![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17558 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-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x000000020d030c80 (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.pdb_lib._load_libs, chimerax.surface._surface, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._imagingmath, lxml._elementpath, lxml.etree (total: 116)
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"uptime" : 210000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,12",
"coalitionID" : 9713,
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"captureTime" : "2025-05-06 14:38:09.8066 +0800",
"codeSigningMonitor" : 1,
"incident" : "83A3A1AC-4E67-48C4-AA60-F9C62CE58058",
"pid" : 66663,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-06 11:12:10.7233 +0800",
"procStartAbsTime" : 4926319738723,
"procExitAbsTime" : 5044574196843,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "0304A793-D291-B174-D326-F22CCB4C6004",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["selectedSiriLanguageIneligible","accessNotGranted","countryBillingIneligible","siriAssetIsNotReady","regionIneligible","selectedLanguageDoesNotMatchSelectedSiriLanguage","countryLocationIneligible","notOptedIn"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "6781FE31-4400-4296-8A53-A58C9EE1CDA3",
"wakeTime" : 460,
"sleepWakeUUID" : "14417F19-6A2B-4E1F-9B38-DFA7AFF8B975",
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"vmRegionInfo" : "0x8f0000081c0 is not in any region. Bytes after previous region: 9345848869313 Bytes before following region: 95726231060032\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000088f0000081c0","rawCodes":[1,150564373561792],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000088f0000081c0 -> 0x000008f0000081c0 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":66663},
"ktriageinfo" : "VM - (arg = 0x0) Page has error bit set\nCL - (arg = 0x0) cluster_pagein past EOF\nAPFS - (arg = 0x3b12001600200040) cluster_pagein() failed\nVM - (arg = 0x1900000016) Filesystem pagein returned an error in vnode_pagein\nVM - (arg = 0x0) Page has error bit set\n",
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.7G resident=0K(0%) swapped_out_or_unallocated=1.7G(100%)\nWritable regions: Total=3.4G written=22.4M(1%) resident=1799K(0%) swapped_out=20.7M(1%) unallocated=3.3G(99%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 896K 7 \nActivity Tracing 256K 1 \nCG image 1712K 45 \nColorSync 608K 32 \nCoreAnimation 3824K 148 \nCoreGraphics 96K 6 \nCoreServices 624K 2 \nCoreUI image data 4624K 47 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.5G 117 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 656K 41 \nStack 194.4M 42 \nStack Guard 56.0M 1 \nVM_ALLOCATE 248.5M 246 \nVM_ALLOCATE (reserved) 384.0M 5 reserved VM address space (unallocated)\n__AUTH 5486K 695 \n__AUTH_CONST 77.2M 942 \n__CTF 824 1 \n__DATA 36.5M 1157 \n__DATA_CONST 37.9M 1164 \n__DATA_DIRTY 2775K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 659.0M 218 \n__OBJC_RO 61.3M 1 \n__OBJC_RW 2391K 1 \n__TEXT 1.0G 1014 \n__TEXT (graphics) 292.7M 171 \n__TPRO_CONST 128K 2 \ndyld private memory 10.3M 84 \nmapped file 317.6M 75 \npage table in kernel 1799K 1 \nshared memory 3216K 26 \n=========== ======= ======= \nTOTAL 5.9G 6665 \nTOTAL, minus reserved VM space 5.6G 6665 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "7716f60e15e4c73a9ec5caae164f3269fd386287",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "67648e5334a82511f4acf879",
"factorPackIds" : {
},
"deploymentId" : 240000008
},
{
"rolloutId" : "60f8ddccefea4203d95cbeef",
"factorPackIds" : {
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"deploymentId" : 240000025
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],
"experiments" : [
{
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"experimentId" : "67f46b1a73932228c9baf274",
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}
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}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/suxining/Downloads/8wix.pdb1
8wix.pdb1 title:
Cryo-em structure of alligator haemoglobin In carbonmonoxy form [more info...]
