![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17696 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 (last modified by )
The following bug report has been submitted:
Platform: macOS-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001fc52fac0 (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, openmm._openmm, openmm.app.internal.compiled, 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, 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, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PIL._imagingmath, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, PIL._webp (total: 121)
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{
"uptime" : 160000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac13,1",
"coalitionID" : 1277,
"osVersion" : {
"train" : "macOS 14.4.1",
"build" : "23E224",
"releaseType" : "User"
},
"captureTime" : "2025-05-16 09:22:33.2797 +0800",
"codeSigningMonitor" : 1,
"incident" : "6301F210-D73F-41EC-A7F9-040DB958B78B",
"pid" : 11993,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-15 09:57:32.3573 +0800",
"procStartAbsTime" : 3006544653752,
"procExitAbsTime" : 4008317055815,
"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":"76FE78C1-201A-5F49-ADFA-10F0B74B8E9F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "127FC16E-3970-D18B-F1C5-9EA938FF4171",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 10,
"sleepWakeUUID" : "392715EA-36A3-4B70-BB72-BA2E87F3F885",
"sip" : "enabled",
"vmRegionInfo" : "0x4433e94a9978 is not in any region. Bytes after previous region: 74508711663993 Bytes before following region: 30563368265352\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, 0x0000c433e94a9978","rawCodes":[1,215727236356472],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000c433e94a9978 -> 0x00004433e94a9978 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":11993},
"vmregioninfo" : "0x4433e94a9978 is not in any region. Bytes after previous region: 74508711663993 Bytes before following region: 30563368265352\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 =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/admin/Desktop/FGH-allS DNA.cxs"
Log from Wed May 14 14:35:55 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/admin/Desktop/FGH-allS DNA.cxs"
Log from Wed May 14 13:57:59 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
[deleted to fit within ticket limits]
> hbonds sel showDist true restrict cross select true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2_All-S_DNA_ir-F.pdb
66 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A LYS 428 NZ /D GLU 68 OE2 /A LYS 428 3HZ 3.542 2.919
/D ASN 12 ND2 /K DT 14 OP1 /D ASN 12 2HD2 3.351 2.512
/D LYS 24 NZ /K DC 12 O2 /D LYS 24 1HZ 2.578 1.977
/D LYS 24 NZ /K DC 12 OP2 /D LYS 24 3HZ 2.831 2.079
/D ARG 87 NH2 /B GLU 435 O /D ARG 87 1HH2 3.528 2.879
/D TYR 346 OH /K DG 13 OP1 /D TYR 346 HH 3.427 2.705
/D GLN 373 NE2 /E ASP 823 OD1 /D GLN 373 1HE2 3.310 2.483
/D GLN 373 NE2 /E ASP 823 OD2 /D GLN 373 1HE2 3.125 2.459
/D ARG 420 NE /E ASP 827 OD2 /D ARG 420 HE 3.242 2.483
/E ARG 230 NH1 /D SER 221 OG /E ARG 230 1HH1 3.066 2.357
/J DG 11 N1 /K DC 30 N3 /J DG 11 H1 2.872 2.075
/J DG 11 N2 /K DC 30 N3 /J DG 11 H21 3.565 2.917
/J DG 11 N2 /K DC 30 O2 /J DG 11 H21 2.647 1.840
/J DG 12 N1 /K DC 29 N3 /J DG 12 H1 2.866 2.019
/J DG 12 N2 /K DC 29 N3 /J DG 12 H21 3.618 2.961
/J DG 12 N2 /K DC 29 O2 /J DG 12 H21 2.764 1.927
/J DT 13 N3 /K DA 27 N1 /J DT 13 H3 2.922 2.262
/J DC 15 N4 /K DG 26 O6 /J DC 15 H41 2.871 2.054
/J DT 16 N3 /K DA 25 N1 /J DT 16 H3 2.743 2.012
/J DC 17 N4 /K DG 24 O6 /J DC 17 H41 2.883 2.046
/J DC 18 N4 /K DG 23 O6 /J DC 18 H41 2.912 2.055
