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Opened 9 months ago
Closed 9 months ago
#16777 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2.1-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
Thread 0x00000002a307f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a2073000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a1067000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a005b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029f04f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029e043000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029d037000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029c02b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029b01f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029a013000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000299007000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001df079000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 54)
{"app_name":"ChimeraX","timestamp":"2025-02-03 17:24:02.00 -0800","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.2.1 (23C71)","roots_installed":0,"name":"ChimeraX","incident_id":"BEFC59E5-9C36-4F68-BF25-4181A632FA42"}
{
"uptime" : 870000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 486399,
"osVersion" : {
"train" : "macOS 14.2.1",
"build" : "23C71",
"releaseType" : "User"
},
"captureTime" : "2025-02-03 17:23:47.7893 -0800",
"codeSigningMonitor" : 1,
"incident" : "BEFC59E5-9C36-4F68-BF25-4181A632FA42",
"pid" : 64934,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-03 13:20:09.2780 -0800",
"procStartAbsTime" : 20717650046069,
"procExitAbsTime" : 21068487960615,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"67A27C6A-1CA0-5ED5-B061-F2AE14B3FDF5","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4DA9A43F-AD37-F879-248F-454B9E13E2FB",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 15758,
"sleepWakeUUID" : "FACF4A1C-A213-4D1E-BB74-7F8270883148",
"sip" : "enabled",
"vmRegionInfo" : "0x48373aefa948 is not in any region. Bytes after previous region: 78921012848969 Bytes before following region: 26151067080376\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000048373aefa948","rawCodes":[1,79402049186120],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000048373aefa948"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":64934},
"vmregioninfo" : "0x48373aefa948 is not in any region. Bytes after previous region: 78921012848969 Bytes before following region: 26151067080376\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"size" : 49152,
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
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"size" : 3948544,
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
"name" : "Python",
"CFBundleVersion" : "3.11.4"
},
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
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"queue" : "com.apple.main-thread"
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"logWritingSignature" : "ee0b919f363481c22b5bfeff7565367bc6268c83",
"trialInfo" : {
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===== Log before crash start =====
Startup Messages
---
warning | QCoreApplication::postEvent: Unexpected null receiver
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
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/esthernguyen/Downloads/8qfs.pdb format pdb
No such file/path: /Users/esthernguyen/Downloads/8qfs.pdb
> open /Users/esthernguyen/Downloads/8sv8.pdb format pdb
No such file/path: /Users/esthernguyen/Downloads/8sv8.pdb
> open PDB ID 4UN3
'PDB' has no suffix
> open ID 4UN3
'ID' has no suffix
> open 4un3
Summary of feedback from opening 4un3 fetched from pdb
---
notes | Fetching compressed mmCIF 4un3 from http://files.rcsb.org/download/4un3.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
4un3 title:
Crystal structure of Cas9 bound to PAM-containing DNA target [more info...]
Chain information for 4un3 #1
---
Chain | Description | UniProt
A | SGRNA |
B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368
C | TARGET DNA STRAND |
D | NON-TARGET DNA STRAND |
Non-standard residues in 4un3 #1
---
MG — magnesium ion
> save
Missing or invalid "fileName" argument: Expected a file name
> save
Missing or invalid "fileName" argument: Expected a file name
> hide atoms
> show atoms
> hide atoms
> hide cartoons
> show cartoons
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
> select solvent
405 atoms, 405 residues, 1 model selected
> select solvent
405 atoms, 405 residues, 1 model selected
> select H
Nothing selected
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
> select H
Nothing selected
> show target ab
> hide target a
> set bgColor white
> hide target m
> show target m
> close
> close #
Expected a models specifier or a keyword
> open 4un3 format mmcif fromDatabase pdb
4un3 title:
Crystal structure of Cas9 bound to PAM-containing DNA target [more info...]
