![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17528 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-14.6-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 0x00000001fc330f40 (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, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 58)
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{
"uptime" : 280000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,12",
"coalitionID" : 5160,
"osVersion" : {
"train" : "macOS 14.6",
"build" : "23G80",
"releaseType" : "User"
},
"captureTime" : "2025-05-01 10:15:46.8243 -0400",
"codeSigningMonitor" : 1,
"incident" : "45B8FCEF-24B8-4A3D-834E-26F065D5AA2B",
"pid" : 68576,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-29 13:21:22.3550 -0400",
"procStartAbsTime" : 3888559014946,
"procExitAbsTime" : 6769119231820,
"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":"4604459A-99EE-584E-A4BF-AE5488296CB8","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "90B1516C-5BFC-0BCB-BDB5-993A1A9010E0",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 16345,
"sleepWakeUUID" : "B03C92FD-55CB-4341-B03E-7F7DB51EDDB4",
"sip" : "enabled",
"vmRegionInfo" : "0x2cc3eb71b188 is not in any region. Bytes after previous region: 48738944004489 Bytes before following region: 56333135924856\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, 0x0000acc3eb71b188","rawCodes":[1,189957468696968],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000acc3eb71b188 -> 0x00002cc3eb71b188 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":68576},
"vmregioninfo" : "0x2cc3eb71b188 is not in any region. Bytes after previous region: 48738944004489 Bytes before following region: 56333135924856\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 ",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/danielasanchezgiannakis/Desktop/urc lattice.cxs" format session
opened ChimeraX session
> hide #3.1 models
> hide #3.2 models
> hide #3.3 models
> show #3.2 models
> show #3.3 models
> hide #3.2 models
> hide #3.4 models
> show #3.4 models
> hide #3.5 models
> show #3.5 models
> hide #3.5 models
> show #3.5 models
> hide #3.6 models
> show #3.6 models
> hide #3.7 models
> show #3.7 models
> hide #3.8 models
> show #3.8 models
> hide #3.36 models
> show #3.36 models
> camera ortho
> hide #3.36 models
> show #3.36 models
> hide #3.31 models
> show #3.31 models
> hide #3.30 models
> show #3.30 models
> hide #3.30 models
> hide #3.29 models
> show #3.29 models
> hide #3.29 models
> show #3.29 models
> hide #3.28 models
> show #3.28 models
> hide #3.28 models
> hide #3.27 models
> show #3.27 models
> hide #3.27 models
> hide #3.26 models
> hide #3.25 models
> hide #3.24 models
> show #3.24 models
> hide #3.23 models
> show #3.23 models
> hide #3.22 models
> show #3.22 models
> hide #3.21 models
> hide #3.20 models
> show #3.20 models
> hide #3.20 models
> show #3.20 models
> hide #3.19 models
> hide #3.18 models
> show #3.18 models
> hide #3.17 models
> show #3.17 models
> hide #3.16 models
> show #3.16 models
> hide #3.15 models
> hide #3.14 models
> hide #3.13 models
> hide #3.12 models
> hide #3.11 models
> hide #3.10 models
> show #3.10 models
> hide #3.9 models
> show #3.9 models
> hide #3.8 models
> show #3.8 models
> hide #3.7 models
> show #3.7 models
> hide #3.6 models
> show #3.6 models
> hide #3.5 models
> show #3.5 models
> hide #3.4 models
> show #3.4 models
> hide #3.3 models
> show #3.3 models
> hide #3.6 models
> show #3.6 models
> hide #3.3 models
> show #3.3 models
> hide #3.36 models
> show #3.36 models
> hide #3.35 models
> show #3.35 models
> hide #3.34 models
> show #3.34 models
> hide #3.33 models
> show #3.33 models
> hide #3.32 models
> show #3.32 models
> hide #3.31 models
> show #3.31 models
> hide #3.29 models
> show #3.29 models
> hide #3.24 models
> show #3.24 models
> hide #3.23 models
> show #3.23 models
> hide #3.22 models
> show #3.22 models
> hide #3.20 models
> show #3.20 models
> show #3.21 models
> show #3.19 models
> close session
