![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16781 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-13.5-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 0x00000001f6f56080 (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.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, lxml._elementpath, lxml.etree, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath (total: 60)
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"version" : 2,
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"incident" : "F6071705-6C88-45F9-911D-A69CF6B4CDF6",
"pid" : 81209,
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"procLaunch" : "2025-02-03 16:59:26.7124 -0500",
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"procExitAbsTime" : 10544625982619,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BB488BFF-7735-3F07-70AD-320186DB2983",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"codeSigningTrustLevel" : 0,
"wakeTime" : 17250,
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"exception" : {"codes":"0x0000000000000001, 0x00001cf43591def8","rawCodes":[1,31835196350200],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00001cf43591def8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":81209},
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"faultingThread" : 0,
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"source" : "P",
"arch" : "arm64e",
"base" : 6909505536,
"size" : 520184,
"uuid" : "949943e2-52cb-3c95-ab08-7ed984333d03",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6911160320,
"size" : 28668,
"uuid" : "6d458354-3c39-3f35-a3bb-d01a78817b4a",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6964240384,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15794176,
"uuid" : "ab4a163e-3a53-3fde-a88d-130759291adb",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.70.136"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6907453440,
"size" : 583048,
"uuid" : "e7a99595-e0f8-34af-be8b-9347d0d658a4",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6911373312,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5087232,
"uuid" : "b3b2df49-2db8-370e-84ae-e0a2704515b8",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1979"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6927732736,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 10248192,
"uuid" : "b7799cb6-0a3c-3c8b-a185-8cec55845b14",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "1979"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
}
],
"sharedCache" : {
"base" : 6906789888,
"size" : 3553361920,
"uuid" : "9c875b0a-d532-3933-b1f0-f1ea72cedde2"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.7G resident=0K(0%) swapped_out_or_unallocated=1.7G(100%)\nWritable regions: Total=2.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 5440K 8 \nCG image 1264K 60 \nColorSync 592K 30 \nCoreAnimation 544K 34 \nCoreGraphics 144K 9 \nCoreUI image data 5648K 49 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 1.4G 431 \nMALLOC guard page 192K 11 \nMALLOC_MEDIUM (reserved) 640.0M 8 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.6M 40 \nStack 200.8M 40 \nVM_ALLOCATE 305.4M 213 \nVM_ALLOCATE (reserved) 128.0M 3 reserved VM address space (unallocated)\n__AUTH 1930K 398 \n__AUTH_CONST 29.5M 636 \n__CTF 824 1 \n__DATA 20.9M 788 \n__DATA_CONST 40.5M 795 \n__DATA_DIRTY 2039K 247 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 832.6M 157 \n__OBJC_RO 66.4M 1 \n__OBJC_RW 2012K 1 \n__TEXT 890.9M 814 \ndyld private memory 320K 4 \nmapped file 228.2M 58 \nshared memory 3200K 28 \n=========== ======= ======= \nTOTAL 4.8G 4880 \nTOTAL, minus reserved VM space 4.0G 4880 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "89ffc6da225233b246bd7954fb6dafde7d7db9d1",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "62fe74515312cd4599bd3c80",
"factorPackIds" : {
"MYRIAD_BOOSTS" : "62fe74805312cd4599bd3c81"
},
"deploymentId" : 240000006
},
{
"rolloutId" : "6297d96be2c9387df974efa4",
"factorPackIds" : {
},
"deploymentId" : 240000032
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Chimera-Image/local_res.cxs"
Opened P2_J174_map_flipped_nosharp.mrc as #6, grid size 224,224,224, pixel
0.832, shown at level 0.0255, step 1, values float32
Opened cryosparc_P2_J178_map_locres.mrc z flip as #9, grid size 224,224,224,
pixel 0.832, shown at level 2.77, step 1, values float32
Log from Mon Feb 3 16:57:41 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Chimera-Image/local_res.cxs"
Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel
0.832, shown at level 0.0526, step 1, values float32
Opened cryosparc_P2_J77_004_volume_map.mrc as #3, grid size 224,224,224, pixel
0.832, shown at level 0.0661, step 1, values float32
Opened cryosparc_P2_J135_map_locres.mrc as #4, grid size 224,224,224, pixel
0.832, shown at level 3.23, step 1, values float32
Map values for surface "surface": minimum 0, mean 2.002, maximum 3.728
Log from Wed Jan 29 13:58:14 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Chimera-Image/Overview.cxs"
Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel
0.832, shown at level 0.0526, step 1, values float32
Log from Mon Jan 27 14:41:44 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Chimera-Image/Overview_mrc.cxs"
Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel
0.832, shown at level 0.0526, step 1, values float32
Log from Sun Jan 26 23:19:58 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Chimera-Image/Overview_mrc.cxs"
Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel
0.832, shown at level 0.0526, step 1, values float32
Log from Sun Jan 26 22:49:43 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Chimera-Image/Overview_mrc.cxs"
Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel
0.832, shown at level 0.0623, step 1, values float32
Log from Sun Jan 26 22:19:26 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Chimera-Image/side_view_1.cxs"
Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel
0.832, shown at level 0.0623, step 1, values float32
Log from Sun Jan 26 22:02:04 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Chimera-Image/Overview_mrc.cxs"
Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel
0.832, shown at level 0.0914, step 1, values float32
Log from Mon Jan 13 14:04:48 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Chimera-Image/Overview_Helix_fixed.cxs"
Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel
0.832, shown at level 0.0599, step 1, values float32
Log from Sun Jan 12 22:11:30 2025 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/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Model_building_Mac/P2_J74_map_flipped_nosharp.mrc"
Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel
0.832, shown at level 0.0599, step 1, values float32
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-16.pdb"
Chain information for P2_J73_map_flipped_nosharp-coot-16.pdb #2
---
Chain | Description
A | No description available
B C D | No description available
> set bgColor white
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> lighting soft
> lighting full
> lighting soft
