C3_CP_flexregion_VOP.seg - 4 regions, 3 surfaces
> hide #!2 models
> show #!2 models
> hide #2.1 models
> show #2.1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #2.3 models
> hide #2.2 models
> hide #2.1 models
> hide #!2 models
Segmenting C3_seg_fullres.mrc, density threshold 0.031178
Showing 93 region surfaces
1194 watershed regions, grouped to 93 regions
Showing C3_seg_fullres.seg - 93 regions, 93 surfaces
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #1.8
1 model selected
> color #1.8 orange
No visible atoms or bonds selected
> ui tool show "Color Zone"
No atoms chosen for color zoning
> hide #!3 models
> color #1.8 yellow
> select clear
> select #1.8
1 model selected
No visible atoms or bonds selected
> color #1.8 purple
> color sel red
> color sel violet
> color sel beige
> color sel 255,233,332
> color sel 255,233,10
> color sel 255,23,10
> color sel 255,13,10
> color sel 255,100,10
> color sel 255,100,50
> color sel 25,100,50
> color sel 200,100,50
> color sel 100,100,50
> color sel 100,300,50
> color sel 100,200,50
> color sel 100,200,0
> color sel 100,200,100
> color sel 100,200,70
> color sel 100,20,70
> color sel 100,30,70
> color sel 10,30,70
> color sel 10,30,100
> color sel 10,30,200
> color sel 10,30,120
> color sel 10,30,10
> ui tool show "Color Actions"
> color sel blue target s
> color sel light sea green target s
> color sel magenta target s
> color sel light gray target s
> color sel gray target s
> color sel light gray target s
Drag select of 1771, 11387 of 53416 triangles, 1764, 9191 of 26468 triangles,
1775, 9756 of 27996 triangles, 1779, 27571 of 28024 triangles, 1773, 23211 of
29672 triangles, 1792, 190 of 23100 triangles, 1794, 17084 of 17244 triangles,
1783, 1190 of 19976 triangles, 1785, 3002 of 21812 triangles, 1795, 13734 of
19400 triangles, 1753, 7695 of 17808 triangles, 1770, 1776, 10772 of 20780
triangles, 1768, 4775 of 13152 triangles, 1727, 1788, 6613 of 12068 triangles,
1787, 7877 of 12456 triangles, 1742, 1648, 3846 of 10040 triangles, 1677, 9972
of 11084 triangles, 1729, 3798 of 10700 triangles, 1751, 4509 of 8792
triangles
> select #1.14
1 model selected
> select add #1.1
2 models selected
> select add #1.52
3 models selected
> select add #1.30
4 models selected
> ui tool show "Segment Map"
Grouped 4 regions
> color sel 10,30,10
> select add #1.70
2 models selected
> select subtract #1.70
1 model selected
> select subtract #1.1
Nothing selected
> select add #1.1
1 model selected
Ungrouped to 4 regions
> select #1.52
1 model selected
> select add #1.54
2 models selected
> select add #1.25
3 models selected
Grouped 3 regions
> color sel 10,30,60
> select add #1.30
2 models selected
Grouped 2 regions
> color sel 10,30,60
> select #1.33
1 model selected
> select add #1.70
2 models selected
> select add #1.16
3 models selected
> select add #1.28
4 models selected
> select add #1.94
5 models selected
> select add #1.32
6 models selected
> select add #1.14
7 models selected
> select add #1.41
8 models selected
> select add #1.68
9 models selected
> select add #1.21
10 models selected
> select add #1.36
11 models selected
> select add #1.18
12 models selected
> select subtract #1.21
11 models selected
> select add #1.21
12 models selected
> select add #1.69
13 models selected
> select add #1.45
14 models selected
> select add #1.71
15 models selected
> select add #1.84
16 models selected
> select add #1.74
17 models selected
> select add #1.63
18 models selected
Grouped 18 regions
> select add #1.67