Chain information for 4un3 #1
---
Chain | Description | UniProt
A | SGRNA |
B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368
C | TARGET DNA STRAND |
D | NON-TARGET DNA STRAND |
Non-standard residues in 4un3 #1
---
MG — magnesium ion
> set bgColor black
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color plum
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> color red
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select /B:1239
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B:1240
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:1239
5 atoms, 4 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> color sel pink
> select clezr
Expected an objects specifier or a keyword
> select clear
> center
Unknown command: center
> select clear
> select all
13629 atoms, 13708 bonds, 140 pseudobonds, 1839 residues, 5 models selected
> center sel
Unknown command: center sel
> center sel
Unknown command: center sel
> show solvent
> delete solvent
> hydrogen
Unknown command: modelcif hydrogen
> set bgColor white
> ui tool show "Show Sequence Viewer"
> sequence chain /D
Alignment identifier is 1/D
> ui tool show "Show Sequence Viewer"
> color lightblue
> select chain a
Expected an objects specifier or a keyword
> select /A
1736 atoms, 1942 bonds, 48 pseudobonds, 85 residues, 3 models selected
> select /B
10694 atoms, 10877 bonds, 14 pseudobonds, 1310 residues, 3 models selected
> color sel light blue
> clear sel
Unknown command: clear sel
> clear
Unknown command: clear
> select clear
> select /B
10694 atoms, 10877 bonds, 14 pseudobonds, 1310 residues, 3 models selected
> color sel blue
> color sel orange
> delete sel
Undo failed, probably because structures have been modified.
> show /B
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> open new
'new' has no suffix
> open 4un3
4un3 title:
Crystal structure of Cas9 bound to PAM-containing DNA target [more info...]
Chain information for 4un3 #2
---
Chain | Description | UniProt
A | SGRNA |
B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368
C | TARGET DNA STRAND |
D | NON-TARGET DNA STRAND |
Non-standard residues in 4un3 #2
---
MG — magnesium ion
> close session
> open 4un3 format mmcif fromDatabase pdb
4un3 title:
Crystal structure of Cas9 bound to PAM-containing DNA target [more info...]
Chain information for 4un3 #1
---
Chain | Description | UniProt
A | SGRNA |
B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368
C | TARGET DNA STRAND |
D | NON-TARGET DNA STRAND |
Non-standard residues in 4un3 #1
---
MG — magnesium ion
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
> color sel orange
> clear sel
Unknown command: clear sel
> select cler
Expected an objects specifier or a keyword
> select clear
> hide cartoons
> show cartoons
> hide cartoons
> show cartoons
> select /A
1882 atoms, 1942 bonds, 58 pseudobonds, 231 residues, 3 models selected
> color sel blue
> clear sel
Unknown command: clear sel
> select clear
> select /C
578 atoms, 634 bonds, 39 residues, 1 model selected
> color sel pink
> color sel darkred pink
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel hot pink
> select clear
> select /D
229 atoms, 255 bonds, 13 residues, 1 model selected
> color sel green
> select clear
> hide /B
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
> hide sel
> hide sel cartoons
> undo
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> color /B orange
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> select solvent
405 atoms, 405 residues, 1 model selected
> select solvent
405 atoms, 405 residues, 1 model selected
> delete sel
> show atoms
> hide atoms
> show atoms
> hide atoms
> undo
> select H
Nothing selected
> select solvent
Nothing selected
> select /D
227 atoms, 255 bonds, 11 residues, 1 model selected
> select clear
> select H
Nothing selected
> ui tool show "Show Sequence Viewer"
> color /A pink
> color /A steelblue
> color /C yellow green
> color / D red
> ui tool show Distances
Exactly two atoms must be selected!
No distances to delete!