> open /Users/danielasanchezgiannakis/Downloads/1T6B11RY_refine_22.pdb
Chain information for 1T6B11RY_refine_22.pdb #1
---
Chain | Description
A | No description available
C | No description available
D | No description available
G | No description available
Computing secondary structure
> camera ortho
> color bychain
> style ball
Changed 779 atom styles
> style stick
Changed 779 atom styles
> style ball
Changed 779 atom styles
> nucleotides atoms
> style nucleic stick
Changed 697 atom styles
> style sphere
Changed 779 atom styles
> style sphere
Changed 779 atom styles
> style ball
Changed 779 atom styles
> style ball
Changed 779 atom styles
> lighting full
> ui tool show "Unit Cell"
> unitcell #1
> unitcell outline #1
> unitcell outline #1 close
> unitcell #1 cells 3,3,3
> unitcell #1 cells 2,2,2
> unitcell delete #1
> unitcell #1 cells 2,2,2
> unitcell #1
> unitcell #1 cells 1,2,1
> select
> #1/C#2.1/C#2.2/C#2.3/C#2.4/C#2.5/C#2.6/C#2.7/C#2.8/C#2.9/C#2.10/C#2.11/C#2.12/C
2067 atoms, 2210 bonds, 65 residues, 13 models selected
> color sel #5c4eb3ff
> select clear
> select
> #1/D#2.1/D#2.2/D#2.3/D#2.4/D#2.5/D#2.6/D#2.7/D#2.8/D#2.9/D#2.10/D#2.11/D#2.12/D
2067 atoms, 2223 bonds, 65 residues, 13 models selected
> color sel #c27de1ff
> color sel #c17be1ff
> color sel #c675e2ff
> color sel #d465e1ff
> color sel #d564e0ff
> color sel #d85edfff
> color sel #d85edeff
> color sel #d85bdaff
> color sel #d85bd9ff
> color sel #d85cddff
> color sel #d85edeff
> color sel #d85fe2ff
> color sel #d262e1ff
> color sel #d263e1ff
> color sel #d264e1ff
> color sel #cf65e1ff
> color sel #cf66e1ff
> color sel #d367e1ff
> color sel #d567e1ff
> color sel #d566e1ff
> color sel #d767e2ff
> color sel #d868e2ff
> color sel #d867e1ff
> color sel #d867ddff
> color sel #d867dcff
> color sel #d867daff
> color sel #d868d7ff
> color sel #d867d6ff
> color sel #d866d6ff
> color sel #d765d2ff
> color sel #d764d1ff
> color sel #d862d1ff
> color sel #d861d2ff
> color sel #d860d2ff
> select
> #1/G#2.1/G#2.2/G#2.3/G#2.4/G#2.5/G#2.6/G#2.7/G#2.8/G#2.9/G#2.10/G#2.11/G#2.12/G
2444 atoms, 2626 bonds, 78 residues, 13 models selected
> select clear
> unitcell #1 cells 1,2,2
> color /a mediumblue
> color #3230e3ff
> select
> #1/C#2.1/C#2.2/C#2.3/C#2.4/C#2.5/C#2.6/C#2.7/C#2.8/C#2.9/C#2.10/C#2.11/C#2.12/C#2.13/C#2.14/C#2.15/C#2.16/C#2.17/C#2.18/C#2.19/C#2.20/C#2.21/C#2.22/C#2.23/C#2.24/C
3975 atoms, 4250 bonds, 125 residues, 25 models selected
> select
> #1/D#2.1/D#2.2/D#2.3/D#2.4/D#2.5/D#2.6/D#2.7/D#2.8/D#2.9/D#2.10/D#2.11/D#2.12/D#2.13/D#2.14/D#2.15/D#2.16/D#2.17/D#2.18/D#2.19/D#2.20/D#2.21/D#2.22/D#2.23/D#2.24/D
3975 atoms, 4275 bonds, 125 residues, 25 models selected
> color sel #d976deff
> color sel #d975b0ff
> color sel #d872dcff
> color sel #d762ccff
> color sel #d946caff
> color sel #d85dd1ff
> color sel #db40c3ff
> select
> #1/G#2.1/G#2.2/G#2.3/G#2.4/G#2.5/G#2.6/G#2.7/G#2.8/G#2.9/G#2.10/G#2.11/G#2.12/G#2.13/G#2.14/G#2.15/G#2.16/G#2.17/G#2.18/G#2.19/G#2.20/G#2.21/G#2.22/G#2.23/G#2.24/G
4700 atoms, 5050 bonds, 150 residues, 25 models selected
> color sel #a2e691ff
> color sel #428c35ff
> color sel #4a9b55ff
> color sel #59bd51ff
> color sel #5ca836ff
> color sel #499932ff
> color sel #4a9b3bff
> color sel #4b9f3aff
> color sel #51ac39ff
> color sel #51ab3eff
> color sel #51ab40ff
> color sel #52ad42ff
> color sel #52ae42ff
> color sel #52ae4cff
> color sel #52ae4dff
> color sel #52ae4fff
> color sel #52ae5dff
> color sel #52ae5eff
> color sel #52ae60ff
> color sel #52ae62ff
> color sel #52ad62ff
> color sel #51ab62ff
> color sel #4da45dff
> color sel #4da25bff
> color sel #499b51ff
> color sel #479548ff
> color sel #479546ff
> color sel #489846ff
> color sel #489744ff
> color sel #489845ff
> color sel #489844ff
> color sel #489843ff
> color sel #499a44ff
> color sel #4a9c40ff
> color sel #4a9c3eff
> color sel #4b9f3bff
> color sel #4ca037ff
> color sel #4ca036ff
> color sel #4ca034ff
> color sel #4ca134ff
> color sel #4da134ff
> color sel #4ea134ff
> color sel #50a135ff
> color sel #51a134ff
> color sel #54a135ff
> color sel #59a135ff
