![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16746 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-12.3-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 0x000000010f0f6600 (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.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.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 61)
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{
"uptime" : 2900000,
"procLaunch" : "2025-01-30 19:48:39.4973 -0500",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "iMac20,1",
"procStartAbsTime" : 2990833854704017,
"coalitionID" : 19312,
"osVersion" : {
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"build" : "21E230",
"releaseType" : "User"
},
"captureTime" : "2025-01-30 20:48:12.0781 -0500",
"incident" : "82FDF6F8-6F44-4CA9-B254-1F5AA6FF124F",
"bug_type" : "309",
"pid" : 60207,
"procExitAbsTime" : 2994406061520514,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"82A60AD4-CF32-513B-B21B-F8412D0563CC","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "AE180AAD-FFAB-EBB6-B212-9119B2982CE1",
"wakeTime" : 296509,
"bridgeVersion" : {"build":"19P4242","train":"6.4"},
"sleepWakeUUID" : "3A2451E5-1CDE-4E47-A418-38586742069B",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4377268224\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104e7d000-104e81000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"isCorpse" : 1,
"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4377268224\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104e7d000-104e81000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/akw/Desktop/session-6.cxs
Opened egelman-helix-300box.mrc as #1, grid size 300,300,300, pixel 0.876,
shown at level 0.118, step 1, values float32
Opened 20231130_dimer-segmented-from-helix-MAP-256box.mrc as #3, grid size
256,256,256, pixel 0.876,0.876,0.876, shown at level 0.00805, step 1, values
float32
Log from Thu Dec 12 01:43:15 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/akw/Desktop/session-6.cxs
Opened egelman-helix-300box.mrc as #1, grid size 300,300,300, pixel 0.876,
shown at level 0.118, step 1, values float32
Opened 20231130_dimer-segmented-from-helix-MAP-256box.mrc as #3, grid size
256,256,256, pixel 0.876,0.876,0.876, shown at level 0.00805, step 1, values
float32
Log from Wed Dec 11 17:42:09 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/akw/Desktop/session-4.cxs
Opened egelman-helix-300box.mrc as #1, grid size 300,300,300, pixel 0.876,
shown at level 0.0576, step 1, values float32
Opened 20231130_dimer-segmented-from-helix-MAP-256box.mrc as #3, grid size
256,256,256, pixel 0.876,0.876,0.876, shown at level 0.00805, step 1, values
float32
Log from Wed Dec 11 00:35:51 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Volumes/LabUSB/CryoEM-Structure/khg-paper-cryoem-structure-3.cxs
Opened egelman-helix-300box.mrc as #1, grid size 300,300,300, pixel 0.876,
shown at level 0.142, step 1, values float32
Opened 20231130_dimer-segmented-from-helix-MAP-256box.mrc as #3, grid size
256,256,256, pixel 0.876,0.876,0.876, shown at level 0.00805, step 1, values
float32
Log from Fri Dec 6 16:57:31 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/neherlab/Desktop/khg-paper-cryoem-structure.cxs
Opened egelman-helix-300box.mrc as #1, grid size 300,300,300, pixel 0.876,
shown at level 0.116, step 2, values float32
Log from Fri Oct 11 15:38:55 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Volumes/LabUSB/CryoEM-Structure/egelman-helix-300box.mrc
Opened egelman-helix-300box.mrc as #1, grid size 300,300,300, pixel 0.876,