> ui tool show "Add Hydrogens"
> addh #!1
Summary of feedback from adding hydrogens to 4un3 #1
---
warnings | Not adding hydrogens to /A A 1 P because it is missing heavy-atom bond partners
Not adding hydrogens to /B LYS 797 CB because it is missing heavy-atom bond
partners
notes | Termini for 4un3 (#1) chain A determined from SEQRES records
Termini for 4un3 (#1) chain B determined from SEQRES records
Termini for 4un3 (#1) chain C determined from SEQRES records
Termini for 4un3 (#1) chain D determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /B LYS 4, /B THR 386, /B
SER 719, /B ASN 776, /B GLY 1030, /B LYS 1059, /B GLU 1253
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /B ASP 384, /B LYS 710, /B
ARG 765, /B ASP 1012, /B ILE 1050, /B HIS 1241, /B GLN 1364
Chain-initial residues that are not actual 5' termini: /A A 1, /D DA 2
1358 hydrogen bonds
Adding 'H' to /B LYS 4
Adding 'H' to /B THR 386
Adding 'H' to /B SER 719
Adding 'H' to /B ASN 776
Adding 'H' to /B GLY 1030
2 messages similar to the above omitted
/B GLN 1364 is not terminus, removing H atom from 'C'
/D DA 2 is not terminus, removing H atom from O5'
12183 hydrogens added
> ui tool show
Missing or invalid "toolName" argument: Expected a text string
> ui tool show "Show Sequence Viewer"
> ui tool show "Add Hydrogens"
> addh #!1
Summary of feedback from adding hydrogens to 4un3 #1
---
warnings | Not adding hydrogens to /A A 1 P because it is missing heavy-atom bond partners
Not adding hydrogens to /B LYS 797 CB because it is missing heavy-atom bond
partners
notes | Termini for 4un3 (#1) chain A determined from SEQRES records
Termini for 4un3 (#1) chain B determined from SEQRES records
Termini for 4un3 (#1) chain C determined from SEQRES records
Termini for 4un3 (#1) chain D determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /B LYS 4, /B THR 386, /B
SER 719, /B ASN 776, /B GLY 1030, /B LYS 1059, /B GLU 1253
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /B ASP 384, /B LYS 710, /B
ARG 765, /B ASP 1012, /B ILE 1050, /B HIS 1241, /B GLN 1364
Chain-initial residues that are not actual 5' termini: /A A 1, /D DA 2
1287 hydrogen bonds
/B GLN 1364 is not terminus, removing H atom from 'C'
/D DA 2 is not terminus, removing H atom from O5'
0 hydrogens added
> ui tool show H-Bonds
> hbonds sel reveal true
Atom specifier selects no atoms
> select /B
21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected
> ui tool show H-Bonds
> hbonds sel reveal true
1130 hydrogen bonds found
> select clear
> undo
Undo failed, probably because structures have been modified.
> hide atoms
> undo
> show atoms
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> delete all
> open 4un3 format mmcif fromDatabase pdb
4un3 title:
Crystal structure of Cas9 bound to PAM-containing DNA target [more info...]
Chain information for 4un3 #1
---
Chain | Description | UniProt
A | SGRNA |
B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368
C | TARGET DNA STRAND |
D | NON-TARGET DNA STRAND |
Non-standard residues in 4un3 #1
---
MG — magnesium ion
> select solvent
405 atoms, 405 residues, 1 model selected
> delete sel
Undo failed, probably because structures have been modified.