> color #1 #b2b2b280 models
> color #1 #b2b2b252 models
> ui mousemode right zoom
> ui tool show "Side View"
> hide #!1 models
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #2/C:24
Nothing selected
> select #2/C:240
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 24 atom styles
> select H
9145 atoms, 1108 residues, 1 model selected
> ~select
Nothing selected
> select H
9145 atoms, 1108 residues, 1 model selected
> delete sel
> select #2/C:240
11 atoms, 10 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
2 hydrogen bonds found
> select #2/C:240|#2/B:298
19 atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected
> show #!1 models
> view #2/C:240|#2/B:298
> graphis selection color black
Unknown command: graphis selection color black
> graphics selection color black
> color #1 #d6d6d6ff models
> color #1 #d6d6d646 models
> color #1 #76d6ffff models
> color #1 #76d6ff0f models
> color sel bychain
> select add #2
8922 atoms, 9075 bonds, 2 pseudobonds, 1108 residues, 2 models selected
> color sel bychain
> color sel byhetero
> view #2/C:240|#2/B:298
> select subtract #2
Nothing selected
> view #2/C:240|#2/B:298
> select #2/C:240|#2/B:298
19 atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected
> color #1 #76d6ff31 models
> color #1 #76d6ff49 models
> color #1 darkgrey models
> color #1 #a9a9a9de models
> color #1 #a9a9a93e models
> color #1 #a9a9a936 models
> color #1 #a9a9a935 models
> color #1 #a9a9a936 models
> lighting flat
[Repeated 1 time(s)]
> lighting soft
> hide #!1 models
> setattr #2/B:348-357 res ss_type 1
Assigning ss_type attribute to 10 items
> show #!1 models
> view #2/C:240|#2/B:298
> save "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Chimera-Image/240-298_SaltBridge.cxs"
> save "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Chimera-Image/240-298_SaltBridge.png" width 1020 height 778
> supersample 3
> lighting soft
[Repeated 1 time(s)]
> lighting flat
> lighting soft
> view #2
> hide #!1 models
> setattr #2/C:89-103res ss_type 1
Missing or invalid "attrValue" argument: Expected a text string
> setattr #2/C:89-103 res ss_type 1
Assigning ss_type attribute to 15 items
> setattr #2/C:108-120 res ss_type 1
Assigning ss_type attribute to 13 items
> show #!1 models
> select up
284 atoms, 284 bonds, 1 pseudobond, 35 residues, 2 models selected
> select up
4460 atoms, 4536 bonds, 1 pseudobond, 554 residues, 2 models selected
> select up
8922 atoms, 9075 bonds, 2 pseudobonds, 1108 residues, 2 models selected
> select up
8922 atoms, 9075 bonds, 2 pseudobonds, 1108 residues, 2 models selected
> select up
8922 atoms, 9075 bonds, 2 pseudobonds, 1108 residues, 4 models selected
> view #2
> save "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Chimera-Image/Overview_Helix_fixed.cxs"
——— End of log from Sun Jan 12 22:11:30 2025 ———
opened ChimeraX session
> close #2
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-18.pdb"
Chain information for P2_J73_map_flipped_nosharp-coot-18.pdb #2
---
Chain | Description
A | No description available
B C D | No description available
> color bychain
> setattr #5:90-101|#5:108-120|#5:293-310|#5:341-357|#5:313-331 res ss_type 1
Assigning ss_type attribute to 0 items
> setattr #2:90-101|#2:108-120|#2:293-310|#2:341-357|#2:313-331 res ss_type 1
Assigning ss_type attribute to 316 items
> hide #!1 models
> setattr #2:310-316|#2:293-312 res ss_type 0
Assigning ss_type attribute to 96 items
> setattr #2:297-304 res ss_type 0
Assigning ss_type attribute to 32 items
> setattr #2:297-304 res ss_type 1
Assigning ss_type attribute to 32 items
> setattr #2:297-304 res ss_type 0
Assigning ss_type attribute to 32 items
> setattr #2:297-303 res ss_type 1
Assigning ss_type attribute to 28 items
> setattr #2:329 res ss_type 1
Assigning ss_type attribute to 4 items
> setattr #2:329 res ss_type 1
Assigning ss_type attribute to 4 items
> setattr #2:330-331 res ss_type 0
Assigning ss_type attribute to 8 items
> setattr #2:330-334 res ss_type 0
Assigning ss_type attribute to 20 items
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/model and maps from Emily/InvEd79CL_C1.pdb"
Chain information for InvEd79CL_C1.pdb #3
---
Chain | Description
A C | No description available
B D | No description available
Computing secondary structure
> tile
2 models tiled
> select add #3
18446 atoms, 18608 bonds, 1124 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.48089,-0.4225,0.76827,61.224,-0.67867,0.37541,0.63125,-28.025,-0.55512,-0.82496,-0.10621,208.16
> view matrix models
> #3,-0.71647,-0.33539,-0.61171,301.29,0.39514,0.52754,-0.75204,-22.962,0.57493,-0.78052,-0.24544,102.8
> view matrix models
> #3,-0.75359,-0.60534,-0.25625,295.6,0.051562,0.3342,-0.94109,45.663,0.65532,-0.72241,-0.22064,87.416
> view matrix models
> #3,-0.75628,-0.63923,-0.13934,288.06,-0.059577,0.27938,-0.95833,63.177,0.65153,-0.71647,-0.24938,89.923
> view matrix models
> #3,0.30717,0.10181,0.94619,17.611,0.81457,0.48597,-0.31672,-101.71,-0.49207,0.86803,0.066344,41.029
> view matrix models
> #3,0.4214,0.16776,0.89122,5.4443,0.74905,0.4896,-0.44634,-83.517,-0.51122,0.85565,0.080661,42.714
> view matrix models
> #3,0.46047,0.25973,0.84882,-2.4988,0.6976,0.48544,-0.52698,-70.569,-0.54892,0.8348,0.042339,51.824
> view matrix models
> #3,0.35127,0.36487,0.86225,-1.6834,0.83813,0.28794,-0.46328,-73.71,-0.41732,0.88541,-0.20467,56.803
> view matrix models
> #3,0.59118,0.50311,0.63039,-16.548,0.61842,0.21898,-0.75472,-18.886,-0.51775,0.83602,-0.18168,69.086
> view matrix models
> #3,0.6299,0.38635,0.67377,-14.442,0.52605,0.42599,-0.73607,-28.974,-0.5714,0.81809,0.065093,53.444
> view matrix models
> #3,0.39001,0.14428,0.90944,8.961,0.79636,0.44299,-0.4118,-87.475,-0.46228,0.88484,0.057871,37.352
> view matrix models
> #3,0.35766,0.23924,0.90269,4.722,0.75911,0.48851,-0.43024,-85.915,-0.54391,0.83912,-0.0068889,55.456
> view matrix models
> #3,0.24448,0.32778,0.91257,7.685,0.68388,0.60891,-0.40192,-91.207,-0.68741,0.72235,-0.075295,86.235
> view matrix models
> #3,0.23012,0.36364,0.90267,6.9748,0.7258,0.55376,-0.40811,-90.16,-0.64827,0.74907,-0.1365,85.595
> color sel bychain
> setattr #2:82-84|#2:118-119 res ss_type 0
Assigning ss_type attribute to 20 items
> view matrix models
> #3,0.44735,0.67801,-0.58325,94.196,-0.053756,-0.63058,-0.77426,123.63,-0.89274,0.37772,-0.24565,152.12
> view matrix models
> #3,0.39568,0.84702,-0.35495,64.041,0.0047469,-0.38838,-0.92149,110.47,-0.91837,0.36293,-0.15769,147.92
> setattr #2:108-120 res ss_type 1
Assigning ss_type attribute to 52 items
> setattr #2:118 res ss_type 1
Assigning ss_type attribute to 4 items
> setattr #2:120 res ss_type 0
Assigning ss_type attribute to 4 items
> select subtract #3
Nothing selected
> hide #3 models
> setattr #2:341 res ss_type 0
Assigning ss_type attribute to 4 items
> show #3 models
> setattr #2:330 res ss_type 1
Assigning ss_type attribute to 4 items
> hide #3 models
> view #2
> close #3
> show #!1 models
> hide #!1 models
> show #!1 models
> select add #2
17967 atoms, 18121 bonds, 1108 residues, 1 model selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.79303,-0.59721,-0.12018,234.34,-0.60352,0.79706,0.021628,69.88,0.082877,0.089685,-0.99252,155.71