2 models selected
Grouped 2 regions
> color sel 10,30,20
> color sel 20,30,20
> color sel 5,30,20
> color sel 5,90,20
> color sel 5,80,20
> color sel 5,60,20
> color sel 5,30,20
> color sel 5,40,20
> select clear
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
> close #2
Drag select of 1665, 1778, 1774, 1681, 1790, 1445, 1219, 1786, 17711 of 18200
triangles, 1789, 5385 of 17656 triangles, 1755, 16288 of 18440 triangles,
1781, 2255 of 14200 triangles, 1717, 1633, 1478, 14216 of 15280 triangles,
1730, 3445 of 11544 triangles, 1664, 10204 of 11892 triangles, 1595, 6535 of
10488 triangles, 1634, 7620 of 9724 triangles, 1706, 7727 of 9312 triangles,
1800, 8971 of 9856 triangles, 1628, 8513 of 9192 triangles, 1489, 1799, 264 of
9260 triangles, 1005, 1660, 3383 of 8160 triangles, 1801, 5407 of 6328
triangles, 1747
> select subtract #1.43
26 models selected
Grouped 26 regions
Drag select of 1762, 34288 of 35804 triangles, 1763, 25996 of 31096 triangles,
1765, 19198 of 34204 triangles, 1761, 12516 of 30876 triangles, 1759, 284 of
29364 triangles, 1772, 8152 of 21396 triangles, 1777, 10396 of 16584
triangles, 1701, 14344 of 14804 triangles, 1789, 10402 of 17656 triangles,
1671, 8570 of 15096 triangles, 1583, 9975 of 12772 triangles, 1561, 7781 of
10280 triangles, 1798, 8335 of 10032 triangles, 1724, 7507 of 10072 triangles,
1641, 519 of 9160 triangles, 1202, 6526 of 8616 triangles, 1743, 4579 of 9204
triangles, 1791, 1459, 3261 of 6352 triangles, 1807, 3422 of 241392 triangles
Drag select of 1762, 32457 of 35804 triangles, 1763, 23739 of 31096 triangles,
1765, 16811 of 34204 triangles, 1761, 11418 of 30876 triangles, 1759, 33 of
29364 triangles, 1772, 7397 of 21396 triangles, 1777, 9460 of 16584 triangles,
1701, 13855 of 14804 triangles, 1789, 9056 of 17656 triangles, 1671, 7324 of
15096 triangles, 1583, 9279 of 12772 triangles, 1561, 7110 of 10280 triangles,
1798, 8262 of 10032 triangles, 1724, 6696 of 10072 triangles, 1641, 221 of
9160 triangles, 1202, 5548 of 8616 triangles, 1743, 3954 of 9204 triangles,
1791, 9187 of 9280 triangles, 1459, 2669 of 6352 triangles, 1807, 2115 of
241392 triangles
> select subtract #1.9
19 models selected
> select subtract #1.22
18 models selected
> select subtract #1.10
17 models selected
Grouped 17 regions
> select clear
> select #1.8
1 model selected
> select add #1.14
2 models selected
> select add #1.2
3 models selected
> select add #1.9
4 models selected
> select #1.10
1 model selected
> select #1.9
1 model selected
> select add #1.2
2 models selected
> select add #1.14
3 models selected
> select add #1.8
4 models selected
> select ~sel & ##selected
Nothing selected
> select #1.14
1 model selected
> select add #1.2
2 models selected
> select add #1.9
3 models selected
> select add #1.8
4 models selected
Grouped 27 regions
> color sel indigo target s
> color sel cornflower blue target s
> select clear
> select #1.14
1 model selected
> color sel coral target s
> color sel gold target s
> color sel orange target s
> color sel goldenrod target s
> select clear
> hide #1.2 models
> hide #1.1 models
> show #1.2 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.2 models
> show #1.2 models
> hide #1.1 models
> hide #1.8 models
> hide #1.9 models
> hide #1.14 models
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
> hide #!1 models
Can only have one displayed volume when erasing
> show #!3 models
> hide #!3 models
> show #!1 models
> show #1.1 models
> show #1.8 models
> show #1.9 models