> select all
13224 atoms, 13708 bonds, 125 pseudobonds, 1434 residues, 5 models selected
> ui tool show "Add Hydrogens"
> addh #!1
Summary of feedback from adding hydrogens to 4un3 #1
---
warnings | Not adding hydrogens to /A A 1 P because it is missing heavy-atom bond partners
Not adding hydrogens to /B LYS 797 CB because it is missing heavy-atom bond
partners
notes | Termini for 4un3 (#1) chain A determined from SEQRES records
Termini for 4un3 (#1) chain B determined from SEQRES records
Termini for 4un3 (#1) chain C determined from SEQRES records
Termini for 4un3 (#1) chain D determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /B LYS 4, /B THR 386, /B
SER 719, /B ASN 776, /B GLY 1030, /B LYS 1059, /B GLU 1253
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /B ASP 384, /B LYS 710, /B
ARG 765, /B ASP 1012, /B ILE 1050, /B HIS 1241, /B GLN 1364
Chain-initial residues that are not actual 5' termini: /A A 1, /D DA 2
1358 hydrogen bonds
Adding 'H' to /B LYS 4
Adding 'H' to /B THR 386
Adding 'H' to /B SER 719
Adding 'H' to /B ASN 776
Adding 'H' to /B GLY 1030
2 messages similar to the above omitted
/B GLN 1364 is not terminus, removing H atom from 'C'
/D DA 2 is not terminus, removing H atom from O5'
12183 hydrogens added
> select all H
Expected a keyword
> select clear
> select hydrogen
Expected an objects specifier or a keyword
> select hydrogens
Expected an objects specifier or a keyword
> select H
12183 atoms, 1426 residues, 1 model selected
> select clear
> set bgColor black
> set bgColor white
> select /B
21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected
> color /B dark green
> select clear
> color /A dark magenta
> color /C orange
> color /D deep pink
> color /D deeppink blue
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color /D blue
> color /D cadet blue
> color /D dark blue
> color /C cadet blue
> hide /B
> show/B
Unknown command: show/B
> show /B
> hide /B
> hide cartoons
> show cartoons
> hide cartoons
> show cartoons
> hide cartoons
> show cartoons
> select /B
21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected
> hide sel
> select /B
21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected
> hide cartoons
> show sel cartoons
> select clear
> show sel cartoons
> select clear
> cartoon
> hide #!1 models
> show #!1 models
> select add #1
25407 atoms, 25891 bonds, 125 pseudobonds, 1434 residues, 5 models selected
> select subtract #1
Nothing selected
> select /B
21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected
> hide sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> select /C:17
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /C:17-22
193 atoms, 208 bonds, 6 residues, 1 model selected
> select /C:13
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /C:13-18
190 atoms, 204 bonds, 6 residues, 1 model selected
> select /C:6
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /C:6-11
188 atoms, 200 bonds, 6 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /D
Alignment identifier is 1/D
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /C:2
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /C:2-5
128 atoms, 138 bonds, 4 residues, 1 model selected
> select /C:5
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /C:5-7
92 atoms, 98 bonds, 3 residues, 1 model selected
> select /D:5
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /D:5-7
98 atoms, 105 bonds, 3 residues, 1 model selected
> select /C:10
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /C:10-19
318 atoms, 341 bonds, 10 residues, 1 model selected
> select /C:6
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /C:6-8
92 atoms, 98 bonds, 3 residues, 1 model selected
> select /D:5
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /D:5-7
98 atoms, 105 bonds, 3 residues, 1 model selected
> color sel red
> name sel "PAM"
"sel" is reserved and cannot be redefined
> select /B
21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected
> show /B
> show sel cartoons
> hide sel atoms
> select clear
> ui tool show Distances
Exactly two atoms must be selected!
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select clear
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select subtract /D:6
Nothing selected
Drag select of 3 residues
Drag select of 2 residues
> select /D:7
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:5