> color sel #5ca235ff
> color sel #5fa035ff
> color sel #60a035ff
> color sel #62a035ff
> color sel #629f35ff
> color sel #649f35ff
> color sel #649f34ff
> color sel #669f34ff
> color sel #649f34ff
> color sel #619e34ff
> color sel #5f9e34ff
> color sel #5a9e34ff
> select clear
> camera ortho
> hide #2.2 models
> show #2.2 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.24 models
> show #2.24 models
> hide #2.23 models
> show #2.23 models
> hide #2.23 models
> hide #2.22 models
> show #2.22 models
> hide #2.21 models
> hide #2.20 models
> show #2.20 models
> hide #2.20 models
> show #2.20 models
> hide #2.19 models
> show #2.19 models
> hide #2.19 models
> hide #2.18 models
> hide #2.17 models
> hide #2.16 models
> show #2.16 models
> hide #2.16 models
> show #2.16 models
> hide #2.16 models
> show #2.16 models
> hide #2.16 models
> hide #2.15 models
> hide #2.14 models
> hide #2.13 models
> hide #2.12 models
> show #2.12 models
> hide #2.12 models
> hide #2.11 models
> show #2.11 models
> hide #2.10 models
> hide #2.9 models
> show #2.9 models
> hide #2.8 models
> hide #2.7 models
> show #2.7 models
> hide #2.6 models
> hide #2.5 models
> show #2.5 models
> hide #2.5 models
> hide #2.4 models
> show #2.4 models
> hide #2.4 models
> hide #2.3 models
> show #2.3 models
> hide #2.3 models
> hide #2.2 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.24 models
> show #2.24 models
> hide #2.22 models
> show #2.22 models
> hide #2.20 models
> show #2.20 models
> hide #2.11 models
> show #2.11 models
> hide #2.9 models
> show #2.9 models
> hide #2.7 models
> show #2.7 models
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #2.24 models
> show #2.24 models
> hide #2.22 models
> show #2.22 models
> log metadata #1
The model has no metadata
> log chains #1
Chain information for 1T6B11RY_refine_22.pdb #1
---
Chain | Description
A | No description available
C | No description available
D | No description available
G | No description available
> select #1/C:1-5
159 atoms, 170 bonds, 5 residues, 1 model selected
> lighting full
> lighting shadows false
> camera ortho
> hide #1 models
> show #1 models
> hide #1 models
> hide #!2 models
> show #!2 models
> hide #2.1 models
> hide #2.24 models
> show #2.24 models
> hide #2.22 models
> hide #2.20 models
> show #2.20 models
> hide #2.20 models
> hide #2.11 models
> hide #2.9 models
> show #2.9 models
> hide #2.7 models
> save "/Users/danielasanchezgiannakis/Documents/nyu/spring 2025/1T6B11.cxs"
> save "/Users/danielasanchezgiannakis/Documents/nyu/spring 2025/DX tile
> 1T6B11.png" width 394 height 455 supersample 3 transparentBackground true
> show #2.23 models
> hide #2.23 models
> show #2.22 models
> show #2.21 models
> hide #2.21 models
> show #2.20 models
> show #2.19 models
> hide #2.19 models
> show #2.18 models
> hide #2.18 models
> show #2.17 models
> hide #2.17 models
> show #2.16 models
> hide #2.16 models
> show #2.15 models
> hide #2.15 models
> show #2.14 models
> hide #2.14 models
> show #2.14 models
> hide #2.14 models
> show #2.13 models
> hide #2.13 models
> show #2.12 models
> hide #2.12 models
> show #2.11 models
> show #2.10 models
> hide #2.10 models
> show #2.8 models
> hide #2.8 models
> show #2.7 models
> show #2.8 models
> show #2.6 models
> show #2.5 models
> show #2.4 models
> show #2.3 models
> show #2.2 models
> show #2.1 models
> show #2.23 models
> show #2.21 models
> show #2.19 models
> show #2.18 models
> show #2.17 models
> show #2.16 models
> show #2.15 models
> show #2.14 models
> show #2.13 models
> show #2.12 models
> show #2.10 models
> show #1 models
> hide #1 models
> unitcell #1 cells 2,2,2
> unitcell #1 cells 3,2,2
> unitcell #1 cells 3,3,3
> unitcell #1 cells 3,3,1
> unitcell #1 cells 3,2,1
> unitcell #1 cells 3,3,1
> unitcell #1 cells 3,1,1
> unitcell #1 cells 3,2,1
> unitcell #1 cells 1,2,1
> unitcell #1 cells 3,2,1
> unitcell #1 cells 4,2,1
> unitcell #1 cells 2,2,1
> unitcell #1 cells 2,2,2
> unitcell #1 cells 3,3,3
> ui tool show "Side View"