> show #1.14 models
> select #1.14
1 model selected
> color sel sandy brown target s
> color sel deep sky blue target s
> color sel olive target s
> color sel 237, 201, 175
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select clear
> select #1.14
1 model selected
> color sel 237, 201, 175
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel byidentity 237, 201, 175
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel byidentity surfaces 237, 201, 175
Expected ',' or a keyword
> color sel byidentity surfaces 237, 201, 175, surfaces
Expected ',' or a keyword
> color sel byidentity surfaces 237,201,175
Expected ',' or a keyword
> select clear
> select subtract #1.14
Nothing selected
> select add #1.14
1 model selected
> color sel 200,200,3
> color sel 237,201,175
> select clear
> color sel 237,201,125
> color sel 237,201,105
> color sel 237,20,175
> select #1.14
1 model selected
> color sel 237,201,115
> select #1.8
1 model selected
> color sel 204,115,94
> select #1.1
1 model selected
> select clear
> select #1.1
1 model selected
> color sel 139,152,120
> select clear
> set bgColor black
> set bgColor white
> select #1.2
1 model selected
> color sel 116,132,173
> select #1.9
1 model selected
> select clear
> select #1.9
1 model selected
> color sel 139.152,120
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel 139,152,120
> select clear
> select #1.1
1 model selected
> color sel 8B9878
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel #8B9878
> select clear
> select #1.14
1 model selected
> select #1.9
1 model selected
> color sel #7484AD
> select #1.2
1 model selected
> color sel #CC735E
> select #1.8
1 model selected
> select clear
> select #1.14
1 model selected
> color sel #EDC9AF
> select clear
> select #1.8
1 model selected
> color sel #C69094
> select clear
> select #1.1
1 model selected
> color sel #CC735E
> color sel #EDC9AF
> select #1.14
1 model selected
> color sel #8B9878
> select clear
> select #1.8
1 model selected
> color sel #C69094
> color sel #CC735E
> select #1.2
1 model selected
> color sel #C69094
> select #1.2
1 model selected
> select clear
Drag select of 1756, 42 of 36688 triangles, 1806, 135 of 231904 triangles,
1809, 379 of 453136 triangles
> select #1.8
1 model selected
> color sel #B35C49
> color sel #E27A5F
> color sel #A75345
> select clear
> color sel #C4684A
> select #1.8
1 model selected
> color sel #C4684A
> select clear
> undo
> color sel #A75345
> select clear
> select #1.8
1 model selected
No visible atoms or bonds selected
> ui tool show "Color Actions"
> color sel dark salmon target s
> color sel salmon target s
> color sel peru target s
> color sel dark goldenrod target s
> color sel chocolate target s
> color sel seashell target s
> color sel moccasin target s
> color sel peach puff target s
> color sel old lace target s
> color sel light goldenrod yellow target s
> color sel mint cream target s
> color sel wheat target s
> select clear
> select #1.8
1 model selected
> color sel khaki target s
> color sel sky blue target s
> color sel light sky blue target s
> color sel pale turquoise target s
> color sel silver target s
> select clear
> save /Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/working.cxs includeMaps
> true
> save /Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/Images/Fig1a.png width
> 4000 height 3047 supersample 4 transparentBackground true
Drag select of 1807, 1808, 104913 of 178300 triangles, 1809, 57 of 453136
triangles
> select #1.2
1 model selected