shown at level 0.192, step 2, values float32
> volume #1 level 0.1156
> open /Volumes/LabUSB/CryoEM-Structure/IandJ.pdb
Summary of feedback from opening /Volumes/LabUSB/CryoEM-Structure/IandJ.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 64 HIS A 71 1 8
Start residue of secondary structure not found: HELIX 2 2 TRP A 94 GLU A 106 1
13
Start residue of secondary structure not found: HELIX 3 3 PRO A 125 PHE A 149
1 25
Start residue of secondary structure not found: HELIX 4 4 TYR A 161 ALA A 171
1 11
Start residue of secondary structure not found: HELIX 5 5 ASP A 262 LYS A 268
1 7
427 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (57 )
Cannot find LINK/SSBOND residue CYS (246 )
Cannot find LINK/SSBOND residue CYS (294 )
Cannot find LINK/SSBOND residue CYS (308 )
Cannot find LINK/SSBOND residue CYS (448 )
75 messages similar to the above omitted
Chain information for IandJ.pdb #2
---
Chain | Description
I J | No description available
> select add #2
13594 atoms, 13782 bonds, 868 residues, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.76629,-0.62579,0.14558,151.31,0.63634,0.7705,-0.037475,-109.76,-0.088718,0.12136,0.98864,1.3347
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.76629,-0.62579,0.14558,29.699,0.63634,0.7705,-0.037475,-202.73,-0.088718,0.12136,0.98864,-143.58
> view matrix models
> #2,0.76629,-0.62579,0.14558,41.34,0.63634,0.7705,-0.037475,-220.86,-0.088718,0.12136,0.98864,-144.45
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule IandJ.pdb (#2) to map egelman-helix-300box.mrc (#1) using 13594
atoms
average map value = 0.07346, steps = 204
shifted from previous position = 2.41
rotated from previous position = 19.9 degrees
atoms outside contour = 9988, contour level = 0.11563
Position of IandJ.pdb (#2) relative to egelman-helix-300box.mrc (#1)
coordinates:
Matrix rotation and translation
0.93052266 -0.36618758 0.00585159 -15.31543785
0.36604431 0.93043576 0.01734523 -198.88648151
-0.01179613 -0.01399819 0.99983244 -140.05885987
Axis -0.04275375 0.02407225 0.99879560
Axis point 504.53247009 -154.36497997 0.00000000
Rotation angle (degrees) 21.50346116
Shift along axis -144.02302456
> select subtract #2
Nothing selected
> color #2 #9437ffff
> color zone #1 near #2 distance 4
> color zone #1 near #2 distance 3
> select add #2
13594 atoms, 13782 bonds, 868 residues, 1 model selected
> view matrix models
> #2,0.93052,-0.36619,0.0058516,-15.291,0.36604,0.93044,0.017345,-198.66,-0.011796,-0.013998,0.99983,-144.86
> fitmap #2 inMap #1
Fit molecule IandJ.pdb (#2) to map egelman-helix-300box.mrc (#1) using 13594
atoms
average map value = 0.1375, steps = 56
shifted from previous position = 1.5
rotated from previous position = 2.05 degrees
atoms outside contour = 6748, contour level = 0.11563
Position of IandJ.pdb (#2) relative to egelman-helix-300box.mrc (#1)
coordinates:
Matrix rotation and translation
0.94076379 -0.33860304 0.01764840 -26.86855672
0.33865095 0.94091203 0.00029064 -188.53442556
-0.01670400 0.00570323 0.99984421 -149.04283603
Axis 0.00798146 0.05065634 0.99868425
Axis point 504.40694109 -163.85487466 0.00000000
Rotation angle (degrees) 19.82041430
Shift along axis -158.61164696
> color zone #1 near #2 distance 3
> color zone #1 near #2 distance 2.8
> color zone #1 near #2 distance 2.5
> color zone #1 near #2 distance 2.3
> color zone #1 near #2 distance 2
> color zone #1 near #2 distance 2.2
> color zone #1 near #2 distance 2.3
> hide #2 models
> set bgColor white
> lighting full
> view
> view orient
> turn x 90
> turn y 90
[Repeated 1 time(s)]
> turn y 15
[Repeated 1 time(s)]