> save "/Users/danielasanchezgiannakis/Documents/nyu/spring 2025/1T6B11
> cavity.png" width 394 height 513 supersample 3
> save "/Users/danielasanchezgiannakis/Documents/nyu/spring 2025/cavity 1T6B11
> no background.png" width 394 height 513 supersample 3 transparentBackground
> true
> save "/Users/danielasanchezgiannakis/Documents/nyu/spring 2025/bigger cavity
> lol.png" width 894 height 742 supersample 3
> save "/Users/danielasanchezgiannakis/Documents/nyu/spring 2025/again
> lol.png" width 894 height 742 supersample 3 transparentBackground true
> style #2.1-162 sphere
Changed 126198 atom styles
> style #2.1-162 ball
Changed 126198 atom styles
> style #2.1-162 sphere
Changed 126198 atom styles
> lighting full
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> nucleotides #2.1-162 atoms
> style nucleic & #2.1-162 stick
Changed 112914 atom styles
> style #2.1-162 ball
Changed 126198 atom styles
> style #2.1-162 sphere
Changed 126198 atom styles
> style #2.1-162 ball
Changed 126198 atom styles
> style #2.1-162 stick
Changed 126198 atom styles
> style #2.1-162 ball
Changed 126198 atom styles
> style #2.1-162 sphere
Changed 126198 atom styles
> save "/Users/danielasanchezgiannakis/Documents/nyu/spring 2025/attempt 2
> space filling.png" width 894 height 742 supersample 3 transparentBackground
> true
> style #2.1-162 ball
Changed 126198 atom styles
> save "/Users/danielasanchezgiannakis/Documents/nyu/spring 2025/ballandstick
> cavity 1T6B11.png" width 894 height 742 supersample 3
> save "/Users/danielasanchezgiannakis/Documents/nyu/spring 2025/NO BACKGROUND
> PLS.png" width 894 height 742 supersample 3 transparentBackground true
> unitcell #1 cells 2,2,2
> hide #2.48 models
> show #2.48 models
> hide #2.47 models
> hide #2.46 models
> hide #2.45 models
> show #2.45 models
> hide #2.45 models
> hide #2.44 models
> hide #2.43 models
> hide #2.42 models
> hide #2.41 models
> hide #2.40 models
> hide #2.39 models
> hide #2.38 models
> show #2.38 models
> hide #2.38 models
> hide #2.37 models
> hide #2.36 models
> hide #2.35 models
> hide #2.34 models
> hide #2.33 models
> hide #2.32 models
> hide #2.31 models
> hide #2.30 models
> hide #2.29 models
> hide #2.28 models
> hide #2.27 models
> hide #2.26 models
> hide #2.25 models
> hide #2.24 models
> show #2.24 models
> hide #2.23 models
> show #2.23 models
> hide #2.22 models
> show #2.22 models
> hide #2.22 models
> hide #2.21 models
> show #2.21 models
> hide #2.20 models
> show #2.20 models
> hide #2.20 models
> hide #2.19 models
> hide #2.18 models
> hide #2.17 models
> hide #2.16 models
> hide #2.15 models
> hide #2.14 models
> hide #2.13 models
> hide #2.12 models
> hide #2.11 models
> hide #2.10 models
> hide #2.9 models
> hide #2.8 models
> hide #2.7 models
> hide #2.6 models
> hide #2.5 models
> hide #2.4 models
> hide #2.3 models
> hide #2.2 models
> hide #2.1 models
> hide #!2 models
> show #!2 models
> hide #2.48 models
> show #2.48 models
> hide #2.24 models
> show #2.24 models
> hide #2.24 models
> hide #2.23 models
> ui tool show "Side View"
> view orient
> save "/Users/danielasanchezgiannakis/Documents/nyu/spring 2025/base
> stacking.png" width 894 height 742 supersample 3 transparentBackground true
> close session
> open /Users/danielasanchezgiannakis/Documents/1T5_12_blunt_refine_63.pdb
Chain information for 1T5_12_blunt_refine_63.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Computing secondary structure
> style ball
Changed 492 atom styles
> nucleotides atoms
> style nucleic stick
Changed 492 atom styles
> style ball
Changed 492 atom styles
> camera ortho
> color bychain
> ui tool show "Unit Cell"
> unitcell #1
> unitcell #1 cells 3,3,3
> select
> #1/A#2.1/A#2.2/A#2.3/A#2.4/A#2.5/A#2.6/A#2.7/A#2.8/A#2.9/A#2.10/A#2.11/A#2.12/A#2.13/A#2.14/A#2.15/A#2.16/A#2.17/A#2.18/A#2.19/A#2.20/A#2.21/A#2.22/A#2.23/A#2.24/A#2.25/A#2.26/A#2.27/A#2.28/A#2.29/A#2.30/A#2.31/A#2.32/A#2.33/A#2.34/A#2.35/A#2.36/A#2.37/A#2.38/A#2.39/A#2.40/A#2.41/A#2.42/A#2.43/A#2.44/A#2.45/A#2.46/A#2.47/A#2.48/A#2.49/A#2.50/A#2.51/A#2.52/A#2.53/A#2.54/A#2.55/A#2.56/A#2.57/A#2.58/A#2.59/A#2.60/A#2.61/A#2.62/A#2.63/A#2.64/A#2.65/A#2.66/A#2.67/A#2.68/A#2.69/A#2.70/A#2.71/A#2.72/A#2.73/A#2.74/A#2.75/A#2.76/A#2.77/A#2.78/A#2.79/A#2.80/A#2.81/A