> select add #1.9
2 models selected
> ui mousemode right "translate selected atoms"
> ui mousemode right "translate selected models"
> view matrix models
> #1.9,0.99985,-0.016312,0.0062197,2.2529,0.016385,0.99979,-0.012011,0.0068709,-0.0060225,0.012111,0.99991,-0.89591,#1.2,0.99985,-0.016312,0.0062197,2.2529,0.016385,0.99979,-0.012011,0.0068709,-0.0060225,0.012111,0.99991,-0.89591
> view matrix models
> #1.9,0.997,-0.0765,0.012196,11.759,0.074437,0.98966,0.12259,-26.216,-0.021447,-0.12131,0.99238,24.479,#1.2,0.997,-0.0765,0.012196,11.759,0.074437,0.98966,0.12259,-26.216,-0.021447,-0.12131,0.99238,24.479
> view matrix models
> #1.9,0.997,-0.0765,0.012196,13.782,0.074437,0.98966,0.12259,-20.851,-0.021447,-0.12131,0.99238,24.26,#1.2,0.997,-0.0765,0.012196,13.782,0.074437,0.98966,0.12259,-20.851,-0.021447,-0.12131,0.99238,24.26
> view matrix models
> #1.9,0.99212,-0.12018,0.035411,18.359,0.1049,0.95133,0.28977,-43.201,-0.068512,-0.28377,0.95644,63.236,#1.2,0.99212,-0.12018,0.035411,18.359,0.1049,0.95133,0.28977,-43.201,-0.068512,-0.28377,0.95644,63.236
> view matrix models
> #1.9,0.99212,-0.12018,0.035411,18.958,0.1049,0.95133,0.28977,-39.499,-0.068512,-0.28377,0.95644,58.722,#1.2,0.99212,-0.12018,0.035411,18.958,0.1049,0.95133,0.28977,-39.499,-0.068512,-0.28377,0.95644,58.722
> view matrix models
> #1.9,0.9966,-0.081759,0.01031,15.595,0.078057,0.97668,0.19999,-26.662,-0.02642,-0.1985,0.97974,35.015,#1.2,0.9966,-0.081759,0.01031,15.595,0.078057,0.97668,0.19999,-26.662,-0.02642,-0.1985,0.97974,35.015
> view matrix models
> #1.9,0.9966,-0.081759,0.01031,14.668,0.078057,0.97668,0.19999,-29.877,-0.02642,-0.1985,0.97974,36.98,#1.2,0.9966,-0.081759,0.01031,14.668,0.078057,0.97668,0.19999,-29.877,-0.02642,-0.1985,0.97974,36.98
> select #1.9
1 model selected
> view matrix models
> #1.9,0.99218,-0.12289,0.02187,20.247,0.11078,0.94767,0.29943,-46.721,-0.057524,-0.29467,0.95387,62.067
> view matrix models
> #1.9,0.99218,-0.12289,0.02187,20.864,0.11078,0.94767,0.29943,-45.006,-0.057524,-0.29467,0.95387,61.474
> select clear
> save /Users/jawh0004/Desktop/SLU/Manuscripts/C3_TiO2/Images/Fig1b.png width
> 4000 height 3047 supersample 4 transparentBackground true
> select #1.9
1 model selected
> select #1.2
1 model selected
> select add #1.9
2 models selected
> view matrix models
> #1.9,0.96349,-0.26518,-0.0369,57.436,0.25492,0.86646,0.42926,-72.352,-0.081859,-0.42299,0.90243,93.968,#1.2,0.97256,-0.23027,-0.033166,49.267,0.22795,0.91466,0.33382,-61.94,-0.046532,-0.33222,0.94205,67.661
> view matrix models
> #1.9,0.96349,-0.26518,-0.0369,61.456,0.25492,0.86646,0.42926,-64.066,-0.081859,-0.42299,0.90243,92.224,#1.2,0.97256,-0.23027,-0.033166,53.288,0.22795,0.91466,0.33382,-53.654,-0.046532,-0.33222,0.94205,65.917
> select #1.9
1 model selected
> view matrix models
> #1.9,0.91739,-0.37029,-0.14591,104.07,0.3957,0.80922,0.43426,-78.337,-0.04273,-0.45612,0.88889,93.533
> view matrix models
> #1.9,0.91739,-0.37029,-0.14591,103.19,0.3957,0.80922,0.43426,-78.017,-0.04273,-0.45612,0.88889,91.794
> select clear
> select #1.9
1 model selected
> select clear
> save /Users/jawh0004/Desktop/SLU/Manuscripts/C3_TiO2/Images/Fig1c.png width
> 4000 height 3047 supersample 4 transparentBackground true
> save
> /Users/jawh0004/Desktop/SLU/Manuscripts/C3_TiO2/Images/Manuscript_working.cxs
> includeMaps true
> close #1#3
> open
> /Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/C3_inactive_working.pdb
C3_inactive_working.pdb title:
Human complement component C3 [more info...]