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:7
33 atoms, 35 bonds, 1 residue, 1 model selected
Drag select of 3 residues, 1 shapes
> show sel target ab
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel atoms
> style sel stick
Changed 98 atom styles
> style sel ball
Changed 98 atom styles
> style sel sphere
Changed 98 atom styles
> style sel stick
Changed 98 atom styles
> style sel ball
Changed 98 atom styles
> style sel ball
Changed 98 atom styles
> ui tool show Contacts
> contacts sel ignoreHiddenModels true
161 contacts
> undo
> ui tool show Contacts
> select clear
Drag select of 19 pseudobonds
> delete sel
> hide sel
Drag select of 16 pseudobonds
> hide sel
Drag select of 11 pseudobonds
> hide sel
> view clip false
> select add #1.4
161 pseudobonds, 1 model selected
> delete sel
> hide sel
> select subtract #1.4
Nothing selected
> hide #1.4 models
> show #1.4 models
> hide #1.4 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:7
33 atoms, 35 bonds, 1 residue, 1 model selected
Drag select of 3 residues
> select /D:5
32 atoms, 33 bonds, 1 residue, 1 model selected
> select add /D:6
65 atoms, 68 bonds, 2 residues, 1 model selected
> select add /D:7
98 atoms, 103 bonds, 3 residues, 1 model selected
> select /B
21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected
> select add /D:5
21592 atoms, 21776 bonds, 14 pseudobonds, 1311 residues, 3 models selected
> select add /D:6
21625 atoms, 21811 bonds, 14 pseudobonds, 1312 residues, 3 models selected
> select add /D:7
21658 atoms, 21846 bonds, 14 pseudobonds, 1313 residues, 3 models selected
> ui tool show Contacts
> contacts sel distanceOnly 4.0 ignoreHiddenModels true
93051 distances
> select clear
> show #1.4 models
> hide #1.4 models
> show #1.4 models
> hide #1.4 models
> select /B
21560 atoms, 21743 bonds, 86549 pseudobonds, 1310 residues, 4 models selected
> hide #!1 models
> show #!1 models
> select add /D:5
21592 atoms, 21776 bonds, 86549 pseudobonds, 1311 residues, 4 models selected
> select add /D:6
21625 atoms, 21811 bonds, 86549 pseudobonds, 1312 residues, 4 models selected
> select add /D:7
21658 atoms, 21846 bonds, 86549 pseudobonds, 1313 residues, 4 models selected
> ui tool show Distances
> ui tool show Contacts
> contacts sel restrict both distanceOnly 4.0 ignoreHiddenModels true
86965 distances
> show #1.4 models
> select add #1.4
21658 atoms, 21846 bonds, 86979 pseudobonds, 1313 residues, 4 models selected
> select subtract #1.4
21658 atoms, 21846 bonds, 14 pseudobonds, 1313 residues, 3 models selected
> select add #1.4
21658 atoms, 21846 bonds, 86979 pseudobonds, 1313 residues, 4 models selected
> delete sel
> undo
Undo failed, probably because structures have been modified.
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> open 4un3 format mmcif fromDatabase pdb
4un3 title:
Crystal structure of Cas9 bound to PAM-containing DNA target [more info...]
Chain information for 4un3 #2
---
Chain | Description | UniProt
A | SGRNA |
B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368
C | TARGET DNA STRAND |
D | NON-TARGET DNA STRAND |
Non-standard residues in 4un3 #2
---
MG — magnesium ion
> cloe
Unknown command: cloe
> cloeclose
Unknown command: cloeclose
> close
> open 4un3 format mmcif fromDatabase pdb
4un3 title:
Crystal structure of Cas9 bound to PAM-containing DNA target [more info...]
Chain information for 4un3 #1
---
Chain | Description | UniProt
A | SGRNA |
B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368
C | TARGET DNA STRAND |
D | NON-TARGET DNA STRAND |
Non-standard residues in 4un3 #1
---
MG — magnesium ion
> color /B slate blue
> color/A red
Unknown command: color/A red
> color /A red
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color /A yellow green
> color /B steel blue
> color /C coral
> color /D orange
> color /D orangered
> color /D tomato
> color /D dark orange
> color /C crimson
> color /C tomato
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
> hide sel
> show sel
> hide sel
> hide sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> select /C:9
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /C:9-11
60 atoms, 65 bonds, 3 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /D
Alignment identifier is 1/D
> select /D:5
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /D:5-7
64 atoms, 71 bonds, 3 residues, 1 model selected
> color sel red
> color sel crimson
> color sel teal