> view matrix models
> #2,-0.7841,-0.61773,-0.059968,262.12,-0.61213,0.78568,-0.089479,19.264,0.10239,-0.033453,-0.99418,156.55
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.87348,0.36279,0.32468,-15.966,-0.40507,0.9115,0.071283,-25.477,-0.27009,-0.19378,0.94313,39.423
> view matrix models
> #2,0.6866,0.68476,0.2443,-21.42,-0.71396,0.69849,0.048727,24.92,-0.13727,-0.20787,0.96848,26.179
> view matrix models
> #2,0.65914,0.68984,0.29944,-24.074,-0.70888,0.70287,-0.058842,33.294,-0.25106,-0.17348,0.9523,34.985
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.65914,0.68984,0.29944,-55.58,-0.70888,0.70287,-0.058842,94.601,-0.25106,-0.17348,0.9523,43.834
> view matrix models
> #2,-0.92993,-0.31103,0.1962,190.88,0.284,-0.94635,-0.15413,168.23,0.23362,-0.087606,0.96837,-10.543
> view matrix models
> #2,-0.69836,-0.69612,0.16648,210.81,0.68819,-0.71697,-0.11107,99.941,0.19668,0.037005,0.97977,-18.676
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.4353,0.87727,0.20226,-43.306,-0.8943,0.44722,-0.015047,131.4,-0.10365,-0.17433,0.97922,28.877
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.4353,0.87727,0.20226,-46.161,-0.8943,0.44722,-0.015047,136.54,-0.10365,-0.17433,0.97922,28.628
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.89932,0.21352,0.38161,124.06,-0.24576,-0.96862,-0.037207,208.96,0.36169,-0.12724,0.92357,-14.27
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.75647,-0.098997,-0.64649,87.199,-0.45219,0.63499,-0.62635,130.59,0.47252,0.76615,0.43559,-65.221
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map
P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms
average map value = 0.09697, steps = 124
shifted from previous position = 1.24
rotated from previous position = 12.3 degrees
atoms outside contour = 6623, contour level = 0.059907
Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to
P2_J74_map_flipped_nosharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99999996 0.00014108 0.00025768 186.33283726
-0.00014111 -0.99999998 -0.00013184 186.38559753
0.00025766 -0.00013188 0.99999998 -0.01152858
Axis -0.00015165 0.00008216 -0.99999999
Axis point 93.17299394 93.18622572 0.00000000
Rotation angle (degrees) 179.99191595
Shift along axis -0.00141580
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_Helix_fixed.cxs"
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_Helix_fixed.png" width 923 height 778 supersample 3
> set view z
Expected a keyword
> set view
Expected a keyword
> select subtract #2
Nothing selected
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_Helix_fixed.png" width 923 height 778 supersample 3
> view orient
[Repeated 2 time(s)]
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> view name p1
> view p1
> rainbow polymers palette pubugn
> undo
[Repeated 1 time(s)]
> color bychain
> preset "molecular surfaces" "chain id coloring (opaque)"
Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> hide #!2 models
> show #!2 models
> volume #1 level 0.05506
> color bychain
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide surfaces
> show atoms
[Repeated 1 time(s)]
> hide atoms
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map
P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms
average map value = 0.09696, steps = 88
shifted from previous position = 2.01
rotated from previous position = 9.62 degrees
atoms outside contour = 6092, contour level = 0.055057
Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to
P2_J74_map_flipped_nosharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99999995 0.00004038 0.00030409 186.33580992
-0.00004044 -0.99999998 -0.00019307 186.38795964
0.00030408 -0.00019309 0.99999995 -0.02269610
Axis -0.00023177 0.00015318 -0.99999996
Axis point 93.16979056 93.19209564 0.00000000
Rotation angle (degrees) 179.99768469
Shift along axis 0.00805974
> hide #!1 models
> show #!1 models
> select #2/B
4517 atoms, 4555 bonds, 277 residues, 1 model selected
> hbonds sel reveal true
245 hydrogen bonds found
> hide #!1 models
> view matrix models
> #2,0.59349,-0.78929,-0.15744,125.06,-0.0088879,-0.20203,0.97934,28.362,-0.8048,-0.57982,-0.12692,225.89
> view matrix models
> #2,0.57657,-0.8013,-0.15966,127.93,0.019451,-0.18189,0.98313,23.535,-0.81682,-0.56995,-0.089287,222.86
> show #!1 models
> fitmap #2 inMap #1
Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map
P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms
average map value = 0.09697, steps = 136
shifted from previous position = 0.742
rotated from previous position = 16.3 degrees
atoms outside contour = 6090, contour level = 0.055057
Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to
P2_J74_map_flipped_nosharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99999996 0.00013771 0.00023680 186.33626316
-0.00013773 -0.99999998 -0.00011738 186.38540532
0.00023678 -0.00011742 0.99999998 -0.01543045
Axis -0.00014211 0.00007568 -0.99999999
Axis point 93.17454990 93.18628654 0.00000000
Rotation angle (degrees) 179.99210925
Shift along axis 0.00305471
> select add #2
17967 atoms, 18121 bonds, 245 pseudobonds, 1108 residues, 3 models selected
> select subtract #2
4 models selected
> ui tool show "Side View"
> style stick
Changed 17967 atom styles
> color bypolymer
[Repeated 1 time(s)]
> color bychain
> style stick
Changed 17967 atom styles
> style stick
Changed 17967 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style sphere
Changed 17967 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style stick
Changed 17967 atom styles
> style stick
Changed 17967 atom styles
> color bychain
> color bfactor
17967 atoms, 1108 residues, 4 surfaces, atom bfactor range 30 to 262
> undo
> color zone #1 near #2 distance 4.99
[Repeated 1 time(s)]
> hide #!2 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.08011
> volume #1 level 0.1019
> show #!2 models
> hide #!2 models
> volume #1 level 0.1076
> lighting flat
> lighting full
> lighting soft
> lighting full
> lighting soft
> volume #1 level 0.11
> volume #1 level 0.09224
> show #!2 models
> ui mousemode right "translate selected models"
> select add #2
17967 atoms, 18121 bonds, 245 pseudobonds, 1108 residues, 2 models selected
> view matrix models
> #2,0.86091,-0.5002,0.09295,118.47,0.28124,0.31566,-0.90623,109.43,0.42396,0.80633,0.41243,-54.339
> view p1
> fitmap #2 inMap #1
Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map
P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms
average map value = 0.09697, steps = 48
shifted from previous position = 0.776
rotated from previous position = 0.00678 degrees
atoms outside contour = 9832, contour level = 0.092237
Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to
P2_J74_map_flipped_nosharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99999996 0.00013094 0.00023673 186.33597857
-0.00013100 -0.99999996 -0.00024792 186.40323872
0.00023669 -0.00024796 0.99999996 -0.00201516
Axis -0.00014291 0.00014145 -0.99999998
Axis point 93.17409266 93.19551819 0.00000000
Rotation angle (degrees) 179.99249607
Shift along axis 0.00175156
> fitmap #2 inMap #1
Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map