Chain information for C3_inactive_working.pdb #1
---
Chain | Description | UniProt
A | complement C3 | CO3_HUMAN 1-643
B | complement C3 | CO3_HUMAN 651-1641
Non-standard residues in C3_inactive_working.pdb #1
---
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> close #1
> open
> /Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/manuscript_working.pdb
manuscript_working.pdb title:
\--- [more info...]
Chain information for manuscript_working.pdb #1
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> close #1.1
> 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
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
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
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 "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> 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
> dssp
Computing secondary structure
> open
> /Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/C3_inactive_working.pdb
C3_inactive_working.pdb title:
Human complement component C3 [more info...]
Chain information for C3_inactive_working.pdb #2
---
Chain | Description | UniProt
A | complement C3 | CO3_HUMAN 1-643
B | complement C3 | CO3_HUMAN 651-1641
Non-standard residues in C3_inactive_working.pdb #2
---
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> hide #!2 models
> show #!2 models
> hide #!2 models
> mlp #1
Map values for surface "manuscript_working.pdb_A SES surface": minimum -28.87,
mean -4.223, maximum 24.42
Map values for surface "manuscript_working.pdb_B SES surface": minimum -28.35,
mean -5.005, maximum 25.79
To also show corresponding color key, enter the above mlp command and add key
true
> transparency 50
> transparency #1 10
> transparency #1 80
> transparency #1 50
Drag select of manuscript_working.pdb_A SES surface, 399970 of 401772
triangles, manuscript_working.pdb_B SES surface, 109282 of 800016 triangles,
628 residues
> transparency (#!1 & sel) 30
> select clear
> undo
Drag select of manuscript_working.pdb_A SES surface, manuscript_working.pdb_B
SES surface, 800000 of 800016 triangles, 1474 residues
> transparency (#!1 & sel) 80
> select clear
> transparency #1 50
> transparency #1 0
> select clear
> save /Users/jawh0004/Desktop/SLU/Manuscripts/C3_TiO2/Images/Fig2a.png width
> 4000 height 3047 supersample 4 transparentBackground true
> transparency #1 80
> show #!1 atoms
> hide #!1 atoms
> select clear
> select #1 :755,758,1025,1028
35 atoms, 31 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> select #1 :755,758
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #1 :1025,1028
18 atoms, 16 bonds, 2 residues, 1 model selected
> select ((#1/A & ::polymer_type>0 ) & ((#1/B & ::polymer_type>0 ) :0 ) & ((#1/A & ::polymer_type>0 ) : ui tool show Contacts
> contacts intraRes true ignoreHiddenModels true
14141 contacts
> contacts sel select true makePseudobonds false
2945 contacts
> contacts sel select true makePseudobonds false
5060 contacts
> contacts intraRes true ignoreHiddenModels true
14141 contacts
> volume hide
No volumes specified
> hide sel & #!1 surfaces
> undo
> show sel & #!1 surfaces
> show #!2 models
> hide #!2 models
> hide #1.1 models
> hide #1.2 models
> select #1 :162
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> contacts distanceOnly 4.0 intraRes true ignoreHiddenModels true
22045 distances
> select #1 :1021-1033
101 atoms, 101 bonds, 183 pseudobonds, 13 residues, 2 models selected
> show sel atoms
> undo
> select #1 :160-163
32 atoms, 31 bonds, 48 pseudobonds, 4 residues, 2 models selected
> show sel atoms
> undo
> select clear
> close #3
> select #1/B:758@CD
1 atom, 1 residue, 1 model selected