8446 atoms, 9348 bonds, 410 residues, 82 models selected
> select
> #1/B#2.1/B#2.2/B#2.3/B#2.4/B#2.5/B#2.6/B#2.7/B#2.8/B#2.9/B#2.10/B#2.11/B#2.12/B#2.13/B#2.14/B#2.15/B#2.16/B#2.17/B#2.18/B#2.19/B#2.20/B#2.21/B#2.22/B#2.23/B#2.24/B#2.25/B#2.26/B#2.27/B#2.28/B#2.29/B#2.30/B#2.31/B#2.32/B#2.33/B#2.34/B#2.35/B#2.36/B#2.37/B#2.38/B#2.39/B#2.40/B#2.41/B#2.42/B#2.43/B#2.44/B#2.45/B#2.46/B#2.47/B#2.48/B#2.49/B#2.50/B#2.51/B#2.52/B#2.53/B#2.54/B#2.55/B#2.56/B#2.57/B#2.58/B#2.59/B#2.60/B#2.61/B#2.62/B#2.63/B#2.64/B#2.65/B#2.66/B#2.67/B#2.68/B#2.69/B#2.70/B#2.71/B#2.72/B#2.73/B#2.74/B#2.75/B#2.76/B#2.77/B#2.78/B#2.79/B#2.80/B#2.81/B
11972 atoms, 13448 bonds, 574 residues, 82 models selected
> color sel #5a9e34ff
> color sel #a98fffff
> select
> #1/A#2.1/A#2.2/A#2.3/A#2.4/A#2.5/A#2.6/A#2.7/A#2.8/A#2.9/A#2.10/A#2.11/A#2.12/A#2.13/A#2.14/A#2.15/A#2.16/A#2.17/A#2.18/A#2.19/A#2.20/A#2.21/A#2.22/A#2.23/A#2.24/A#2.25/A#2.26/A#2.27/A#2.28/A#2.29/A#2.30/A#2.31/A#2.32/A#2.33/A#2.34/A#2.35/A#2.36/A#2.37/A#2.38/A#2.39/A#2.40/A#2.41/A#2.42/A#2.43/A#2.44/A#2.45/A#2.46/A#2.47/A#2.48/A#2.49/A#2.50/A#2.51/A#2.52/A#2.53/A#2.54/A#2.55/A#2.56/A#2.57/A#2.58/A#2.59/A#2.60/A#2.61/A#2.62/A#2.63/A#2.64/A#2.65/A#2.66/A#2.67/A#2.68/A#2.69/A#2.70/A#2.71/A#2.72/A#2.73/A#2.74/A#2.75/A#2.76/A#2.77/A#2.78/A#2.79/A#2.80/A#2.81/A
8446 atoms, 9348 bonds, 410 residues, 82 models selected
> color sel #a98fffff
> unitcell #1 cells 2,2,2
> select
> #1/A#2.1/A#2.2/A#2.3/A#2.4/A#2.5/A#2.6/A#2.7/A#2.8/A#2.9/A#2.10/A#2.11/A#2.12/A#2.13/A#2.14/A#2.15/A#2.16/A#2.17/A#2.18/A#2.19/A#2.20/A#2.21/A#2.22/A#2.23/A#2.24/A
2575 atoms, 2850 bonds, 125 residues, 25 models selected
> unitcell #1 cells 2,3,2
> unitcell #1 cells 2,3,3
> unitcell #1 cells 3,3,3
> unitcell #1 cells 2,2,2
> hide #2.1 models
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> hide #2.5 models
> hide #2.6 models
> hide #2.7 models
> hide #2.8 models
> hide #2.9 models
> hide #2.10 models
> hide #2.11 models
> hide #2.12 models
> hide #2.13 models
> hide #2.14 models
> show #2.14 models
> show #2.13 models
> hide #2.14 models
> show #2.14 models
> hide #2.15 models
> show #2.15 models
> hide #2.16 models
> show #2.16 models
> hide #2.17 models
> show #2.17 models
> hide #2.17 models
> show #2.17 models
> hide #2.18 models
> show #2.18 models
> hide #2.19 models
> show #2.19 models
> hide #2.19 models
> show #2.19 models
> hide #2.20 models
> show #2.20 models
> hide #2.20 models
> show #2.20 models
> hide #2.20 models
> show #2.20 models
> hide #2.21 models
> show #2.21 models
> hide #2.21 models
> show #2.21 models
> hide #2.22 models
> show #2.22 models
> hide #2.23 models
> show #2.23 models
> hide #2.24 models
> show #2.24 models
> hide #2.24 models
> show #2.24 models
> hide #1 models
> unitcell #1 cells 4,4,4
> select clear
> unitcell #1 cells 2,2,2
> unitcell #1 cells 2,2,3
> unitcell #1 cells 3,2,3
> unitcell #1 cells 2,3,3
> save "/Users/danielasanchezgiannakis/Documents/nyu/spring 2025/1T512B.cxs"
> close session
> open "/Users/danielasanchezgiannakis/Documents/nyu/spring 2025/1T6B11.cxs"
> format session
opened ChimeraX session
> show #2.8 models
> hide #2.8 models
> show #2.10 models
> hide #2.10 models
> show #2.1 models
> hide #2.1 models
> ui tool show "Unit Cell"
> unitcell #2.9
> unitcell #2.9 cells 2,2,2
> unitcell #2.9 cells 3,3,3
> unitcell #2.9 cells 2,2,2
> view orient
> save "/Users/danielasanchezgiannakis/Documents/nyu/spring 2025/side view
> 1T6B.png" width 894 height 742 supersample 3 transparentBackground true
> close session
> open "/Users/danielasanchezgiannakis/Desktop/urc lattice.cxs" format session
opened ChimeraX session
> graphics silhouettes false
> graphics silhouettes true
> nucleotides atoms
> style nucleic stick
Changed 33345 atom styles
> nucleotides atoms
> style nucleic stick
Changed 33345 atom styles
> ui tool show "Unit Cell"