/J DC 19 N4 /K DG 22 O6 /J DC 19 H41 2.913 2.068
/J DA 20 N6 /K DT 21 O4 /J DA 20 H61 2.931 2.082
/J DG 21 N1 /K DC 20 N3 /J DG 21 H1 2.900 2.056
/J DG 21 N2 /K DC 20 N3 /J DG 21 H21 3.636 2.980
/J DG 21 N2 /K DC 20 O2 /J DG 21 H21 2.807 1.988
/J DT 22 N3 /K DA 19 N1 /J DT 22 H3 2.802 1.952
/J DC 23 N4 /K DG 18 O6 /J DC 23 H41 2.902 2.043
/J DA 24 N6 /K DT 17 O4 /J DA 24 H61 2.883 2.080
/J DC 25 N4 /K DG 16 O6 /J DC 25 H42 2.906 2.051
/J DG 26 N1 /K DC 15 N3 /J DG 26 H1 2.912 2.079
/J DG 26 N2 /K DC 15 N3 /J DG 26 H21 3.655 3.001
/J DG 26 N2 /K DC 15 O2 /J DG 26 H21 2.829 2.003
/J DA 27 N6 /K DT 14 O4 /J DA 27 H61 3.420 2.797
/J DG 29 N1 /K DG 13 N7 /J DG 29 H1 3.247 2.523
/J DT 30 N3 /K DA 11 N1 /J DT 30 H3 3.126 2.507
/K DC 9 N4 /J DA 34 N6 /K DC 9 H41 3.080 2.473
/K DA 10 N6 /J DT 31 O4 /K DA 10 H62 3.679 3.012
/K DA 11 N6 /J DT 30 O4 /K DA 11 H61 3.027 2.305
/K DC 15 N4 /J DG 26 O6 /K DC 15 H41 2.898 2.040
/K DG 16 N1 /J DC 25 N3 /K DG 16 H1 2.871 2.086
/K DG 16 N2 /J DC 25 N3 /K DG 16 H21 3.611 2.979
/K DG 16 N2 /J DC 25 O2 /K DG 16 H21 2.742 1.921
/K DT 17 N3 /J DA 24 N1 /K DT 17 H3 2.832 2.216
/K DG 18 N1 /J DC 23 N3 /K DG 18 H1 2.860 2.001
/K DG 18 N2 /J DC 23 N3 /K DG 18 H21 3.586 2.925
/K DG 18 N2 /J DC 23 O2 /K DG 18 H21 2.741 1.892
/K DA 19 N6 /J DT 22 O4 /K DA 19 H61 2.923 2.067
/K DC 20 N4 /J DG 21 O6 /K DC 20 H41 2.908 2.051
/K DT 21 N3 /J DA 20 N1 /K DT 21 H3 2.892 2.032
/K DG 22 N1 /J DC 19 N3 /K DG 22 H1 2.892 2.051
/K DG 22 N2 /J DC 19 N3 /K DG 22 H21 3.632 2.981
/K DG 22 N2 /J DC 19 O2 /K DG 22 H21 2.769 1.927
/K DG 23 N1 /J DC 18 N3 /K DG 23 H1 2.876 2.027
/K DG 23 N2 /J DC 18 N3 /K DG 23 H21 3.618 2.963
/K DG 23 N2 /J DC 18 O2 /K DG 23 H21 2.745 1.894
/K DG 24 N1 /J DC 17 N3 /K DG 24 H1 2.884 2.045
/K DG 24 N2 /J DC 17 N3 /K DG 24 H21 3.630 2.981
/K DG 24 N2 /J DC 17 O2 /K DG 24 H21 2.792 1.940
/K DA 25 N6 /J DT 16 O4 /K DA 25 H61 3.017 2.373
/K DG 26 N1 /J DC 15 N3 /K DG 26 H1 2.895 2.273
/K DG 26 N2 /J DC 15 N3 /K DG 26 H21 3.677 3.125
/K DG 26 N2 /J DC 15 O2 /K DG 26 H21 2.815 2.156
/K DA 27 N6 /J DT 13 O4 /K DA 27 H61 2.869 2.246
/K DC 29 N4 /J DG 12 O6 /K DC 29 H41 2.885 2.033
/K DC 30 N4 /J DG 11 O6 /K DC 30 H41 2.992 2.235
66 hydrogen bonds found
> select ((/J & ::polymer_type>0 ) & ((/D & ::polymer_type>0 ) :<3.5)) | ((/D & ::polymer_type>0 ) & ((/J & ::polymer_type>0 ) :<3.5))
344 atoms, 353 bonds, 13 residues, 1 model selected
> select ((/J & ::polymer_type>0 ) & ((/D & ::polymer_type>0 ) :<3.5)) | ((/D & ::polymer_type>0 ) & ((/J & ::polymer_type>0 ) :<3.5))
344 atoms, 353 bonds, 13 residues, 1 model selected
> help help:user/selectcontacts.html
> contacts sel select true makePseudobonds false
405 contacts
> ui tool show Contacts
> select clear
> hide atoms
> ui tool show H-Bonds
> size pseudobondRadius +0.5
Changed 66 pseudobond radii
> show atoms
> size pseudobondRadius -0.5
Changed 66 pseudobond radii
> size pseudobondRadius -0.1
Cannot reduce pseudobond radius to <= 0
> size pseudobondRadius -0.1
Cannot reduce pseudobond radius to <= 0
> size pseudobondRadius -0.1
Cannot reduce pseudobond radius to <= 0
> size pseudobondRadius \- 0.1
Invalid "pseudobondRadius" argument: Expected a number >= 0 or a +/- delta
> size pseudobondRadius /- 0.1
Invalid "pseudobondRadius" argument: Expected a number >= 0 or a +/- delta
> size pseudobondRadius -0.1
Cannot reduce pseudobond radius to <= 0
> size pseudobondRadius -
Invalid "pseudobondRadius" argument: Expected a number >= 0 or a +/- delta
> size pseudobondRadius -1
Cannot reduce pseudobond radius to <= 0
> size pseudobondRadius \- 0.5
Invalid "pseudobondRadius" argument: Expected a number >= 0 or a +/- delta
> size pseudobondRadius \- .5