> hide sel atoms
> undo
> select #1 :755,758
17 atoms, 15 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #1 :1025
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #!1 surfaces
> select #1 :1028
9 atoms, 8 bonds, 1 residue, 1 model selected
> view sel
> view
> view orient
> ui tool show "Side View"
> help help:user/tools/sideview.html
> select #1/B:1025@OE1
1 atom, 1 residue, 1 model selected
> select #1 :1028
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of manuscript_working.pdb_B SES surface, 605 of 800016 triangles,
3 residues
> select clear
Drag select of manuscript_working.pdb_A SES surface, 12 of 401772 triangles,
manuscript_working.pdb_B SES surface, 168 of 800016 triangles
> hide #!1 atoms
> transparency #!1.1-2 30
> save /Users/jawh0004/Desktop/SLU/Manuscripts/C3_TiO2/Images/Fig2a_zoom.png
> width 4000 height 3047 supersample 4 transparentBackground true
> view matrix models
> #1.1,0.97583,0.001583,-0.21851,30.269,-0.00058159,0.99999,0.0046473,-0.47783,0.21852,-0.0044079,0.97582,-25.806,#1.2,0.97583,0.001583,-0.21851,30.269,-0.00058159,0.99999,0.0046473,-0.47783,0.21852,-0.0044079,0.97582,-25.806
> undo
> view sel
> view matrix models
> #1.1,1,0,0,-4.8757,0,1,0,2.477,0,0,1,-10.77,#1.2,1,0,0,-4.8757,0,1,0,2.477,0,0,1,-10.77
> undo
> save
> /Users/jawh0004/Desktop/SLU/Manuscripts/C3_TiO2/Images/Manuscript_working_Fig2.cxs
> includeMaps true
> close #1-2#1.1-2
> open
> /Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/cryosparc_P3_J112_009_volume_map_half_A.mrc
Opened cryosparc_P3_J112_009_volume_map_half_A.mrc as #1, grid size
400,400,400, pixel 0.648, shown at level 0.0385, step 2, values float32
> open
> /Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/cryosparc_P3_J112_009_volume_map_half_B.mrc
Opened cryosparc_P3_J112_009_volume_map_half_B.mrc as #2, grid size
400,400,400, pixel 0.648, shown at level 0.0386, step 2, values float32
> open
> /Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/C3_CP_flexregion_VOP.mrc
Opened C3_CP_flexregion_VOP.mrc as #3, grid size 400,400,400, pixel 0.648,
shown at level 0.0324, step 2, values float32
> hide #!3 models
> open
> /Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/cryosparc_P3_J115_006_LocalRefvolume_flexregion.mrc
Opened cryosparc_P3_J115_006_LocalRefvolume_flexregion.mrc as #4, grid size
400,400,400, pixel 0.648, shown at level 0.0179, step 2, values float32
> open
> /Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/cryosparc_P3_J112_009_volume_map.mrc
Opened cryosparc_P3_J112_009_volume_map.mrc as #5, grid size 400,400,400,
pixel 0.648, shown at level 0.0158, step 2, values float32
> hide #!4 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> hide #!5 models
> open
> /Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/cryosparc_P2_J69_008_volume_map.mrc
Opened cryosparc_P2_J69_008_volume_map.mrc as #6, grid size 200,200,200, pixel
1.3, shown at level 0.0522, step 1, values float32
> open
> /Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/cryosparc_P2_J72_map_sharp.mrc
Opened cryosparc_P2_J72_map_sharp.mrc as #7, grid size 200,200,200, pixel 1.3,
shown at level 0.0573, step 1, values float32
> hide #!6 models
> close #6-7
> show #!1 models
> show #!2 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> close #4
> show #!3 models
> hide #!3 models
> close #3
> close #1-2,5
> open
> /Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/LocalResolution_25/cryosparc_P3_J112_009_volume_map_full.ccp4
Opened cryosparc_P3_J112_009_volume_map_full.ccp4 as #1, grid size
400,400,400, pixel 0.648, shown at level 0.0158, step 2, values float32
> volume #1 step 1
> hide #!1 models
> open