> unitcell #1.1
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> hide #3.2 models
> hide #3.3 models
> hide #3.4 models
> hide #3.5 models
> hide #3.6 models
> hide #3.7 models
> show #3.7 models
> show #3.6 models
> hide #3.6 models
> show #3.5 models
> hide #3.5 models
> show #3.4 models
> hide #3.4 models
> show #3.3 models
> hide #3.3 models
> show #3.2 models
> hide #3.2 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> select
> #1.1/A#1.2/A#1.3/A#3.1/A#3.2/A#3.3/A#3.4/A#3.5/A#3.6/A#3.7/A#3.8/A#3.9/A
2940 atoms, 3300 bonds, 144 residues, 12 models selected
> color (#1.1-3#3.1,7-9 & sel) #a390ffff
> color (#1.1-3#3.1,7-9 & sel) #a791ffff
> color (#1.1-3#3.1,7-9 & sel) #ac92ffff
> color (#1.1-3#3.1,7-9 & sel) #b092ffff
> color (#1.1-3#3.1,7-9 & sel) #b592ffff
> color (#1.1-3#3.1,7-9 & sel) #b692ffff
> color (#1.1-3#3.1,7-9 & sel) #c18effff
> color (#1.1-3#3.1,7-9 & sel) #c38dffff
> color (#1.1-3#3.1,7-9 & sel) #c58cffff
> color (#1.1-3#3.1,7-9 & sel) #c78bffff
> color (#1.1-3#3.1,7-9 & sel) #ce86ffff
> color (#1.1-3#3.1,7-9 & sel) #d084ffff
> color (#1.1-3#3.1,7-9 & sel) #d381ffff
> color (#1.1-3#3.1,7-9 & sel) #d481ffff
> color (#1.1-3#3.1,7-9 & sel) #d581ffff
> color (#1.1-3#3.1,7-9 & sel) #d280ffff
> color (#1.1-3#3.1,7-9 & sel) #d180ffff
> color (#1.1-3#3.1,7-9 & sel) #d080ffff
> color (#1.1-3#3.1,7-9 & sel) #cf80ffff
> color (#1.1-3#3.1,7-9 & sel) #d080ffff
> color (#1.1-3#3.1,7-9 & sel) #d280ffff
> color (#1.1-3#3.1,7-9 & sel) #d680ffff
> color (#1.1-3#3.1,7-9 & sel) #da7fffff
> color (#1.1-3#3.1,7-9 & sel) #df7fffff
> color (#1.1-3#3.1,7-9 & sel) #e07fffff
> color (#1.1-3#3.1,7-9 & sel) #e37fffff
> color (#1.1-3#3.1,7-9 & sel) #e581ffff
> color (#1.1-3#3.1,7-9 & sel) #e582ffff
> color (#1.1-3#3.1,7-9 & sel) #e785ffff
> color (#1.1-3#3.1,7-9 & sel) #e888ffff
> color (#1.1-3#3.1,7-9 & sel) #e98affff
> color (#1.1-3#3.1,7-9 & sel) #ea8cffff
> color (#1.1-3#3.1,7-9 & sel) #ec8fffff
> color (#1.1-3#3.1,7-9 & sel) #f097ffff
> color (#1.1-3#3.1,7-9 & sel) #faa7ffff
> color (#1.1-3#3.1,7-9 & sel) #ffaefeff
> color (#1.1-3#3.1,7-9 & sel) #ffbedfff
> color (#1.1-3#3.1,7-9 & sel) #ffbed8ff
> color (#1.1-3#3.1,7-9 & sel) #ffb8b6ff
> color (#1.1-3#3.1,7-9 & sel) #ffbab4ff
> color (#1.1-3#3.1,7-9 & sel) #ffbeaeff
> color (#1.1-3#3.1,7-9 & sel) #ffbfacff
> color (#1.1-3#3.1,7-9 & sel) #ffc397ff
> color (#1.1-3#3.1,7-9 & sel) #ffc391ff
> color (#1.1-3#3.1,7-9 & sel) #ffc390ff
> color (#1.1-3#3.1,7-9 & sel) #ffc38eff
> color (#1.1-3#3.1,7-9 & sel) #ffc38cff
> color (#1.1-3#3.1,7-9 & sel) #ffc38bff
> color (#1.1-3#3.1,7-9 & sel) #ffc389ff
> color (#1.1-3#3.1,7-9 & sel) #ffc387ff
> color (#1.1-3#3.1,7-9 & sel) #ffc385ff
> color (#1.1-3#3.1,7-9 & sel) #ffc382ff
> color (#1.1-3#3.1,7-9 & sel) #ffc280ff
> color (#1.1-3#3.1,7-9 & sel) #ffc27eff
> color (#1.1-3#3.1,7-9 & sel) #ffc27bff
> color (#1.1-3#3.1,7-9 & sel) #ffc27aff
> color (#1.1-3#3.1,7-9 & sel) #ffc279ff
> color (#1.1-3#3.1,7-9 & sel) #ffc178ff
> color (#1.1-3#3.1,7-9 & sel) #ffc177ff
> color (#1.1-3#3.1,7-9 & sel) #ffc178ff
> color (#1.1-3#3.1,7-9 & sel) #ffbd77ff
> color (#1.1-3#3.1,7-9 & sel) #ffb975ff
> color (#1.1-3#3.1,7-9 & sel) #ffb874ff
> color (#1.1-3#3.1,7-9 & sel) #ffb371ff
> color (#1.1-3#3.1,7-9 & sel) #ffb270ff
> color (#1.1-3#3.1,7-9 & sel) #ffb170ff
> color (#1.1-3#3.1,7-9 & sel) #ffaf6fff
> color (#1.1-3#3.1,7-9 & sel) #ffae6eff
> color (#1.1-3#3.1,7-9 & sel) #ffad6eff
> color (#1.1-3#3.1,7-9 & sel) #ffad6dff
> color (#1.1-3#3.1,7-9 & sel) #ffac6cff
> color (#1.1-3#3.1,7-9 & sel) #ffab6bff
> color (#1.1-3#3.1,7-9 & sel) #ffaa6bff
> color (#1.1-3#3.1,7-9 & sel) #ffa96aff
> color (#1.1-3#3.1,7-9 & sel) #ffaa6aff
> color (#1.1-3#3.1,7-9 & sel) #ffa96aff
> color (#1.1-3#3.1,7-9 & sel) #ffa869ff
> color (#1.1-3#3.1,7-9 & sel) #ffa769ff
> color (#1.1-3#3.1,7-9 & sel) #ffa668ff
> color (#1.1-3#3.1,7-9 & sel) #ffa467ff
> color (#1.1-3#3.1,7-9 & sel) #ffa366ff
> color (#1.1-3#3.1,7-9 & sel) #ffa266ff
> color (#1.1-3#3.1,7-9 & sel) #ff9f64ff
> color (#1.1-3#3.1,7-9 & sel) #ff9e64ff