P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms
average map value = 0.09696, steps = 28
shifted from previous position = 0.00609
rotated from previous position = 0.0118 degrees
atoms outside contour = 9832, contour level = 0.092237
Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to
P2_J74_map_flipped_nosharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99999991 0.00013328 0.00040667 186.32680752
-0.00013342 -0.99999993 -0.00036541 186.41549141
0.00040662 -0.00036547 0.99999987 -0.00684003
Axis -0.00022742 0.00019991 -0.99999995
Axis point 93.16961923 93.20153329 0.00000000
Rotation angle (degrees) 179.99235953
Shift along axis 0.00173211
> fitmap #2 inMap #1
Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map
P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms
average map value = 0.09697, steps = 40
shifted from previous position = 0.0161
rotated from previous position = 0.0153 degrees
atoms outside contour = 9819, contour level = 0.092237
Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to
P2_J74_map_flipped_nosharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99999995 0.00014329 0.00027422 186.32188104
-0.00014332 -0.99999998 -0.00013440 186.39201925
0.00027419 -0.00013444 0.99999997 -0.01654028
Axis -0.00015957 0.00008319 -0.99999998
Axis point 93.16761954 93.18933375 0.00000000
Rotation angle (degrees) 179.99178926
Shift along axis 0.00231578
> hide #!2 models
> show #!2 models
> hide #!2 models
> view p1
> select add #1
17967 atoms, 18121 bonds, 245 pseudobonds, 1108 residues, 8 models selected
> show #!2 models
> view p1
> fitmap #2 inMap #1
Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map
P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms
average map value = 0.09697, steps = 52
shifted from previous position = 0.726
rotated from previous position = 0.0123 degrees
atoms outside contour = 9816, contour level = 0.092237
Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to
P2_J74_map_flipped_nosharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99999989 0.00014690 0.00043305 186.30481430
-0.00014701 -0.99999996 -0.00025432 186.40234758
0.00043301 -0.00025439 0.99999989 -0.01954564
Axis -0.00023840 0.00014279 -0.99999996
Axis point 93.15925756 93.19432790 0.00000000
Rotation angle (degrees) 179.99158024
Shift along axis 0.00174627
> fitmap #2 inMap #1
Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map
P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms
average map value = 0.09697, steps = 40
shifted from previous position = 0.0142
rotated from previous position = 0.00931 degrees
atoms outside contour = 9833, contour level = 0.092237
Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to
P2_J74_map_flipped_nosharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99999995 0.00014052 0.00029053 186.33155559
-0.00014057 -0.99999998 -0.00017639 186.39851600
0.00029050 -0.00017644 0.99999996 -0.01392357
Axis -0.00016815 0.00010450 -0.99999998
Axis point 93.17232811 93.19271049 0.00000000
Rotation angle (degrees) 179.99194762
Shift along axis 0.00207069
> fitmap #2 inMap #1
Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map
P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms
average map value = 0.09696, steps = 28
shifted from previous position = 0.00582
rotated from previous position = 0.0119 degrees
atoms outside contour = 9834, contour level = 0.092237
Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to
P2_J74_map_flipped_nosharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99999991 0.00013421 0.00040367 186.32795998
-0.00013435 -0.99999993 -0.00035125 186.41449296
0.00040361 -0.00035131 0.99999988 -0.00786976
Axis -0.00022575 0.00019272 -0.99999996
Axis point 93.17023895 93.20099055 0.00000000
Rotation angle (degrees) 179.99230615
Shift along axis 0.00173094
> select subtract #2
6 models selected
> select subtract #1
Nothing selected
> hide #!2 models
> volume #1 level 0.09143
> view p1
> view name p1
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_mrc.png" width 923 height 778 supersample 3
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_mrc.cxs"
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> surface dust #1 size 8.32
[Repeated 3 time(s)]
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> view p1
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_mrc.cxs"
——— End of log from Mon Jan 13 14:04:48 2025 ———
opened ChimeraX session
> view name p1
> view
> lighting shadows false
> volume #1 level 0.09143
> volume #1 level 0.06675
> volume #1 level 0.06011
> volume #1 level 0.08573
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> select add #2
17967 atoms, 18121 bonds, 245 pseudobonds, 1108 residues, 2 models selected
> hide sel atoms
> ~hbonds
> show #!1 models
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map
P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms
average map value = 0.09696, steps = 156
shifted from previous position = 0.633
rotated from previous position = 23.7 degrees
atoms outside contour = 9212, contour level = 0.085735
Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to
P2_J74_map_flipped_nosharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99999996 0.00013775 0.00023762 186.33969735
-0.00013778 -0.99999998 -0.00015605 186.39740178
0.00023760 -0.00015609 0.99999998 -0.01109390
Axis -0.00014227 0.00009354 -0.99999999
Axis point 93.17626917 93.19228265 0.00000000
Rotation angle (degrees) 179.99210671
Shift along axis 0.00201851
> color zone #1 near sel & #2 distance 4.99
> volume #1 level 0.06553
> volume #1 level 0.06391
> volume #1 level 0.0728
> volume #1 level 0.0623
> ui mousemode right zoom
> select subtract #2
4 models selected
> view name p1
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_mrc.cxs"
> view p1
> turn y 60
> view p1
> hide #!1 models
> turn y 90
> turn y -90
> show #!1 models
> hide #!1 models
> show #!1 models
> view p1
> turn y 60
> hide #!1 models
> select
> #1/b:270|#1/b:261-262|#1/b:217-218|#1/b:179|#1/a:270|#1/a:261-262|#1/a:217-218|#1/a:179|#1/a:175
Nothing selected
> select
> #2/b:270|#2/b:261-262|#2/b:217-218|#2/b:179|#2/a:270|#2/a:261-262|#2/a:217-218|#2/a:179|#2/a:175
246 atoms, 240 bonds, 13 residues, 1 model selected
> show sel cartoons
> show sel atoms
> view sel
> select H
9034 atoms, 1093 residues, 1 model selected
> delete sel
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
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 default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> show atoms
> hide atoms
> select
> #2/b:270|#2/b:261-262|#2/b:217-218|#2/b:179|#2/a:270|#2/a:261-262|#2/a:217-218|#2/a:179|#2/a:175
113 atoms, 107 bonds, 13 residues, 1 model selected
> show sel atoms
> transparency #2 50 cartoons/
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency #2 50 cartoons
> view sel
> transparency #2 0 cartoons
> view sel
> ui tool show "Side View"
> show #!1 models
> turn y -60
> view p1
> turn y 60
> view p1
> turn y 50
> view sel
> hide #!1 models
> show #!1 models
> view p1
> turn y 45
> view sel
> hide #!1 models
> view p1
> turn y 40
> view sel
> view p1