Invalid "pseudobondRadius" argument: Expected a number >= 0 or a +/- delta
> hide atoms
> size pseudobondRadius .5
Changed 66 pseudobond radii
> show atoms
> size pseudobondRadius .1
Changed 66 pseudobond radii
> size pseudobondRadius 0.3
Changed 66 pseudobond radii
> size pseudobondRadius 0.2
Changed 66 pseudobond radii
> hbonds /J /D saltOnly=false, restrict=cross, select=true, reveal=true,
> showDist=true, color=green, radius=0.1, dashes=5, name=j_d_hbonds
Expected a keyword
> ui tool show Shell
> hbonds #J to #D color green distance true radius 0.1 dashes 5 name
> j_d_hbonds
Expected a keyword
> hide atoms
> hbonds /j restrict /d
6 hydrogen bonds found
> hbonds /j restrict /d reveal true
6 hydrogen bonds found
> `open help:user/tutorials/binding-sites.html`
Unknown command: `open help:user/tutorials/binding-sites.html`
> open help:user/tutorials/binding-sites.html
Opened help:user/tutorials/binding-sites.html
> label @@display
> hbonds /j restrict /e reveal true
0 hydrogen bonds found
> hbonds /j restrict /d/e reveal true
6 hydrogen bonds found
> hbonds /j/k restrict /d/e reveal true
11 hydrogen bonds found
> abel @@display
Unknown command: abel @@display
> abel @@display
Unknown command: abel @@display
> label @@display
> size pseudobondRadius 0.2
Changed 11 pseudobond radii
> hbonds /j/k restrict /d/e reveal true name 1
11 hydrogen bonds found
> select 1
Expected an objects specifier or a keyword
> label height 1.0
> select add #1
65734 atoms, 66619 bonds, 22 pseudobonds, 4000 residues, 4 models selected
> color (#!1 & sel) byhetero
> select clear
> save "/Users/admin/Desktop/FGH-allS DNA.cxs"
——— End of log from Wed May 14 10:48:39 2025 ———
opened ChimeraX session
> label height 2.0
> color label
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> label color red
> label color yellow
> save "/Users/admin/Desktop/FGH-allS DNA.cxs"
> select /K:24@O4'
1 atom, 1 residue, 1 model selected
> label delete
> select /D:344@CZ
1 atom, 1 residue, 1 model selected
> select clear
> select add /D:360
17 atoms, 17 bonds, 1 residue, 1 model selected
> select add /E:302@CZ
18 atoms, 17 bonds, 2 residues, 1 model selected
> label sel
> label delete
> lighting soft
> lighting simple
> lighting soft
> set bgColor white
> lighting full
> lighting soft
> set bgColor black
> lighting shadows true intensity 0.5
> graphics silhouettes true
> lighting flat
> lighting full
> lighting soft
> label @ca
> label delete
> select clear
> view hbood
Expected an objects specifier or a view name or a keyword
> view /j/k
> lighting full
> set bgColor white
> lighting full
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> select /D:336@CG
1 atom, 1 residue, 1 model selected
> select /D:9@CD
1 atom, 1 residue, 1 model selected
> select clear
> select /E:299
10 atoms, 9 bonds, 1 residue, 1 model selected
> select add /D:98
17 atoms, 19 bonds, 1 residue, 1 model selected
> select /D:9,12
36 atoms, 34 bonds, 2 residues, 1 model selected
> select /D:9,12,264,267,336,344,364
145 atoms, 138 bonds, 7 residues, 1 model selected
> select /D:9,12,264,267,336,344,346
142 atoms, 136 bonds, 7 residues, 1 model selected
> select /D:9,12,24,267,336,344,346,302
167 atoms, 161 bonds, 8 residues, 1 model selected
> select /D:9,12,24,267,336,344,346, /E:302
Expected an objects specifier or a keyword
> select /D:9,12,24,267,336,344,346 /E:302
171 atoms, 164 bonds, 8 residues, 1 model selected
> save "/Users/admin/Desktop/FGH-allS DNA.cxs"
> abel @@display
Unknown command: abel @@display
> label @@display
> label @display
> label delete
> label @display
[Repeated 1 time(s)]
> label sel
> label height 1.0
> label color yellow
> label height 2.0
> label height 1.5
> label color black