> color (#1.1-3#3.1,7-9 & sel) #ff9e63ff
> color (#1.1-3#3.1,7-9 & sel) #ff9d62ff
> color (#1.1-3#3.1,7-9 & sel) #ff9b60ff
> color (#1.1-3#3.1,7-9 & sel) #ff995fff
> color (#1.1-3#3.1,7-9 & sel) #ff975dff
> color (#1.1-3#3.1,7-9 & sel) #ff965cff
> color (#1.1-3#3.1,7-9 & sel) #ff985dff
> color (#1.1-3#3.1,7-9 & sel) #ffa58fff
> color (#1.1-3#3.1,7-9 & sel) #ffa6a6ff
> color (#1.1-3#3.1,7-9 & sel) #ffb6ceff
> color (#1.1-3#3.1,7-9 & sel) #d098ffff
> color (#1.1-3#3.1,7-9 & sel) #c691ffff
> color (#1.1-3#3.1,7-9 & sel) #c08bffff
> color (#1.1-3#3.1,7-9 & sel) #b484ffff
> color (#1.1-3#3.1,7-9 & sel) #ab7affff
> color (#1.1-3#3.1,7-9 & sel) #ab79ffff
> color (#1.1-3#3.1,7-9 & sel) #a977ffff
> color (#1.1-3#3.1,7-9 & sel) #a875ffff
> color (#1.1-3#3.1,7-9 & sel) #a672ffff
> color (#1.1-3#3.1,7-9 & sel) #a571ffff
> color (#1.1-3#3.1,7-9 & sel) #a36effff
> color (#1.1-3#3.1,7-9 & sel) #a36dffff
> color (#1.1-3#3.1,7-9 & sel) #a26bffff
> color (#1.1-3#3.1,7-9 & sel) #a169ffff
> color (#1.1-3#3.1,7-9 & sel) #a068ffff
> color (#1.1-3#3.1,7-9 & sel) #9e64ffff
> color (#1.1-3#3.1,7-9 & sel) #9e63ffff
> color (#1.1-3#3.1,7-9 & sel) #9a5dffff
> color (#1.1-3#3.1,7-9 & sel) #995cffff
> color (#1.1-3#3.1,7-9 & sel) #995bffff
> color (#1.1-3#3.1,7-9 & sel) #9a5bffff
> color (#1.1-3#3.1,7-9 & sel) #9b5cffff
> color (#1.1-3#3.1,7-9 & sel) #a462ffff
> color (#1.1-3#3.1,7-9 & sel) #a966ffff
> color (#1.1-3#3.1,7-9 & sel) #ff7718ff
> color (#1.1-3#3.1,7-9 & sel) #ff7400ff
> color (#1.1-3#3.1,7-9 & sel) #ff7100ff
> color (#1.1-3#3.1,7-9 & sel) #ff7404ff
> color (#1.1-3#3.1,7-9 & sel) #ff7c13ff
> color (#1.1-3#3.1,7-9 & sel) #ff7f1aff
> color (#1.1-3#3.1,7-9 & sel) #ff8123ff
> color (#1.1-3#3.1,7-9 & sel) #ff822eff
> color (#1.1-3#3.1,7-9 & sel) #ff8336ff
> color (#1.1-3#3.1,7-9 & sel) #ff833dff
> color (#1.1-3#3.1,7-9 & sel) #ff833eff
> color (#1.1-3#3.1,7-9 & sel) #ff8340ff
> color (#1.1-3#3.1,7-9 & sel) #ff8441ff
> color (#1.1-3#3.1,7-9 & sel) #ff8f44ff
> color (#1.1-3#3.1,7-9 & sel) #ff9144ff
> color (#1.1-3#3.1,7-9 & sel) #ff9245ff
> color (#1.1-3#3.1,7-9 & sel) #ff9346ff
> color (#1.1-3#3.1,7-9 & sel) #ff9446ff
> color (#1.1-3#3.1,7-9 & sel) #ff9546ff
> color (#1.1-3#3.1,7-9 & sel) #ff9647ff
> color (#1.1-3#3.1,7-9 & sel) #ff9748ff
> color (#1.1-3#3.1,7-9 & sel) #ff9648ff
> color (#1.1-3#3.1,7-9 & sel) #ff9649ff
> color (#1.1-3#3.1,7-9 & sel) #ff9549ff
> color (#1.1-3#3.1,7-9 & sel) #ff934aff
> color (#1.1-3#3.1,7-9 & sel) #ff924dff
> color (#1.1-3#3.1,7-9 & sel) #ff924fff
> color (#1.1-3#3.1,7-9 & sel) #ff9355ff
> color (#1.1-3#3.1,7-9 & sel) #ff9c5aff
> color (#1.1-3#3.1,7-9 & sel) #ff9f59ff
> color (#1.1-3#3.1,7-9 & sel) #ffa059ff
> color (#1.1-3#3.1,7-9 & sel) #ffa058ff
> color (#1.1-3#3.1,7-9 & sel) #ffa158ff
> color (#1.1-3#3.1,7-9 & sel) #ffa057ff
> color (#1.1-3#3.1,7-9 & sel) #ff9f56ff
> color (#1.1-3#3.1,7-9 & sel) #ff9e55ff
> color (#1.1-3#3.1,7-9 & sel) #ff9b52ff
> color (#1.1-3#3.1,7-9 & sel) #ff9950ff
> color (#1.1-3#3.1,7-9 & sel) #ff974eff
> color (#1.1-3#3.1,7-9 & sel) #ff984dff
> select
> #1.1/B#1.2/B#1.3/B#3.1/B#3.2/B#3.3/B#3.4/B#3.5/B#3.6/B#3.7/B#3.8/B#3.9/B
1692 atoms, 1884 bonds, 84 residues, 12 models selected
> color (#1.1-3#3.1,7-9 & sel) #ffa24dff
> color (#1.1-3#3.1,7-9 & sel) #ffb073ff
> color (#1.1-3#3.1,7-9 & sel) #ffb691ff
> color (#1.1-3#3.1,7-9 & sel) #ffbeaaff
> color (#1.1-3#3.1,7-9 & sel) #ffbdacff
> color (#1.1-3#3.1,7-9 & sel) #ffbcacff
> color (#1.1-3#3.1,7-9 & sel) #ffbaadff
> color (#1.1-3#3.1,7-9 & sel) #ffb7b3ff
> color (#1.1-3#3.1,7-9 & sel) #fffbcdff
> color (#1.1-3#3.1,7-9 & sel) #faffceff
> color (#1.1-3#3.1,7-9 & sel) #f5ffcfff
> color (#1.1-3#3.1,7-9 & sel) #dbffc7ff
> color (#1.1-3#3.1,7-9 & sel) #c5ffe8ff
> color (#1.1-3#3.1,7-9 & sel) #bae6ffff
> color (#1.1-3#3.1,7-9 & sel) #b6dfffff
> color (#1.1-3#3.1,7-9 & sel) #b3daffff
> color (#1.1-3#3.1,7-9 & sel) #abc9ffff
> color (#1.1-3#3.1,7-9 & sel) #a9c6ffff
> color (#1.1-3#3.1,7-9 & sel) #a8c5ffff
> color (#1.1-3#3.1,7-9 & sel) #a8c4ffff
> color (#1.1-3#3.1,7-9 & sel) #a6c2ffff
> color (#1.1-3#3.1,7-9 & sel) #a6c1ffff