> view name p1
> turn y 40
> view name p2
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> view sel
[Repeated 4 time(s)]
> view name p3
> transparency #2 80 cartoons
> view name p3
> transparency #2 60 cartoons
> transparency #2 75cartoons
Missing or invalid "percent" argument: Expected a number
> transparency #2 75 cartoons
> view name p3
> hide #2/c|#2/d
> select #2/c|#2/d
4460 atoms, 4536 bonds, 554 residues, 1 model selected
> hide sel cartoons
> view name p3
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB-
> hydrophobic.cxs"
> size stickRadius +.1
Changed 9087 bond radii
> size stickRadius +.1
Changed 9087 bond radii
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB-
> hydrophobic-stick-thick.cxs"
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB-
> hydrophobic-stick-thick.png" width 938 height 879 supersample 3
> undo
[Repeated 1 time(s)]
> redo
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB-
> hydrophobic-stick-thick-1.png" width 938 height 879 supersample 3
> lighting flat
[Repeated 3 time(s)]
> lighting full
> lighting flat
> graphics silhouettes false
> select
> #2/b:270|#2/b:261-262|#2/b:217-218|#2/b:179|#2/a:270|#2/a:261-262|#2/a:217-218|#2/a:179|#2/a:175
113 atoms, 107 bonds, 13 residues, 1 model selected
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting simple
> lighting full
> transparency #2 80 cartoons
> transparency #2 90 cartoons
> transparency #2 85 cartoons
> transparency #2 60 cartoons
> transparency #2 75 cartoons
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB-
> hydrophobic-stick-thick-1.cxs"
> size stickRadius +.1
Changed 9087 bond radii
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB-
> hydrophobic-stick-thick-1.cxs"
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB-
> hydrophobic-stick-thick-1.png" width 938 height 879 supersample 3
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> transparency #2 60 cartoons
> view p3
[Repeated 1 time(s)]
> show #!1 models
> hide #!1 models
> view p3
> show #!1 models
> hide #!1 models
> view name p3
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB-
> hydrophobic-stick-thick-2.png" width 938 height 879 supersample 3
> transparency #2 80 cartoons
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB-
> hydrophobic-stick-thick-2.png" width 938 height 879 supersample 3
> show #!1 models
> view p2
> view p3
[Repeated 1 time(s)]
> turn y -40
> turn y 40
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/side_view_1.cxs"
——— End of log from Sun Jan 26 22:02:04 2025 ———
opened ChimeraX session
> view p2
> view p1
> view p4
Expected an objects specifier or a view name or a keyword
> view p4
Expected an objects specifier or a view name or a keyword
> view p3
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> view name p4
[Repeated 1 time(s)]
> turn y -30
> view p1
> undo
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> view p1
> undo
> lighting shadows false
> view p1
> undo
> view p4
[Repeated 2 time(s)]
> view p1
> view p3
> view p1
> turn y -15
> view p1
> undo
> view p1-1
Expected an objects specifier or a view name or a keyword
> view name p1-1
> view p4
> turn y -45
> view p1-1
> undo
> view p1-1
> turn y 40
> view p4
> undo
[Repeated 1 time(s)]
> redo
> view p4
> undo
> view name p4-2
> view p4
> view p4-2
> view p3
> view p4
> view p3
> view p4
> view p1
> view p1-1
> turn y 45
> view p3
> view p4
> view p3
> view p4-1
Expected an objects specifier or a view name or a keyword
> view p4-2
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_p4-2.png" width 938 height 879 supersample 3
> turn y -45
> turn y 40
> view p4
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_p4.png" width 938 height 879 supersample 3
> view p1
> view p1-1
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_p1-1.png" width 938 height 879 supersample 3
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_mrc.cxs"
——— End of log from Sun Jan 26 22:19:26 2025 ———
opened ChimeraX session
> volume #1 level 0.0526
> volume #1 level 0.06209
> volume #1 level 0.0526
> volume #1 level 0.04406
> volume #1 level 0.0526
> view p1-1
> undo
> view p1-1
> undo
> view p1-1
[Repeated 2 time(s)]
> view p3
> ui tool show "Side View"
> view p3
> hide #!1 models
> show #!1 models
> show #!2 models
> select add #2
8933 atoms, 9087 bonds, 1108 residues, 1 model selected
> select subtract #2
4 models selected
> select add #2
8933 atoms, 9087 bonds, 1108 residues, 1 model selected
> select subtract #2
4 models selected
> hide #!1 models
> select
> #2/b:270|#2/b:261-262|#2/b:217-218|#2/b:179|#2/a:270|#2/a:261-262|#2/a:217-218|#2/a:179|#2/a:175
113 atoms, 107 bonds, 13 residues, 1 model selected
> graphics selection color black
> graphics selection color green
> graphics selection color black
> view p4
> show #!1 models
> hide #!2 models
> show #!2 models
> volume #1 level 0.0526
> volume #1 level 0.06311
> view p1-1
> volume #1 level 0.05341
> view p1-1
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_p1-1-2.png" width 938 height 879 supersample 3
> view p4
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_p4-2.png" width 938 height 879 supersample 3
> hide #!2 models
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_p4-2.png" width 938 height 879 supersample 3
> view p1-1
> view p1
> view p1-1
> view p1
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_p1.png" width 938 height 879 supersample 3
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_mrc.cxs"
> view p5
Expected an objects specifier or a view name or a keyword
> turn x 90
> view name p5
[Repeated 1 time(s)]
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/p5-top_view.png" width 938 height 879 supersample 3
> volume #1 level 0.0526
[Repeated 1 time(s)]
> view p5
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_mrc.cxs"
——— End of log from Sun Jan 26 22:49:43 2025 ———
opened ChimeraX session
> lighting shadows true
> lighting flat
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/p5-top_view-1.png" width 1035 height 879 supersample 3
> view p4
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_p4-1.png" width 1035 height 879 supersample 3
> view p1-1
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
[Repeated 2 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_p1-1_1.png" width 1035 height 879 supersample 3
[Repeated 1 time(s)]
> view p1
> lighting soft
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_p1.png" width 1035 height 879 supersample 3
> view p4
> lighting soft
[Repeated 2 time(s)]
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_p4.png" width 1035 height 879 supersample 3
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_mrc.cxs"
> view p3
> show #!2 models
> hide #!1 models
> size stickRadius +.1
Changed 9087 bond radii
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB-
> hydrophobic-stick-thick-3.png" width 1035 height 879 supersample 3
> 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
> transparency #2 0 cartoons
> select
> #2/b:270|#2/b:261-262|#2/b:217-218|#2/b:179|#2/a:270|#2/a:261-262|#2/a:217-218|#2/a:179|#2/a:175
113 atoms, 107 bonds, 13 residues, 1 model selected