> turn y 5
> save /Users/neherlab/Desktop/khg-paper-cryoem-structure.cxs
——— End of log from Fri Oct 11 15:38:55 2024 ———
opened ChimeraX session
> show #2 models
> hide #2 models
> select subtract #2
Nothing selected
> select add #2
13594 atoms, 13782 bonds, 868 residues, 1 model selected
> show #2 models
> hide #!1 models
> graphics silhouettes true
> select subtract #2
Nothing selected
> select #2/I,J:246-269
718 atoms, 718 bonds, 48 residues, 1 model selected
> color #2/I,J:246-269 yellow
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color #2/I,J:246-269 gold
> select clear
> turn y 180
> open /Volumes/LabUSB/CryoEM-Structure/20231130_dimer-segmented-from-helix-
> MAP-256box.mrc
Opened 20231130_dimer-segmented-from-helix-MAP-256box.mrc as #3, grid size
256,256,256, pixel 0.876,0.876,0.876, shown at level 0.00805, step 1, values
float32
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit map 20231130_dimer-segmented-from-helix-MAP-256box.mrc in map egelman-
helix-300box.mrc using 167699 points
correlation = 0.4491, correlation about mean = 0.08124, overlap = 1078
steps = 260, shift = 28.8, angle = 21.1 degrees
Position of 20231130_dimer-segmented-from-helix-MAP-256box.mrc (#3) relative
to egelman-helix-300box.mrc (#1) coordinates:
Matrix rotation and translation
0.93520941 0.32888530 -0.13121668 6.84267416
-0.33690918 0.94051345 -0.04389371 30.32792885
0.10897506 0.08525791 0.99038150 -21.06759020
Axis 0.17950636 -0.33383977 -0.92538018
Axis point 99.70475446 4.62128701 -0.00000000
Rotation angle (degrees) 21.08429426
Shift along axis 10.59916523
> select add #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.93521,0.32889,-0.13122,19.207,-0.33691,0.94051,-0.043894,38.214,0.10898,0.085258,0.99038,-15.453
> fitmap #3 inMap #1
Fit map 20231130_dimer-segmented-from-helix-MAP-256box.mrc in map egelman-
helix-300box.mrc using 167699 points
correlation = 1, correlation about mean = 1, overlap = 3307
steps = 148, shift = 7.6, angle = 21.1 degrees
Position of 20231130_dimer-segmented-from-helix-MAP-256box.mrc (#3) relative
to egelman-helix-300box.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 -0.00010603 -0.00006061 39.43083226
0.00010604 0.99999999 0.00008940 -15.79518287
0.00006060 -0.00008941 0.99999999 7.00577045
Axis -0.59068847 -0.40040599 0.70054420
Axis point 194523.93940707 304687.20038210 0.00000000
Rotation angle (degrees) 0.00867223
Shift along axis -12.05900032
> color zone #3 near #2 distance 2.3
> color zone #3 near #2 distance 4
> color zone #3 near #2 distance 4.5
> color zone #3 near #2 distance 5
> color zone #3 near #2 distance 6
> transparency sel 50
> select subtract #3
Nothing selected
> turn y 180
[Repeated 1 time(s)]
> turn y 90
> ui mousemode right translate
> turn y 90
[Repeated 2 time(s)]
> hide #!3 models
> graphics silhouettes true width 5 color black
> graphics silhouettes true width 3 color black
> color #2/I,J:420-424 tomato
> color #2/I,J:412-427 tomato
> graphics silhouettes true width 3.5 color black
> graphics silhouettes true width 4color black
Invalid "width" argument: Expected a number
> graphics silhouettes true width 4 color black
> save /Volumes/LabUSB/CryoEM-Structure/khg-paper-cryoem-structure-2.cxs
> color #2/I,J:413-427 tomato
> open /Volumes/LabUSB/CryoEM-
> Structure/RSR80_chainsrenamed_real_space_refined_083.pdb
Chain information for RSR80_chainsrenamed_real_space_refined_083.pdb #4
---
Chain | Description
A B C D E F G H I J K L M N O P Q R | No description available
> show #!1 models
> select add #4