> /Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/LocalResolution_25/cryosparc_P3_J112_009_volume_map_local_resolution.ccp4
Opened cryosparc_P3_J112_009_volume_map_local_resolution.ccp4 as #2, grid size
400,400,400, pixel 0.648, shown at level 3.23, step 2, values float32
> volume #2 step 1
> volume #2 level 3.242
> close #2
> show #!1 models
Must specify one map, got 0
> hide #!1 models
> open
> "/Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/LocalResolution_25/cryosparc_P3_J112_009_volume_map_full
> copy.mrc"
Opened cryosparc_P3_J112_009_volume_map_full copy.mrc as #2, grid size
400,400,400, pixel 0.648, shown at level 0.0158, step 2, values float32
> color sample #2 map #2 palette
> 2.1,purple:2.5,indigo:2.8,blue:3.3,cyan:3.5,lime:3.8,yellow:4.3,red:5.0,salmon:6.5,pink
Map values for surface "surface": minimum -0.01653, mean 0.01505, maximum
0.03591
> color sample #1 map #2 palette
> 2.1,purple:2.5,indigo:2.8,blue:3.3,cyan:3.5,lime:3.8,yellow:4.3,red:5.0,salmon:6.5,pink
Map values for surface "surface": minimum 0.01579, mean 0.01579, maximum
0.0158
> color sample #2 map #2 palette
> 2.1,purple:2.5,indigo:2.8,blue:3.3,cyan:3.5,lime:3.8,yellow:4.3,red:5.0,salmon:6.5,pink
Map values for surface "surface": minimum -0.01653, mean 0.01505, maximum
0.03591
> volume #2 step 1
> volume #2 level 0.01663
> close #1
> open
> "/Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/LocalResolution_25/cryosparc_P3_J112_009_volume_map_local_resolution
> copy.mrc"
Opened cryosparc_P3_J112_009_volume_map_local_resolution copy.mrc as #1, grid
size 400,400,400, pixel 0.648, shown at level 3.23, step 2, values float32
> color sample #1 map #2 palette
> 2.1,purple:2.5,indigo:2.8,blue:3.3,cyan:3.5,lime:3.8,yellow:4.3,red:5.0,salmon:6.5,pink
> ui tool show "Surface Color"
> color sample #2.1 map #2 palette
> 2.1,#800080:2.5,#4b0082:2.8,#0000ff:3.3,#00ffff:3.5,#00ff00:3.8,#ffff00:4.3,#ff0000:5,#fa8072
Map values for surface "surface": minimum 0.01663, mean 0.01663, maximum
0.01663
> color sample #2.1 map #2 palette
> 2.1,#0f8e23:2.5,#4b0082:2.8,#0000ff:3.3,#00ffff:3.5,#00ff00:3.8,#ffff00:4.3,#ff0000:5,#fa8072
Map values for surface "surface": minimum 0.01663, mean 0.01663, maximum
0.01663
> color sample #1.1 map #2 palette
> 2.1,#800080:2.5,#4b0082:2.8,#0000ff:3.3,#00ffff:3.5,#00ff00:3.8,#ffff00:4.3,#ff0000:5,#fa8072
> color sample #1.1 map #2 palette
> #800080:#4b0082:#0000ff:#00ffff:#00ff00:#ffff00:#ff0000:#fa8072
> color sample #1.1 map #2 palette
> 0,#800080:0.1429,#4b0082:0.2857,#0000ff:0.4286,#00ffff:0.5714,#00ff00:0.7143,#ffff00:0.8571,#ff0000:1,#fa8072
No surface chosen for coloring
> help help:user/tools/surfacecolor.html
> color sample #1.1 map #2 palette
> 0,#800080:0.1429,#4b0082:0.2857,#0000ff:0.4286,#00ffff:0.5714,#00ff00
> close #1-2
> open
> "/Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/LocalResolution_25/cryosparc_P3_J112_009_volume_map_full
> copy.mrc"
Opened cryosparc_P3_J112_009_volume_map_full copy.mrc as #1, grid size
400,400,400, pixel 0.648, shown at level 0.0158, step 2, values float32
> open
> "/Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/LocalResolution_25/cryosparc_P3_J112_009_volume_map_local_resolution
> copy.mrc"
Opened cryosparc_P3_J112_009_volume_map_local_resolution copy.mrc as #2, grid
size 400,400,400, pixel 0.648, shown at level 3.23, step 2, values float32
> color sample #1 map #2 palette rdylbu key true range 2.1,6.5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> key rdylbu :2.1 :3.2 :4.3 :5.4 :6.5 showTool true
> ui mousemode right "color key"
> color sample #1 map #2 palette rdylbu key true range 2.1,3.0,6.5
Invalid "range" argument: Expected 2-tuple of numbers or 'full'