Chain information for 8wix.pdb1
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
1.1/B 1.2/B | No description available
> info chains
chain id #1.1/A chain_id A
chain id #1.1/B chain_id B
chain id #1.2/A chain_id A
chain id #1.2/B chain_id B
> set bgColor white
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select #1.1/A
1209 atoms, 1187 bonds, 5 pseudobonds, 198 residues, 2 models selected
> color sel mistyrose
> select #1.1/B
1281 atoms, 1253 bonds, 5 pseudobonds, 210 residues, 2 models selected
> color sel thistle
> color sel mediumturquoise
> select #1.1/A
1209 atoms, 1187 bonds, 5 pseudobonds, 198 residues, 2 models selected
> color sel slateblue
> select #1.2/A
1209 atoms, 1187 bonds, 4 pseudobonds, 198 residues, 2 models selected
> color sel aquamarine
> color sel lightskyblue
> select #1.2/B
1281 atoms, 1253 bonds, 4 pseudobonds, 210 residues, 2 models selected
> color sel lightsteelblue
> color sel thistle
> select #1.1/A
1209 atoms, 1187 bonds, 5 pseudobonds, 198 residues, 2 models selected
> color sel plum
> color sel lightcoral
> color sel steelblue
> select #1.2/B
1281 atoms, 1253 bonds, 4 pseudobonds, 210 residues, 2 models selected
> select #1.2/A
1209 atoms, 1187 bonds, 4 pseudobonds, 198 residues, 2 models selected
> select #1.1/B
1281 atoms, 1253 bonds, 5 pseudobonds, 210 residues, 2 models selected
> color sel plum
> select #1.1/A
1209 atoms, 1187 bonds, 5 pseudobonds, 198 residues, 2 models selected
> color sel slateblue
> color sel steelblue
> select #1.1/B
1281 atoms, 1253 bonds, 5 pseudobonds, 210 residues, 2 models selected
> color sel seagreen
> select #1.2/A
1209 atoms, 1187 bonds, 4 pseudobonds, 198 residues, 2 models selected
> select #1.2/B
1281 atoms, 1253 bonds, 4 pseudobonds, 210 residues, 2 models selected
> color sel mediumturquoise
> color sel aquamarine
> color sel palegreen
> color #1.2 #7da977ff
> color #1.2 #89b983ff
> color #1.2 #6d9468ff
> color #1.2 #9fd798ff
> color #1.2 #8bd76cff
> color #1.2 #9cd773ff
> color #1.2 #9ad773ff
> color #1.2 #8dd76cff
> color #1.2 #89d772ff
> select #1.1/A
1209 atoms, 1187 bonds, 5 pseudobonds, 198 residues, 2 models selected
> color sel cornflowerblue
> select #1.1/B
1281 atoms, 1253 bonds, 5 pseudobonds, 210 residues, 2 models selected
> color sel tomato
> select #1.2/A
1209 atoms, 1187 bonds, 4 pseudobonds, 198 residues, 2 models selected
> color sel seagreen
> select #1.2/B
1281 atoms, 1253 bonds, 4 pseudobonds, 210 residues, 2 models selected
> color sel goldenrod
> select ligand
176 atoms, 188 bonds, 8 residues, 2 models selected
> color byelement sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel byelement
> 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
> 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
> select #1.1/A
1209 atoms, 1187 bonds, 5 pseudobonds, 198 residues, 2 models selected
> color sel Medium Orchid
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel #BA55D3
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> color sel #DA70D6
> color sel #FDE6F5
> color sel #DA70D6
> color sel #D494D4
> select #1.1/B
1281 atoms, 1253 bonds, 5 pseudobonds, 210 residues, 2 models selected
> color sel #3CB371
> color sel #9AD29A
> color sel #7EB77E
> select #1.2/A
1209 atoms, 1187 bonds, 4 pseudobonds, 198 residues, 2 models selected
> color sel #C6A77C
> select #1.2/B
1281 atoms, 1253 bonds, 4 pseudobonds, 210 residues, 2 models selected
> color sel lightsteelblue
> color sel lightskyblue
> color sel lsteelblue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel steelblue
> color #1.2 #628fb6ff
> color #1.2 #618eb6ff
> color #1.2 #6594beff
> select #1.2/A
1209 atoms, 1187 bonds, 4 pseudobonds, 198 residues, 2 models selected
> color sel #C6A77C
> lighting flat or adjust shininess 0.