> color (#1.1-3#3.1,7-9 & sel) #a5c0ffff
> color (#1.1-3#3.1,7-9 & sel) #a4beffff
> color (#1.1-3#3.1,7-9 & sel) #a5beffff
> color (#1.1-3#3.1,7-9 & sel) #a6beffff
> color (#1.1-3#3.1,7-9 & sel) #a8beffff
> color (#1.1-3#3.1,7-9 & sel) #a9bdffff
> color (#1.1-3#3.1,7-9 & sel) #acb7ffff
> color (#1.1-3#3.1,7-9 & sel) #b7acffff
> color (#1.1-3#3.1,7-9 & sel) #b7a8ffff
> color (#1.1-3#3.1,7-9 & sel) #aca1ffff
> color (#1.1-3#3.1,7-9 & sel) #9c97ffff
> color (#1.1-3#3.1,7-9 & sel) #9894ffff
> color (#1.1-3#3.1,7-9 & sel) #9090ffff
> color (#1.1-3#3.1,7-9 & sel) #8f8fffff
> color (#1.1-3#3.1,7-9 & sel) #8e8effff
> color (#1.1-3#3.1,7-9 & sel) #8c8cffff
> color (#1.1-3#3.1,7-9 & sel) #8c8bffff
> color (#1.1-3#3.1,7-9 & sel) #8b8cffff
> color (#1.1-3#3.1,7-9 & sel) #9292ffff
> color (#1.1-3#3.1,7-9 & sel) #9192ffff
> color (#1.1-3#3.1,7-9 & sel) #9ca3ffff
> color (#1.1-3#3.1,7-9 & sel) #a8b8ffff
> color (#1.1-3#3.1,7-9 & sel) #b2fff2ff
> color (#1.1-3#3.1,7-9 & sel) #8effabff
> color (#1.1-3#3.1,7-9 & sel) #8affa4ff
> color (#1.1-3#3.1,7-9 & sel) #6eff78ff
> color (#1.1-3#3.1,7-9 & sel) #6cff74ff
> color (#1.1-3#3.1,7-9 & sel) #63ff67ff
> color (#1.1-3#3.1,7-9 & sel) #59ff55ff
> color (#1.1-3#3.1,7-9 & sel) #58ff53ff
> color (#1.1-3#3.1,7-9 & sel) #57ff52ff
> color (#1.1-3#3.1,7-9 & sel) #57ff51ff
> color (#1.1-3#3.1,7-9 & sel) #56ff4fff
> color (#1.1-3#3.1,7-9 & sel) #55ff4dff
> color (#1.1-3#3.1,7-9 & sel) #56ff4fff
> color (#1.1-3#3.1,7-9 & sel) #56ff50ff
> color (#1.1-3#3.1,7-9 & sel) #57ff50ff
> color (#1.1-3#3.1,7-9 & sel) #5aff57ff
> color (#1.1-3#3.1,7-9 & sel) #c9ffe9ff
> color (#1.1-3#3.1,7-9 & sel) #daeeffff
> color (#1.1-3#3.1,7-9 & sel) #d9e9ffff
> color (#1.1-3#3.1,7-9 & sel) #d9e8ffff
> color (#1.1-3#3.1,7-9 & sel) #d5dfffff
> color (#1.1-3#3.1,7-9 & sel) #d4dcffff
> color (#1.1-3#3.1,7-9 & sel) #d3d9ffff
> color (#1.1-3#3.1,7-9 & sel) #ced1ffff
> color (#1.1-3#3.1,7-9 & sel) #cbcdffff
> color (#1.1-3#3.1,7-9 & sel) #bdc4ffff
> color (#1.1-3#3.1,7-9 & sel) #b7c0ffff
> color (#1.1-3#3.1,7-9 & sel) #b3bdffff
> color (#1.1-3#3.1,7-9 & sel) #b0bbffff
> color (#1.1-3#3.1,7-9 & sel) #b0baffff
> color (#1.1-3#3.1,7-9 & sel) #b1baffff
> color (#1.1-3#3.1,7-9 & sel) #b1b9ffff
> color (#1.1-3#3.1,7-9 & sel) #b2b9ffff
> color (#1.1-3#3.1,7-9 & sel) #b1b8ffff
> color (#1.1-3#3.1,7-9 & sel) #b0b7ffff
> color (#1.1-3#3.1,7-9 & sel) #adb4ffff
> color (#1.1-3#3.1,7-9 & sel) #abb2ffff
> color (#1.1-3#3.1,7-9 & sel) #a4aeffff
> color (#1.1-3#3.1,7-9 & sel) #9ca9ffff
> color (#1.1-3#3.1,7-9 & sel) #9ba9ffff
> color (#1.1-3#3.1,7-9 & sel) #9aa7ffff
> color (#1.1-3#3.1,7-9 & sel) #97a1ffff
> color (#1.1-3#3.1,7-9 & sel) #96a1ffff
> color (#1.1-3#3.1,7-9 & sel) #919dffff
> color (#1.1-3#3.1,7-9 & sel) #8e9bffff
> color (#1.1-3#3.1,7-9 & sel) #8896ffff
> color (#1.1-3#3.1,7-9 & sel) #7b89ffff
> color (#1.1-3#3.1,7-9 & sel) #7685ffff
> color (#1.1-3#3.1,7-9 & sel) #7786ffff
> select
> #1.1/C#1.2/C#1.3/C#3.1/C#3.2/C#3.3/C#3.4/C#3.5/C#3.6/C#3.7/C#3.8/C#3.9/C
3420 atoms, 3816 bonds, 168 residues, 12 models selected
> color (#1.1-3#3.1,7-9 & sel) #ea82cdff
> select
> #1.1/D#1.2/D#1.3/D#3.1/D#3.2/D#3.3/D#3.4/D#3.5/D#3.6/D#3.7/D#3.8/D#3.9/D
2208 atoms, 2472 bonds, 108 residues, 12 models selected
> color /d #ff984dff
> select clear
> save "/Users/danielasanchezgiannakis/Documents/nyu/spring 2025/2t7
> dimer.png" width 894 height 742 supersample 3 transparentBackground true
> save "/Users/danielasanchezgiannakis/Documents/nyu/spring 2025/sticky
> ends.png" width 894 height 742 supersample 3 transparentBackground true
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,12
Model Number: MXCV3LL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6 (23G80)
Kernel Version: Darwin 23.6.0
Time since boot: 6 days, 1 hour, 27 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
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 on Mac waking from sleep |
comment:2 by , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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