> select clear
> show cartoons
> hide cartoons
> show cartoons
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
> hide sel cartoons
> select /C:7-8
40 atoms, 44 bonds, 2 residues, 1 model selected
> select /C:7-8
40 atoms, 44 bonds, 2 residues, 1 model selected
> select /C:8-9
41 atoms, 45 bonds, 2 residues, 1 model selected
> select /C:6-9
79 atoms, 87 bonds, 4 residues, 1 model selected
> select /C:8
21 atoms, 23 bonds, 1 residue, 1 model selected
> select /C:6-8
59 atoms, 65 bonds, 3 residues, 1 model selected
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> hide #1.2 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> select add #1
13629 atoms, 13708 bonds, 140 pseudobonds, 1839 residues, 5 models selected
> select subtract #1
Nothing selected
> show cartoons
> select /A
1882 atoms, 1942 bonds, 58 pseudobonds, 231 residues, 3 models selected
> hide sel
> hide sel cartoons
> select /D
229 atoms, 255 bonds, 13 residues, 1 model selected
> select /C
578 atoms, 634 bonds, 39 residues, 1 model selected
> hide /C
> hide sel cartoons
> select add /D:2
596 atoms, 654 bonds, 40 residues, 1 model selected
> select add /D:3
617 atoms, 677 bonds, 41 residues, 1 model selected
Drag select of 1 residues, 2 shapes
> select add /D:3
617 atoms, 677 bonds, 41 residues, 1 model selected
> select add /D:4
638 atoms, 700 bonds, 42 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select add /D:12
660 atoms, 724 bonds, 43 residues, 1 model selected
> select add /D:11
680 atoms, 745 bonds, 44 residues, 1 model selected
> select add /D:9
701 atoms, 768 bonds, 45 residues, 1 model selected
> select add /D:8
721 atoms, 789 bonds, 46 residues, 1 model selected
> select add /D:10
741 atoms, 810 bonds, 47 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select add /D:7
763 atoms, 834 bonds, 48 residues, 1 model selected
> select add /D:5
805 atoms, 855 bonds, 50 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> select subtract /D:7
783 atoms, 831 bonds, 49 residues, 1 model selected
> select subtract /D:6
761 atoms, 831 bonds, 48 residues, 1 model selected
> select subtract /D:5
741 atoms, 810 bonds, 47 residues, 1 model selected
> select add /D:7
763 atoms, 834 bonds, 48 residues, 1 model selected
> select add /D:6
785 atoms, 858 bonds, 49 residues, 1 model selected
> select add /D:5
805 atoms, 879 bonds, 50 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> hide /C
> hide sel cartoons
> show sel atoms
> show sel cartoons
> select clear
> select /D
229 atoms, 255 bonds, 13 residues, 1 model selected
> select /C
578 atoms, 634 bonds, 39 residues, 1 model selected
> hide sel
> hide sel cartoons
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
> hide sel cartoons
> show sel atoms
> hide sel atoms
> show sel cartoons
> select add /D:5
10960 atoms, 10898 bonds, 18 pseudobonds, 1557 residues, 3 models selected
> select add /D:6
10982 atoms, 10922 bonds, 18 pseudobonds, 1558 residues, 3 models selected
> select add /D:7
11004 atoms, 10946 bonds, 18 pseudobonds, 1559 residues, 3 models selected
> label NGG
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> select : in dna
Expected an objects specifier or a keyword
> select /C
578 atoms, 634 bonds, 39 residues, 1 model selected
> select /D
229 atoms, 255 bonds, 13 residues, 1 model selected
> select /D:5-7
64 atoms, 71 bonds, 3 residues, 1 model selected
> label sel
No distances to delete!
> select /B & within 4 of /D:5-7
Expected a keyword
> select /B within 4 of /D:5-7
Expected a keyword
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
> select /B and /D:5-7
Expected a keyword
> select /B & /D:5-7
Nothing selected
> select /B & /D:5-7
Nothing selected
> select /B, /D
Expected an objects specifier or a keyword
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
> select /B with /D
Expected a keyword
> select add /D:5
10960 atoms, 10898 bonds, 18 pseudobonds, 1557 residues, 3 models selected
> select add /D:6
10982 atoms, 10922 bonds, 18 pseudobonds, 1558 residues, 3 models selected
> select add /D:7
11004 atoms, 10946 bonds, 18 pseudobonds, 1559 residues, 3 models selected
> select clear
> select /B add /D:5-7
Expected a keyword
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
> addcharge /D
Using Amber 20 recommended default charges and atom types for standard
residues
1 structure has non-integral total charge.
Details in log.