122346 atoms, 124038 bonds, 7812 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-93.156,0,1,0,-94.185,0,0,1,-2.6872
> view matrix models #4,1,0,0,-92.208,0,1,0,-95.587,0,0,1,-93.689
> fitmap #4 inMap #1
Fit molecule RSR80_chainsrenamed_real_space_refined_083.pdb (#4) to map
egelman-helix-300box.mrc (#1) using 122346 atoms
average map value = 0.1296, steps = 60
shifted from previous position = 2.94
rotated from previous position = 0.0246 degrees
atoms outside contour = 66485, contour level = 0.11563
Position of RSR80_chainsrenamed_real_space_refined_083.pdb (#4) relative to
egelman-helix-300box.mrc (#1) coordinates:
Matrix rotation and translation
0.99999991 -0.00037639 0.00016867 -92.80659779
0.00037641 0.99999992 -0.00011613 -92.90413739
-0.00016862 0.00011619 0.99999998 -92.83846069
Axis 0.27108294 0.39357404 0.87841534
Axis point 96981.13632418 -143405.54567079 0.00000000
Rotation angle (degrees) 0.02455089
Shift along axis -143.27367059
> hide sel atoms
> show sel cartoons
> surface dust #1 size 8.76
> volume #1 step 1
> select clear
> select #4/R
6797 atoms, 6891 bonds, 434 residues, 1 model selected
> hide sel
> hide #2 models
> hide #!1 models
> hide select
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel
> select hide
Expected an objects specifier or a keyword
> hide sel cartoons
> show #!1 models
> hide #!1 models
> color #4 darkgrey
> select #4/I,J
13594 atoms, 13782 bonds, 868 residues, 1 model selected
> color #4 #531b93ff
> undo
> select add #4
122346 atoms, 124038 bonds, 7812 residues, 1 model selected
> select subtract #4
Nothing selected
> select #4/I,J
13594 atoms, 13782 bonds, 868 residues, 1 model selected
> color #4 #9437ffff
> color #4/I,J #9437ffff
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #4 models
> show #!1 models
> transparency #1.1 50
> show #4 models
> ui mousemode right "rotate selected models"
> select add #4
122346 atoms, 124038 bonds, 7812 residues, 1 model selected
> view matrix models
> #4,0.24737,-0.96822,0.036881,285.57,0.95913,0.23929,-0.15104,-103.8,0.13741,0.072735,0.98784,-137.36
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.24737,-0.96822,0.036881,286.95,0.95913,0.23929,-0.15104,-101.22,0.13741,0.072735,0.98784,-149.95
> fitmap #4 inMap #1
Fit molecule RSR80_chainsrenamed_real_space_refined_083.pdb (#4) to map
egelman-helix-300box.mrc (#1) using 122346 atoms
average map value = 0.1296, steps = 192
shifted from previous position = 12.1
rotated from previous position = 13.3 degrees
atoms outside contour = 60380, contour level = 0.11563
Position of RSR80_chainsrenamed_real_space_refined_083.pdb (#4) relative to
egelman-helix-300box.mrc (#1) coordinates:
Matrix rotation and translation
0.40715860 -0.91335746 0.00013720 244.88878665
0.91335746 0.40715861 0.00011883 -164.75881347
-0.00016440 0.00007693 0.99999998 -116.53246470
Axis -0.00002294 0.00016510 0.99999999
Axis point 249.34556201 106.27136078 0.00000000
Rotation angle (degrees) 65.97353305
Shift along axis -116.56528249
> select subtract #4
Nothing selected
> select #4/R
6797 atoms, 6891 bonds, 434 residues, 1 model selected
> show sel cartoons
> select clear
> select #4/A
6797 atoms, 6891 bonds, 434 residues, 1 model selected
> hide sel cartoons
> view matrix models
> #4,0.40716,-0.91336,0.0001372,219.39,0.91336,0.40716,0.00011883,-179.67,-0.0001644,7.6929e-05,1,-130.93
> undo
> ui mousemode right translate
> volume #1 level 0.1423
> hide #!1 models
> show #!1 models
> transparency #1.1 50
> hide #!1 models
> select #4/R
6797 atoms, 6891 bonds, 434 residues, 1 model selected
> hide sel cartoons
> lighting flat
> undo
> lighting full
> select #4/Q,R