> show sel atoms
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
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 default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> select
> #2/b:270|#2/b:261-262|#2/b:217-218|#2/b:179|#2/a:270|#2/a:261-262|#2/a:217-218|#2/a:179|#2/a:175
113 atoms, 107 bonds, 13 residues, 1 model selected
> show sel atoms
> transparency #2 80 cartoons
> graphics silhouettes false
> lighting soft
[Repeated 2 time(s)]
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB-
> hydrophobic-stick-thick-3.png" width 1035 height 879 supersample 3
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB-
> hydrophobic_1.cxs"
> view p5
> show #!1 models
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> view p1-1
> lighting soft
> view p5
> graphics silhouettes false
> graphics silhouettes true
> vew p1-1
Unknown command: vew p1-1
> view p1-1
> lighting soft
[Repeated 2 time(s)]
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_mrc.cxs"
——— End of log from Sun Jan 26 23:19:58 2025 ———
opened ChimeraX session
> view p1-1
> view name p1
> turn y 45
> hide #!1 models
> show #!1 models
> hide #!2 models
> view p1
> turn y 45
> view p3
> hide #!1 models
> show #!2 models
> show #!1 models
> ui tool show "Side View"
> hide #!2 models
> view p3
> show #!2 models
> hide #!1 models
> view name p2-1
> view p2
> show #!1 models
> hide #!1 models
> show #!1 models
> view name p2-2
> view p2
[Repeated 1 time(s)]
> turn y -45
> view p1
> turn y 45
> select
> #2/b:270|#2/b:261-262|#2/b:217-218|#2/b:179|#2/a:270|#2/a:261-262|#2/a:217-218|#2/a:179|#2/a:175
113 atoms, 107 bonds, 13 residues, 1 model selected
> hide #!1 models
> view
> view sel
> view p2
> show #!1 models
> turn y -45
> view p1
> turn y 45
> hide #!1 models
> view sel
> view name p2-1
> show #!1 models
> hide #!1 models
> show #!1 models
> turn y -45
> hide #!1 models
> show #!1 models
> hide #!2 models
> view name p1
> turn y 45
> view name p2
> view p1
> turn x 90
> lighting soft
[Repeated 2 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> view name p3
> view p2
> view sel
> show #!2 models
> hide #!1 models
> view name p2-1
> show #!1 models
> hide #!2 models
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/Overview.cxs"
> view p1
> lighting soft
[Repeated 5 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> view name p1
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_p1.png" width 938 height 879 supersample 3
> turn y 45
> view name p2
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_p2.png" width 938 height 879 supersample 3
> view p3
> view name p3
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-
> Image/Overview_p3-topview.png" width 938 height 879 supersample 3
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/Overview.cxs"
——— End of log from Mon Jan 27 14:41:44 2025 ———
opened ChimeraX session
> view p1
> open /Users/liyanzhu/Downloads/cryosparc_P2_J77_004_volume_map.mrc
Opened cryosparc_P2_J77_004_volume_map.mrc as #3, grid size 224,224,224, pixel
0.832, shown at level 0.0661, step 1, values float32
> open /Users/liyanzhu/Downloads/cryosparc_P2_J135_map_locres.mrc
Opened cryosparc_P2_J135_map_locres.mrc as #4, grid size 224,224,224, pixel
0.832, shown at level 3.23, step 1, values float32
> hide #!1 models
> hide #!4 models
> ui tool show "Surface Color"
> color sample #3.1 map #4 palette
> 2,#0000ff:2.33,#00aaff:2.66,#00ffa9:3,#00ff00:3.33,#aaff00:3.66,#ffaa00:4,#ff0000
Map values for surface "surface": minimum 2.357, mean 2.615, maximum 3.303
> key blue:2.00 #00aaff:2.33 #00ffa9:2.66 lime:3.00 #aaff00:3.33 #ffaa00:3.66
> red:4.00 showTool true
> ui mousemode right "color key"
> key pos 0.77867,0.5034 size 0.0293152,0.253146
> show #!1 models
> view p1
> select add #2
8933 atoms, 9087 bonds, 1108 residues, 1 model selected
> select subtract #2
4 models selected
> select add #3
4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.96397,0.24652,0.099986,150.1,-0.064154,0.14934,-0.9867,183.29,-0.25817,-0.95756,-0.12814,225.38
> view matrix models
> #3,-0.96602,0.23887,0.098691,151.14,-0.064051,0.14868,-0.98681,183.35,-0.2504,-0.9596,-0.12832,224.86
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.96602,0.23887,0.098691,145.11,-0.064051,0.14868,-0.98681,183.83,-0.2504,-0.9596,-0.12832,224.19
> view matrix models
> #3,-0.96602,0.23887,0.098691,147.84,-0.064051,0.14868,-0.98681,183.67,-0.2504,-0.9596,-0.12832,222.34
> view matrix models
> #3,-0.96602,0.23887,0.098691,157.82,-0.064051,0.14868,-0.98681,182.53,-0.2504,-0.9596,-0.12832,215.57
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.98553,0.065635,-0.15628,201.11,0.15561,-0.015247,-0.9877,177.42,-0.067211,-0.99773,0.0048132,188.82
> view matrix models
> #3,-0.8518,0.52387,0.00075561,130.35,0.00788,0.014255,-0.99987,189.65,-0.52381,-0.85168,-0.01627,219.85
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.8518,0.52387,0.00075561,126.96,0.00788,0.014255,-0.99987,190.54,-0.52381,-0.85168,-0.01627,213.59
> view matrix models
> #3,-0.8518,0.52387,0.00075561,122.41,0.00788,0.014255,-0.99987,190.63,-0.52381,-0.85168,-0.01627,213.93
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit map cryosparc_P2_J77_004_volume_map.mrc in map
P2_J74_map_flipped_nosharp.mrc using 112355 points
correlation = 0.999, correlation about mean = 0.9936, overlap = 2249
steps = 76, shift = 2.22, angle = 2.81 degrees
Position of cryosparc_P2_J77_004_volume_map.mrc (#3) relative to
P2_J74_map_flipped_nosharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.46804955 0.88370223 -0.00005218 54.45417383
0.88370222 0.46804956 0.00012372 -32.78150145
0.00013375 0.00001180 -0.99999998 185.28762784
Axis -0.51572078 -0.85675672 -0.00004797
Axis point 37.08755750 0.00000000 92.64645560
Rotation angle (degrees) 179.99378296
Shift along axis -0.00626472
> view p1
> hide #!1 models
> view matrix models
> #3,-0.86002,0.50914,0.033906,114.11,-0.037083,0.0039095,-0.9993,194.77,-0.50892,-0.86068,0.015518,212.89
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/local_res.png"
> width 985 height 879 supersample 3
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/local_res.cxs"
——— End of log from Wed Jan 29 13:58:14 2025 ———
opened ChimeraX session
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Model_building_Mac/P2_J174_map_flipped_nosharp.mrc"
Opened P2_J174_map_flipped_nosharp.mrc as #6, grid size 224,224,224, pixel
0.832, shown at level 0.0255, step 1, values float32
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-36.pdb"
Chain information for P2_J73_map_flipped_nosharp-coot-36.pdb #7
---
Chain | Description
A | No description available
B C D | No description available
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/liyanzhu/Downloads/cryosparc_P2_J178_map_locres.mrc
Opened cryosparc_P2_J178_map_locres.mrc as #8, grid size 224,224,224, pixel
0.832, shown at level 2.77, step 1, values float32
> hide #7 models
> show #7 models
> hide #7 models
> view p1
> volume flip #8
Opened cryosparc_P2_J178_map_locres.mrc z flip as #9, grid size 224,224,224,
pixel 0.832, shown at step 1, values float32
> close #8
> ui tool show "Surface Color"