Here are the structures will non-integral total charge along with the
particular residues from those structures with non-integral total charge:
4un3 #1: /D DA 2: -2.3889, /D DA 3: -2.7752, /D DA 4: -2.7752, /D DT 5:
-2.5246, /D DG 6: -3.0838, /D DG 7: -3.0838, /D DT 8: -2.5246, /D DA 9:
-2.7752, /D DT 10: -2.5246, /D DT 11: -2.5246, /D DG 12: -3.0838, /D HOH 2001:
-0.834, and /D HOH 2002: -0.834
> select add /D
11169 atoms, 11132 bonds, 18 pseudobonds, 1569 residues, 3 models selected
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
> select add /D:5-7
11004 atoms, 10948 bonds, 18 pseudobonds, 1559 residues, 3 models selected
> ui tool show Distances
> ui tool show Contacts
> select :5-7 in DNA
Expected a keyword
> select :5-7 in /D
Expected a keyword
> select :5-7
209 atoms, 227 bonds, 6 pseudobonds, 12 residues, 2 models selected
> select clear
> select :5-7
209 atoms, 227 bonds, 6 pseudobonds, 12 residues, 2 models selected
> select :5-7
209 atoms, 227 bonds, 6 pseudobonds, 12 residues, 2 models selected
> select clear
> select add /D:5
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /D:6
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add /D:7
64 atoms, 69 bonds, 3 residues, 1 model selected
> distance /D:5-7 in /B
Expected a keyword
> distance /D:5-7
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 64 atoms and 0
measurable objects
> ui tool show Distances
> distance style radius 4
> select zone
Missing or invalid "near" argument: empty atom specifier
> select #1.4
1 model selected
> select subtract #1.4
Nothing selected
> hide #1.4 models
> show #1.4 models
> select #1
13629 atoms, 13708 bonds, 140 pseudobonds, 1839 residues, 6 models selected
> select clear
> select /B,/D:5-7
Expected an objects specifier or a keyword
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
> sel/B
Unknown command: sel/B
> select /B-D
11747 atoms, 11766 bonds, 37 pseudobonds, 1608 residues, 4 models selected
> select /B /D:5-7
11004 atoms, 10948 bonds, 18 pseudobonds, 1559 residues, 3 models selected
> select zone /B /D:5-7 cutoff 4
Missing or invalid "range" argument: Expected a number
> select zone /B /D:5-7 4
Selected 673 atoms, 1 surfaces
> label sel
> center
Unknown command: center
> undo
> show #1.4 models
> hide #1.4 models
> select add #1.4
1 model selected
> show #1.4 models
> delete sel
> select delete
Expected an objects specifier or a keyword
> select subtract #1.4
Nothing selected
> hide #1.4 models
> show #1.4 models
> hide #1.4 models
> show #1.4 models
> hide #1.4 models
> delete #1.4
> ui tool show Contacts
> show atoms
> sel/A /C
Unknown command: sel/A /C
> select /A /C
2460 atoms, 2576 bonds, 101 pseudobonds, 270 residues, 3 models selected
> hide sel atoms
> select /D
229 atoms, 255 bonds, 13 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select solvent
405 atoms, 405 residues, 1 model selected
> hide solvent
> select /D:6@O5'
1 atom, 1 residue, 1 model selected
> select /D:7@P
1 atom, 1 residue, 1 model selected
> style sel sphere
Changed 0 atom styles
> select /D
229 atoms, 255 bonds, 13 residues, 1 model selected
> style sel ball
Changed 229 atom styles
> style sel sphere
Changed 229 atom styles
> style sel stick
Changed 229 atom styles
> style sel ball
Changed 229 atom styles
> lighting soft
> lighting simple
> select clear
> view
> view center
Expected an objects specifier or a view name or a keyword
> view
> label #!1 attribute name
> transparency #!1 60
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
> transparency (#!1 & sel) 70
> select clear
> cartoon hide #!1
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
No Surface models open
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
10690 atoms, 10877 bonds, 6 pseudobonds, 1306 residues, 2 models selected
> ui tool show "Color Actions"
> color sel bynucleotide
> color sel byhetero
> color sel byelement
> color sel bynucleotide
> color sel bychain
> color sel bypolymer
> color sel bychain
> color sel bynucleotide
> color sel byelement
> color sel byhetero