13594 atoms, 13782 bonds, 868 residues, 1 model selected
> color #4 #5e5e5eff
> color #4/Q,R #5e5e5eff
> undo
> select clear
> save /Volumes/LabUSB/CryoEM-Structure/khg-paper-cryoem-structure-3.cxs
——— End of log from Fri Dec 6 16:57:31 2024 ———
opened ChimeraX session
> show #!1 models
> hide #4 models
> show #4 models
> hide #4 models
> show #2 models
> hide #2 models
> show #!3 models
> hide #!3 models
> color #1 #919191ff models
> color #1 #797979ff models
> color #1 #919191ff models
> show #2 models
> hide #!1 models
> show #!1 models
> color zone #1 near #2 distance 6
> color zone #1 near #2 distance 4
> color zone #1 near #2 distance 3.5
> ui tool show "Side View"
> hide #2 models
> hide #!1 models
> show #4 models
> show #2 models
> hide #4 models
> save test1.png transparentBackground true
> select add #2
13594 atoms, 13782 bonds, 868 residues, 1 model selected
> select subtract #2
Nothing selected
> color #2 #9437ffff
> color #2/I,J: 246-269 gold
> hide #2 models
> show #4 models
> color #4/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R: 246-269 gold
> turn x 90
> hide #4 models
> show #!1 models
> color zone #1 near #2 distance 3.5
> view
[Repeated 1 time(s)]
> view orient
> select ~sel & ##selected
Nothing selected
> color zone #1 near #4 distance 3.5
> volume #1 level 0.09592
> transparency #1.1 50
> show #4 models
> volume #1 level 0.07834
> color zone #1 near #4 distance 3.5
> volume #1 level 0.06235
> color zone #1 near #4 distance 3.5
> turn y 90
[Repeated 1 time(s)]
> show #!3 models
> hide #!3 models
> undo
[Repeated 2 time(s)]
> transparency #1.1 50
> transparency #1.1 0
> save /Users/akw/Desktop/session-4.cxs
> save session-4-yellow-lid-helix.png transparentBackground true
[Repeated 1 time(s)]
> volume #1 level 0.09592
> color zone #1 near #4 distance 3.5
> volume #1 level 0.05756
> surface dust #1 size 8.76
> surface dust #1 size 9
> surface dust #1 size 10
> surface dust #1 size 11
> save /Users/akw/Desktop/session-4.cxs
——— End of log from Wed Dec 11 00:35:51 2024 ———
opened ChimeraX session
> hide #!1 models
> ui tool show "Side View"
> show #!3 models
> hide #!3 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> hide #4 models
> show #4 models
> color #4 #919191ff
> color #4 #929292ff
> color #4 #919191ff
> color #4 #929292ff
> color #4 darkgrey
> color #4/I,J #9437ffff
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!1 models
> color #1 #929292ff models
> color #1 darkgrey models
> color #1 #929292ff models
> volume #1 level 0.1295
> volume #1 level 0.1183
> hide #4 models
> hide #!1 models
> show #4 models
> color #4/I,J #9437ffff
> show #!1 models
> color zone #1 near #4 distance 3.5
> hide #4 models
> save session-4-purple-dimer-helix-2.png transparentBackground true
> hide #!1 models
> show #4 models
> save session-4-purple-dimer-helix-model-2.png transparentBackground true
> hide #4 models
> show #4 models
> turn x 90
> save session-4-purple-dimer-helix-model-top-2.png transparentBackground true
> hide #4 models
> show #!1 models
> show #4 models
> hide #!1 models
> show #!1 models
> hide #4 models
> save session-4-purple-dimer-helix-top-2.png transparentBackground true
> save /Users/akw/Desktop/session-4-2.cxs
> hide #!1 models
> show #2 models
> hide #2 models
> show #4 models
> turn x 90
[Repeated 2 time(s)]
> select add #4
122346 atoms, 124038 bonds, 7812 residues, 1 model selected
> color #4 silver
> color #4 darkgrey
> hide #4 models
> show #4 models
> select subtract #4
Nothing selected
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color #4/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R:
> 309,310,312,326,327,433,435,437,443,444 royalblue
> color #4/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R:
> 309,310,312,326,327,433,435,437,443,444 limegreen
> color #4/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R:
> 309,310,312,326,327,433,435,437,443,444 turquiose
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #4/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R:
> 309,310,312,326,327,433,435,437,443,444 turquoise
> show #!1 models
> hide #4 models
> color #1 darkgrey models
> color zone #1 near #4 distance 3.5
> turn y 90
[Repeated 5 time(s)]
> save /Users/akw/Desktop/session-6.cxs
——— End of log from Wed Dec 11 17:42:09 2024 ———
opened ChimeraX session
> ui tool show "Side View"
> view orient
> turn x 90
> lighting flat
> hide #!1 models
> show #4 models
> show #!1 models
> hide #4 models
> show #4 models
> hide #4 models
> show #2 models
> hide #2 models
> show #!3 models
> hide #!3 models
> lighting full
> color #3 darkgrey models
> show #!3 models
> hide #!1 models
> undo
[Repeated 2 time(s)]
> save session-6-heparins.png transparentBackground true
> save /Users/akw/Desktop/session-6.cxs
——— End of log from Thu Dec 12 01:43:15 2024 ———
opened ChimeraX session
> turn y 20
> turn y 5
> turn y 3
> undo
> show #2 models
> turn y 30
> turn y 15
> turn y -5
> hide #2 models
> ui tool show "Side View"
> turn y 90
> turn y 45
> ui tool show "Side View"
> lighting soft
> show #4 models
> hide #!1 models
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color #4/A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R:
> 309,310,312,326,327,433,435,437,443,444 dark blue
> show #!1 models
> color zone #1 near #4 distance 3
> color zone #1 near #4 distance 2.5
> color zone #1 near #4 distance 4
> hide #4 models
> volume #1 level 0.1631
> open /Volumes/LabUSB/CryoEM-
> Structure/RSR80_chainsrenamed_real_space_refined_083.pdb
Chain information for RSR80_chainsrenamed_real_space_refined_083.pdb #5
---
Chain | Description
A B C D E F G H I J K L M N O P Q R | No description available
> hide #5 models
> save /Users/akw/Desktop/session-6.cxs
> save hep-darkblue.png transparentBackground true
> view orient
> turn x -90
> save /Users/akw/Desktop/session-6.cxs
> save hep-darkblue.png transparentBackground true
> ui tool show "Scale Bar"
> scalebar color #000000
> save hep-darkblue.png transparentBackground true
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.8.13
OpenGL renderer: AMD Radeon Pro 5500 XT OpenGL Engine
OpenGL vendor: ATI Technologies 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: iMac
Model Identifier: iMac20,1
Processor Name: 8-Core Intel Core i7
Processor Speed: 3.8 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1731.100.130.0.0 (iBridge: 19.16.14242.0.0,0)
OS Loader Version: 540.100.7~14
Software:
System Software Overview:
System Version: macOS 12.3 (21E230)
Kernel Version: Darwin 21.4.0
Time since boot: 68 days 10:11
Graphics/Displays:
AMD Radeon Pro 5500 XT:
Chipset Model: AMD Radeon Pro 5500 XT
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0041
ROM Revision: 113-D3220I-231
VBIOS Version: 113-D322A1XT-012
Option ROM Version: 113-D322A1XT-012
EFI Driver Version: 01.01.231
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL S2421HGF:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: HXYS973
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 9 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 , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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