> color sample #6.1 map #9 palette
> 2,#0000ff:2.33,#00aaff:2.66,#00ffa9:3,#00ff00:3.33,#aaff00:3.66,#ffaa00:4,#ff0000
Map values for surface "surface": minimum 0.1247, mean 2.481, maximum 3.159
Map values for surface "cap near": minimum 2.689, mean 2.761, maximum 2.922
> hide #!9 models
> select add #6
3 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.99169,-0.086803,0.094912,0.68667,-0.10199,-0.081116,0.99147,24.839,-0.078364,-0.99292,-0.089295,193.66
> view matrix models
> #6,0.93262,-0.34975,0.088862,31.215,-0.11896,-0.065481,0.99074,25.026,-0.34069,-0.93455,-0.10267,213.82
> view matrix models
> #6,0.93792,-0.34345,-0.048382,41.956,0.013996,-0.1019,0.9947,15.69,-0.34656,-0.93363,-0.090768,213.25
> ui tool show "Side View"
> view matrix models
> #6,0.92429,-0.3662,0.10761,31.908,-0.10169,0.035484,0.99418,13.713,-0.36789,-0.92986,-0.0044427,207.45
> view matrix models
> #6,0.82143,-0.57019,0.011748,68.76,-0.048041,-0.048654,0.99766,16.254,-0.56828,-0.82007,-0.067358,221.32
> view matrix models
> #6,0.82588,-0.56302,0.030677,66.047,-0.049261,-0.017848,0.99863,13.414,-0.5617,-0.82625,-0.042475,219.14
> view matrix models
> #6,0.83721,-0.54607,0.029765,63.49,-0.054485,-0.029131,0.99809,14.998,-0.54416,-0.83723,-0.054141,219.53
> view matrix models
> #6,0.83839,-0.54453,0.024098,63.725,-0.047706,-0.029266,0.99843,14.35,-0.54297,-0.83823,-0.050513,219.2
> view matrix models
> #6,0.84841,-0.52808,-0.036468,66.475,0.024323,-0.029929,0.99926,7.6286,-0.52877,-0.84867,-0.012547,215.58
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.84841,-0.52808,-0.036468,59.956,0.024323,-0.029929,0.99926,6.9834,-0.52877,-0.84867,-0.012547,219.46
> view matrix models
> #6,0.84841,-0.52808,-0.036468,57.99,0.024323,-0.029929,0.99926,8.0521,-0.52877,-0.84867,-0.012547,216.59
> ui tool show "Fit in Map"
> fitmap #6 inMap #1
Fit map P2_J174_map_flipped_nosharp.mrc in map P2_J74_map_flipped_nosharp.mrc
using 112357 points
correlation = 0.9985, correlation about mean = 0.9916, overlap = 949.3
steps = 120, shift = 8.58, angle = 0.565 degrees
Position of P2_J174_map_flipped_nosharp.mrc (#6) relative to
P2_J74_map_flipped_nosharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999862 0.00165371 -0.00017055 -0.12699015
-0.00165369 0.99999863 0.00011089 0.14531308
0.00017074 -0.00011060 0.99999997 -0.11813288
Axis -0.06646642 -0.10241739 -0.99251846
Axis point 94.67450911 72.41668611 0.00000000
Rotation angle (degrees) 0.09546420
Shift along axis 0.11080706
> fitmap #6 inMap #1
Fit map P2_J174_map_flipped_nosharp.mrc in map P2_J74_map_flipped_nosharp.mrc
using 112357 points
correlation = 0.9985, correlation about mean = 0.9917, overlap = 949.3
steps = 44, shift = 0.0224, angle = 0.00655 degrees
Position of P2_J174_map_flipped_nosharp.mrc (#6) relative to
P2_J74_map_flipped_nosharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999861 0.00166495 -0.00005916 -0.16008130
-0.00166494 0.99999861 0.00008806 0.14679624
0.00005931 -0.00008796 0.99999998 -0.10969143
Axis -0.05275353 -0.03550751 -0.99797609
Axis point 90.49523166 92.65251344 0.00000000
Rotation angle (degrees) 0.09558775
Shift along axis 0.11270191
> undo
> view p1
> hide #!3 models
> show #!1 models
> view matrix models
> #6,0.84841,-0.52808,-0.036468,66.787,0.024323,-0.029929,0.99926,7.6268,-0.52877,-0.84867,-0.012547,218.68
> view matrix models
> #6,0.84841,-0.52808,-0.036468,65.694,0.024323,-0.029929,0.99926,7.6973,-0.52877,-0.84867,-0.012547,217.6
> fitmap #6 inMap #1
Fit map P2_J174_map_flipped_nosharp.mrc in map P2_J74_map_flipped_nosharp.mrc
using 112357 points
correlation = 0.9985, correlation about mean = 0.9917, overlap = 949.3
steps = 72, shift = 2.26, angle = 0.57 degrees
Position of P2_J174_map_flipped_nosharp.mrc (#6) relative to
P2_J74_map_flipped_nosharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999861 0.00166482 0.00007526 -0.16995416
-0.00166481 0.99999861 -0.00005945 0.15898106
-0.00007536 0.00005933 0.99999998 -0.11068197
Axis 0.03561515 0.04516166 -0.99834462
Axis point 92.37975471 104.55095468 0.00000000
Rotation angle (degrees) 0.09554496
Shift along axis 0.11162565
> hide #!1 models
> view p1
> key blue:2.00 #00aaff:2.33 #00ffa9:2.66 lime:3.00 #aaff00:3.33 #ffaa00:3.66
> red:4.00 showTool true
> ui mousemode right "color key"
> ui mousemode right "translate selected models"
> ui mousemode right 'color key'
> key pos 0.795206,0.540049 size 0.0465094,0.267371
> key blue:2.00 #00aaff:2.33 #00ffa9:2.66 lime:3.00 #aaff00:3.33 #ffaa00:3.66
> red:4.00 showTool true
> key fontSize 25
> key fontSize 26
> ui mousemode right "color key"
> show #7 models
> hide #7 models
> close #7
> close #1
> close #2
> close #3
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/local_res.cxs"
> close #4
> save "/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/local_res.cxs"
——— End of log from Mon Feb 3 16:57:41 2025 ———
opened ChimeraX session
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> ui tool show "Surface Color"
> color single #6.1
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-36.pdb"
Chain information for P2_J73_map_flipped_nosharp-coot-36.pdb #1
---
Chain | Description
A | No description available
B C D | No description available
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui mousemode right "rotate selected models"
> close #9
> close #5
> select add #6
3 models selected
> view matrix models
> #6,0.81695,-0.57576,-0.03297,73.543,0.0038903,-0.051667,0.99866,11.595,-0.57669,-0.81599,-0.039969,219.27
> undo
> select subtract #6
Nothing selected
> select add #1
9334 atoms, 9499 bonds, 1148 residues, 1 model selected
> view matrix models
> #1,0.91831,-0.38727,-0.082069,50.634,-0.017246,-0.24625,0.96905,33.887,-0.39549,-0.88847,-0.23281,225.48
> ui tool show "Fit in Map"
> fitmap #1 inMap #6
Fit molecule P2_J73_map_flipped_nosharp-coot-36.pdb (#1) to map
P2_J174_map_flipped_nosharp.mrc (#6) using 9334 atoms
average map value = 0.05463, steps = 144
shifted from previous position = 0.604
rotated from previous position = 15.1 degrees
atoms outside contour = 2140, contour level = 0.025469
Position of P2_J73_map_flipped_nosharp-coot-36.pdb (#1) relative to
P2_J174_map_flipped_nosharp.mrc (#6) coordinates:
Matrix rotation and translation
0.99999999 -0.00014252 -0.00005834 0.02670625
0.00014251 0.99999999 -0.00007736 -0.00783315
0.00005835 0.00007735 1.00000000 -0.01950950
Axis 0.44887923 -0.33857885 0.82696541
Axis point 58.53060814 192.08823093 0.00000000
Rotation angle (degrees) 0.00987411
Shift along axis -0.00149366
> color sel bychain
> color zone #6 near sel & #1 distance 4.99
> lighting soft
> select subtract #1
Nothing selected
> select add #6
3 models selected
> lighting soft
> select subtract #6
Nothing selected
> ui mousemode right zoom
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> view p1
> turn y 180
> ui tool show "Side View"
> hide #1 models
> show #1 models
> hide #!6 models
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> lighting simple
> graphics silhouettes false
> lighting simple
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #1 models
> view #1
No displayed objects specified.