Expected a keyword
> lighting flat or adjust shininess 0
Expected a keyword
> select #8wix.pdb1 group
Expected an objects specifier or a keyword
> select 8wix.pdb1 group
Expected an objects specifier or a keyword
> select all
4980 atoms, 4880 bonds, 18 pseudobonds, 816 residues, 5 models selected
> lighting soft or use ambient occlusion true
Expected a keyword
> set silhouettes true
> set silhouetteWidth 2
> lighting flat
> lighting soft
> shininess 0
Unknown command: shininess 0
> set ambientOcclusion false
Expected a keyword
> set depthCue false
Expected a keyword
> select all
4980 atoms, 4880 bonds, 18 pseudobonds, 816 residues, 5 models selected
> set depthCue false
Expected a keyword
> set ambientOcclusion false
Expected a keyword
> set shadows false
Expected a keyword
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel atoms
> hide sel atoms
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting soft
> lighting full
> ui tool show "Side View"
> set bgColor gray
> set bgColor white
> set bgColor black
> set bgColor white
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting flat
> lighting full
> select #1.2/A
1209 atoms, 1187 bonds, 4 pseudobonds, 198 residues, 2 models selected
> color sel #C6A77C
> show sel atoms
> hide sel atoms
> show ligand
> select ligand
176 atoms, 188 bonds, 8 residues, 2 models selected
> color sel byelement
> label /A text α1
> label #1.1/A text α1
> hide label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> label hide /A
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> undo
> redo
> ui mousemode right label
> label delete
> label #1.1/A text α1
> label delete
> label #1.1/B:3
> label #1.2/A:88
> label #1.2/A:96
> label delete
> ui mousemode right label
> label #1.2/A:37
> label delete
> ui mousemode right translate
> ui mousemode right select
Drag select of 8 residues
Drag select of 11 residues
Drag select of 13 residues
Drag select of 9 residues
Drag select of 17 residues
> save "/Users/suxining/Desktop/Fig 1 A.cxs"
Drag select of 17 residues
> ui mousemode right translate
> label #1.1/A text α1 2dlabel create text "α1 subunit" xpos 0.2 ypos 0.8
> color hotpink
Expected a keyword
> save /Users/suxining/Desktop/HbAM_clean.png supersample 3
> ui mousemode right rotate
> zoom
Pixel size at center of rotation is 0.122
> zoom
Pixel size at center of rotation is 0.119
> zoom
Pixel size at center of rotation is 0.113
> zoom
Pixel size at center of rotation is 0.113
> ui mousemode right translate
> save /Users/suxining/Desktop/HbAM_clean.png supersample 3
> ui mousemode right select
> ~select
Nothing selected
> save /Users/suxining/Desktop/HbAM_clean.png supersample 3
> open "/Users/suxining/Desktop/Fig 1 A.cxs"
opened ChimeraX session
Drag select of 12 residues
Drag select of 4 atoms, 10 residues, 4 bonds
Drag select of 6 residues
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/suxining/Desktop/Fig 1 A.cxs"
Log from Tue May 6 14:21:09 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/suxining/Downloads/8wix.pdb1
8wix.pdb1 title:
Cryo-em structure of alligator haemoglobin In carbonmonoxy form [more info...]
Chain information for 8wix.pdb1
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
1.1/B 1.2/B | No description available
> info chains
chain id #1.1/A chain_id A
chain id #1.1/B chain_id B
chain id #1.2/A chain_id A
chain id #1.2/B chain_id B
> set bgColor white
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select #1.1/A
1209 atoms, 1187 bonds, 5 pseudobonds, 198 residues, 2 models selected
> color sel mistyrose
> select #1.1/B
1281 atoms, 1253 bonds, 5 pseudobonds, 210 residues, 2 models selected
> color sel thistle
> color sel mediumturquoise
> select #1.1/A
1209 atoms, 1187 bonds, 5 pseudobonds, 198 residues, 2 models selected
> color sel slateblue
> select #1.2/A
1209 atoms, 1187 bonds, 4 pseudobonds, 198 residues, 2 models selected
> color sel aquamarine
> color sel lightskyblue
> select #1.2/B
1281 atoms, 1253 bonds, 4 pseudobonds, 210 residues, 2 models selected
> color sel lightsteelblue
> color sel thistle
> select #1.1/A
1209 atoms, 1187 bonds, 5 pseudobonds, 198 residues, 2 models selected
> color sel plum
> color sel lightcoral
> color sel steelblue
> select #1.2/B
1281 atoms, 1253 bonds, 4 pseudobonds, 210 residues, 2 models selected
> select #1.2/A
1209 atoms, 1187 bonds, 4 pseudobonds, 198 residues, 2 models selected
> select #1.1/B
1281 atoms, 1253 bonds, 5 pseudobonds, 210 residues, 2 models selected
> color sel plum
> select #1.1/A
1209 atoms, 1187 bonds, 5 pseudobonds, 198 residues, 2 models selected
> color sel slateblue
> color sel steelblue
> select #1.1/B
1281 atoms, 1253 bonds, 5 pseudobonds, 210 residues, 2 models selected