> color sel bynucleotide
> color sel hot pink
> color sel cornflower blue
> color sel light gray
> color sel gray
> color sel dark gray
> color sel gray
> color sel light gray
> color sel dim gray
> color sel dark gray
> color sel gray
> color sel purple
> color sel light gray
> color sel gray
> color sel bynucleotide
Alignment identifier is 1/B
Destroying pre-existing alignment with identifier 1/B
Alignment identifier is 1/B
> show sel surfaces
> color sel tan
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color sel peachpuff
> color sel palegreen goldrenrod
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel pale goldenrod
> color sel lace
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel old lace
> color sel tan
> ui tool show "Side View"
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting full
> select clear
> transparency #1.5#!1 40
> transparency #1.5#!1 30
> surface style solid
> transparency #1.5#!1 0
> transparency #1.5#!1 10
> transparency #1.5#!1 0
> volume hide
No volumes specified
> nucleotides atoms
> style nucleic stick
Changed 2526 atom styles
> nucleotides fill
> style nucleic stick
Changed 2526 atom styles
> nucleotides slab
> style nucleic stick
Changed 2526 atom styles
> nucleotides tube/slab shape box
> nucleotides tube/slab shape ellipsoid
> nucleotides tube/slab shape muffler
> nucleotides ladder
> nucleotides stubs
> nucleotides ladder
> nucleotides atoms
> style nucleic stick
Changed 2526 atom styles
> nucleotides fill
> style nucleic stick
Changed 2526 atom styles
> nucleotides ladder
> hide surfaces
> show cartoons
> hide cartoons
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel atoms
> hide solvents
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide solvent
> select clear
> select /B
10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> select /D:5-7
64 atoms, 71 bonds, 3 residues, 1 model selected
> show sel cartoons
> select /D
229 atoms, 255 bonds, 13 residues, 1 model selected
> show sel cartoons
> select clear
> ui tool show Contacts
> help help:user/tools/clashes.html
> select sel : select /B /D:5-7
11004 atoms, 10948 bonds, 18 pseudobonds, 1559 residues, 3 models selected
> select /D:5-7
64 atoms, 71 bonds, 3 residues, 1 model selected
> select sel : label sel
> show #1.4 models
> hide #1.4 models
> show #1.4 models
> hide #1.4 models
> hide #1.5 models
> show #1.5 models
> hide #1.5 models
> show #1.5 models
> show #1.4 models
> hide #1.4 models
> hide #1.5 models
> show #1.5 models
> color sel pink
> color sel teal
> select clear
> select add /B:1136
6 atoms, 5 bonds, 1 residue, 1 model selected
Drag select of 4 residues
> select /B:1174
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add /B:1137
18 atoms, 18 bonds, 2 residues, 2 models selected
> select subtract /B:1174
7 atoms, 7 bonds, 1 residue, 2 models selected
> select add /B:1107
16 atoms, 15 bonds, 2 residues, 2 models selected
> select add /B:1136
22 atoms, 20 bonds, 3 residues, 2 models selected
> select add /B:1139
29 atoms, 26 bonds, 4 residues, 2 models selected
> select add /B:1200
38 atoms, 34 bonds, 5 residues, 2 models selected
> select add /B:1216
44 atoms, 39 bonds, 6 residues, 2 models selected
> select add /B:1215
49 atoms, 43 bonds, 7 residues, 2 models selected
> select add /B:1219
58 atoms, 51 bonds, 8 residues, 2 models selected
> select add /B:1221
67 atoms, 59 bonds, 9 residues, 2 models selected
> select add /B:1320
72 atoms, 63 bonds, 10 residues, 2 models selected
> select add /B:1335
83 atoms, 73 bonds, 11 residues, 2 models selected
> select add /B:1333
94 atoms, 83 bonds, 12 residues, 2 models selected
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MYDC2LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 62 days, 7 hours, 9 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
LG HDR 4K:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 30.00Hz
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 , 9 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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