> view #6
> turn y 180
> hide #!6 models
> show #!6 models
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting soft
> ui tool show "Side View"
> show #1 models
> hide #1 models
> view name p1
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-32.pdb"
Chain information for P2_J73_map_flipped_nosharp-coot-32.pdb #2
---
Chain | Description
A | No description available
B C D | No description available
18 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #2
18910 atoms, 19075 bonds, 1148 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.78025,-0.60909,0.14217,64.817,0.15091,-0.037257,-0.98784,167.02,0.60699,0.79222,0.062849,-49.665
> close #2
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-30.pdb"
Chain information for P2_J73_map_flipped_nosharp-coot-30.pdb #2
---
Chain | Description
A | No description available
B C D | No description available
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #2
18438 atoms, 18603 bonds, 1148 residues, 1 model selected
> view matrix models
> #2,0.58535,-0.78332,-0.20923,129.11,-0.23243,0.085108,-0.96888,189.45,0.77675,0.61577,-0.13225,-32.323
> close #2
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-29.pdb"
Chain information for P2_J73_map_flipped_nosharp-coot-29.pdb #2
---
Chain | Description
A | No description available
B C D | No description available
> select add #2
18090 atoms, 18251 bonds, 1108 residues, 1 model selected
> view matrix models
> #2,0.37087,-0.89771,0.23785,121.33,-0.27102,0.14034,0.95229,23.188,-0.88826,-0.41764,-0.19125,223.55
> view matrix models
> #2,0.9576,0.14494,0.249,-30.811,-0.27797,0.23759,0.93074,16.681,0.075738,-0.96049,0.26781,144.62
> view matrix models
> #2,0.88546,-0.30216,0.35307,8.3731,-0.22828,0.37895,0.89682,1.8743,-0.40477,-0.8747,0.26657,181.56
> view matrix models
> #2,0.92256,0.14227,-0.35866,24.794,0.33634,0.15902,0.92822,-33.073,0.18909,-0.97697,0.09885,150.07
> view matrix models
> #2,0.92004,0.16808,-0.35394,22.236,0.35263,0.038633,0.93497,-24.027,0.17083,-0.98502,-0.023727,163.02
> view matrix models
> #2,0.93243,-0.061064,-0.35616,42.482,0.3491,0.40676,0.8442,-49.991,0.09332,-0.91149,0.40059,127.06
> view matrix models
> #2,0.91515,0.11004,-0.38781,30.968,0.38697,0.02978,0.92161,-25.263,0.11297,-0.99348,-0.01533,168.48
> view matrix models
> #2,0.92393,0.3579,-0.13512,-14.456,0.25944,-0.32663,0.90885,20.706,0.28114,-0.87477,-0.39464,174.33
> view matrix models
> #2,0.91489,0.38729,0.11394,-37.686,0.071627,-0.43347,0.89831,49,0.3973,-0.8137,-0.42432,160.4
> view matrix models
> #2,0.86353,0.2137,-0.45677,32.095,0.46825,-0.0035269,0.88359,-26.494,0.18721,-0.97689,-0.10311,167.55
> view matrix models
> #2,0.91162,-0.37785,-0.16178,57.08,0.14549,-0.071496,0.98677,1.028,-0.38442,-0.9231,-0.010204,207.87
> ui tool show "Fit in Map"
> fitmap #2 inMap #6
Fit molecule P2_J73_map_flipped_nosharp-coot-29.pdb (#2) to map
P2_J174_map_flipped_nosharp.mrc (#6) using 18090 atoms
average map value = 0.04209, steps = 108
shifted from previous position = 1.09
rotated from previous position = 11.6 degrees
atoms outside contour = 6535, contour level = 0.025469
Position of P2_J73_map_flipped_nosharp-coot-29.pdb (#2) relative to
P2_J174_map_flipped_nosharp.mrc (#6) coordinates:
Matrix rotation and translation
0.99999838 -0.00179014 -0.00019667 0.16787808
0.00179023 0.99999831 0.00042909 -0.21809681
0.00019590 -0.00042944 0.99999989 0.12973477
Axis -0.23186240 -0.10602232 0.96695351
Axis point 115.43481350 107.87604664 0.00000000
Rotation angle (degrees) 0.10607560
Shift along axis 0.10964600
> view p1
> ui mousemode right zoom
> select subtract #2
Nothing selected
> hide #2 models
> show #2 models
> hide #!6 models
> color #2 bychain
> show #!6 models
> hide #!6 models
> save /Users/liyanzhu/Desktop/Screenshot-p1-cartoon-1.png width 973 height
> 879 supersample 3
> show #!6 models
> lighting soft
> hide #!6 models
> show #!6 models
> hide #2 models
> hide #!6 models
> show #2 models
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> show #!6 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> turn x 90
> hide #!6 models
> show #!6 models
> view p1
> turn x 90
> hide #2 models
> ui tool show "Side View"
> hide #!6 models
> show #2 models
> hide #2 models
> show #!6 models
> show #2 models
> hide #!6 models
> show #!6 models
> volume zone #6 nearAtoms #2/B,A range 2.5
> hide #2 models
> color zone #6 near #2/B,A distance 2.5
> volume zone #6 nearAtoms #2/B,A range 2.9
> select ~sel & ##selected
Nothing selected
> volume zone #6 nearAtoms #2/B,A range 3
> color zone #6 near #2/B,A distance 3
> view p2
> surface dust #6 size 8.32
> volume zone #6 nearAtoms #2/B,A range 3
> color zone #6 near #2/B,A distance 3
> color zone #6 near #2/B,A distance 3.5
> volume zone #6 nearAtoms #2/B,A range 3.5
> volume zone #6 nearAtoms #2/B,A range 3.2
> volume zone #6 nearAtoms #2/B,A range 3.3
> volume zone #6 nearAtoms #2/B,A range 3.2
> volume #6 level 0.02616
> volume zone #6 nearAtoms #2/B,A range 3
> volume zone #6 nearAtoms #2/B,A range 3.1
> volume #6 level 0.0272
> volume #6 level 0.02651
===== 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
> open "/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan
> Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-36.pdb"
Chain information for P2_J73_map_flipped_nosharp-coot-36.pdb #1
---
Chain | Description
A | No description available
B C D | No description available
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
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 Air
Model Identifier: Mac14,15
Model Number: Z18S000LPLL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5 (22G74)
Kernel Version: Darwin 22.6.0
Time since boot: 13 days, 14 hours, 47 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2880 x 1864 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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 , 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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