> color sel seagreen
> select #1.2/A
1209 atoms, 1187 bonds, 4 pseudobonds, 198 residues, 2 models selected
> select #1.2/B
1281 atoms, 1253 bonds, 4 pseudobonds, 210 residues, 2 models selected
> color sel mediumturquoise
> color sel aquamarine
> color sel palegreen
> color #1.2 #7da977ff
> color #1.2 #89b983ff
> color #1.2 #6d9468ff
> color #1.2 #9fd798ff
> color #1.2 #8bd76cff
> color #1.2 #9cd773ff
> color #1.2 #9ad773ff
> color #1.2 #8dd76cff
> color #1.2 #89d772ff
> select #1.1/A
1209 atoms, 1187 bonds, 5 pseudobonds, 198 residues, 2 models selected
> color sel cornflowerblue
> select #1.1/B
1281 atoms, 1253 bonds, 5 pseudobonds, 210 residues, 2 models selected
> color sel tomato
> select #1.2/A
1209 atoms, 1187 bonds, 4 pseudobonds, 198 residues, 2 models selected
> color sel seagreen
> select #1.2/B
1281 atoms, 1253 bonds, 4 pseudobonds, 210 residues, 2 models selected
> color sel goldenrod
> select ligand
176 atoms, 188 bonds, 8 residues, 2 models selected
> color byelement sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel byelement
> 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
> 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
> select #1.1/A
1209 atoms, 1187 bonds, 5 pseudobonds, 198 residues, 2 models selected
> color sel Medium Orchid
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel #BA55D3
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> color sel #DA70D6
> color sel #FDE6F5
> color sel #DA70D6
> color sel #D494D4
> select #1.1/B
1281 atoms, 1253 bonds, 5 pseudobonds, 210 residues, 2 models selected
> color sel #3CB371
> color sel #9AD29A
> color sel #7EB77E
> select #1.2/A
1209 atoms, 1187 bonds, 4 pseudobonds, 198 residues, 2 models selected
> color sel #C6A77C
> select #1.2/B
1281 atoms, 1253 bonds, 4 pseudobonds, 210 residues, 2 models selected
> color sel lightsteelblue
> color sel lightskyblue
> color sel lsteelblue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel steelblue
> color #1.2 #628fb6ff
> color #1.2 #618eb6ff
> color #1.2 #6594beff
> select #1.2/A
1209 atoms, 1187 bonds, 4 pseudobonds, 198 residues, 2 models selected
> color sel #C6A77C
> lighting flat or adjust shininess 0.
Expected a keyword
> lighting flat or adjust shininess 0
Expected a keyword
> select #8wix.pdb1 group
Expected an objects specifier or a keyword
> select 8wix.pdb1 group
Expected an objects specifier or a keyword
> select all
4980 atoms, 4880 bonds, 18 pseudobonds, 816 residues, 5 models selected
> lighting soft or use ambient occlusion true
Expected a keyword
> set silhouettes true
> set silhouetteWidth 2
> lighting flat
> lighting soft
> shininess 0
Unknown command: shininess 0
> set ambientOcclusion false
Expected a keyword
> set depthCue false
Expected a keyword
> select all
4980 atoms, 4880 bonds, 18 pseudobonds, 816 residues, 5 models selected
> set depthCue false
Expected a keyword
> set ambientOcclusion false
Expected a keyword
> set shadows false
Expected a keyword
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting soft
> lighting full
> ui tool show "Side View"
> set bgColor gray
> set bgColor white
> set bgColor black
> set bgColor white
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting flat
> lighting full
> select #1.2/A
1209 atoms, 1187 bonds, 4 pseudobonds, 198 residues, 2 models selected
> color sel #C6A77C
> show sel atoms
[Repeated 2 time(s)]
> hide sel atoms
> show ligand
> select ligand
176 atoms, 188 bonds, 8 residues, 2 models selected
> color sel byelement
> label /A text α1
> label #1.1/A text α1
> hide label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> label hide /A
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> undo
> redo
> ui mousemode right label
[Repeated 2 time(s)]
> label delete
> label #1.1/A text α1
> label delete
> label #1.1/B:3
> label #1.2/A:88
> label #1.2/A:96
> label delete
> ui mousemode right label
> label #1.2/A:37
> label delete
> ui mousemode right translate
> ui mousemode right select
Drag select of 8 residues
Drag select of 11 residues
Drag select of 13 residues
Drag select of 9 residues
Drag select of 17 residues
> save "/Users/suxining/Desktop/Fig 1 A.cxs"
——— End of log from Tue May 6 14:21:09 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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: Mac15,12
Model Number: MXCR3CH/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 8 days, 10 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
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: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2423DE:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 6 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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