> color sample #1 map #2 palette rdylbu key true range 2.1,6.5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> key rdylbu :2.1 :3.2 :4.3 :5.4 :6.5 showTool true
> volume #1 level 0.01579
> volume #2 level 3.293
> key colorTreatment distinct
> volume #2 step 4
> volume #2 step 1
> volume #1 step 1
> volume #2 level 3.227
> volume #1 level 0.01712
> ui mousemode right "translate selected models"
> close #3#1-2
> open
> "/Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/LocalResolution_25/cryosparc_P3_J112_009_volume_map_full
> copy.mrc"
Opened cryosparc_P3_J112_009_volume_map_full copy.mrc as #1, grid size
400,400,400, pixel 0.648, shown at level 0.0158, step 2, values float32
> open
> "/Users/jawh0004/Desktop/SLU/C3/CryoEM/C3_TiO2/C3_working/LocalResolution_25/cryosparc_P3_J112_009_volume_map_local_resolution
> copy.mrc"
Opened cryosparc_P3_J112_009_volume_map_local_resolution copy.mrc as #2, grid
size 400,400,400, pixel 0.648, shown at level 3.23, step 2, values float32
> volume #1 step 1
> volume #2 step 1
> ui tool show "Surface Color"
> color sample #1.1 map #2 palette #ff0000:#f8f7ff:#0d00f5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette 2,#ff0000:4,#f8f7ff:6,#0d00f5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette #ff0000:#f8f7ff:#0d00f5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette 2,#ff0000:3.227,#f8f7ff:3.227,#0d00f5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette 2,#ff0000:3.227,#f8f7ff:10,#0d00f5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette 2,#ff0000:5,#f8f7ff:10,#0d00f5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette 2,#ff0000:3,#f8f7ff:10,#0d00f5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette 2,#ff0000:3,#f8f7ff:4,#0d00f5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette #ff0000:#f8f7ff:#0d00f5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette #ff0000:#f8f7ff:#0d00f5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette 3.223,#ff0000:3.227,#f8f7ff:3.227,#0d00f5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> volume #1 level 0.02056
> color single #1.1
> color sample #1.1 map #2 palette 2.1,#ff0000:2.2,#f8f7ff:2.3,#0d00f5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette 2.1,#ff0000:2.2,#f8f7ff:3,#0d00f5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette 2.1,#ff0000:2.2,#f8f7ff:2.2,#0d00f5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette 2.2,#ff0000:2.2,#f8f7ff:2.2,#0d00f5
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette 2.2,#0fc7cf:2.2,#ffffff:2.2,#9e205e
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette 2.2,#0fc7cf:2.2,#ffffff:3.2,#9e205e
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette 4.2,#0fc7cf:2.2,#ffffff:3.2,#9e205e
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
> color sample #1.1 map #2 palette 4.2,#9e205e:2.2,#ffffff:3.2,#0fc7cf
Map values for surface "surface": minimum 3.227, mean 3.227, maximum 3.227
No surface chosen for coloring
> hide #!2 models
No surface chosen for coloring
> select #1
2 models selected
No surface chosen for coloring
> show #!2 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: MRX43KS/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 11881.41.5
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.1 (23H222)
Kernel Version: Darwin 23.6.0
Time since boot: 6 days, 23 hours
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
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: No
Connection Type: Internal
PHL 329P1:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 6 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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