> select ~sel & ##selected
65563 atoms, 66455 bonds, 22 pseudobonds, 3992 residues, 3 models selected
> save "/Users/admin/Desktop/FGH-allS DNA.cxs"
> select clear
> label height 2.0
> label color yellow
> select clear
> set bgColor black
> select /i/h
Nothing selected
> select /l/m
1051 atoms, 1133 bonds, 33 residues, 1 model selected
> hbonds /l/m restrict /c/f reveal true
0 hydrogen bonds found
> select ~sel & ##selected
64683 atoms, 65486 bonds, 11 pseudobonds, 3967 residues, 2 models selected
> select ~sel & ##selected
1051 atoms, 1133 bonds, 33 residues, 1 model selected
> select ~sel & ##selected
64683 atoms, 65486 bonds, 11 pseudobonds, 3967 residues, 2 models selected
> select clear
> hbonds /l/m restrict /G/f reveal true
4 hydrogen bonds found
> select clear
> size pseudobondRadius 1.5
Changed 15 pseudobond radii
> size pseudobondRadius .5
Changed 15 pseudobond radii
> size pseudobondRadius .2
Changed 15 pseudobond radii
> select /G:339,12,24
60 atoms, 57 bonds, 3 residues, 1 model selected
> label sel
> label sel color yellow height 2.0
> label sel color yellow height 1.5
> save "/Users/admin/Desktop/FGH-allS DNA.cxs"
> select clear
> view list
Named views: 1
> view 1
> view /j/k
> view name 1
> view /m/l
> view name 2
> view
> view name 3
> view list
Named views: 1, 2, 3
> view 3
> save "/Users/admin/Desktop/FGH-allS DNA.cxs"
——— End of log from Wed May 14 13:57:59 2025 ———
opened ChimeraX session
> changechains sel
Missing or invalid "fromIds" argument: Expected a text string
> changechains /E
Missing or invalid "fromIds" argument: Expected a text string
> open 6oej
6oej title:
Crystal structure of the non-neutralizing and ADCC-potent antibody C11 In
complex with hiv-1 clade A/E GP120 [more info...]
Chain information for 6oej #2
---
Chain | Description | UniProt
A G | clade A/E 93TH057 HIV-1 gp120 core | A0A0M3KKW9_9HIV1 44-492
B H | C11 Fab heavy chain |
C L | C11 Fab light chain |
Non-standard residues in 6oej #2
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
6oej mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> changechains glycosylations
Chain IDs of 8 residues changed
> info
6 models
#1, 2_All-S_DNA_ir-F.pdb, shown
65734 atoms, 66619 bonds, 4000 residues, 10 chains (E,A,J,K,B,F,D,G,L,M)
11 1, 4 hydrogen bonds
#1.1, hydrogen bonds, shown, 4 pseudobonds
#1.2, labels, shown, 22 triangles
#1.3, 1, shown, 11 pseudobonds
#2, 6oej, shown
12140 atoms, 12455 bonds, 1556 residues, 6 chains (G,H,L,A,B,C)
10 missing structure
#2.1, missing structure, shown, 10 pseudobonds
> log metadata #2
Metadata for 6oej #2
---
Title | Crystal structure of the non-neutralizing and ADCC-potent antibody C11 In complex with hiv-1 clade A/E GP120
Citation | Tolbert, W.D., Van, V., Sherburn, R., Tuyishime, M., Yan, F., Nguyen, D.N., Stanfield-Oakley, S., Easterhoff, D., Bonsignori, M., Haynes, B.F., Moody, M.A., Ray, K., Ferrari, G., Lewis, G.K., Pazgier, M. (2020). Recognition Patterns of the C1/C2 Epitopes Involved in Fc-Mediated Response in HIV-1 Natural Infection and the RV114 Vaccine Trial. Mbio, 11. PMID: 32605979. DOI: 10.1128/mBio.00208-20
Non-standard residues | BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
Gene sources | Human immunodeficiency virus 1
Homo sapiens
Experimental method | X-ray diffraction
Resolution | 3.45Å
> 6oej title
Unknown command: 6oej title
> Chain information for 6oej #2
Unknown command: Chain information for 6oej #2
> changechains /G G C
Proposed chainID change conflicts with existing residue 6oej #2/C ASN 31
> close #2
> changechains /G G C
Chain IDs of 440 residues changed
> info
4 models
#1, 2_All-S_DNA_ir-F.pdb, shown
65734 atoms, 66619 bonds, 4000 residues, 10 chains (E,A,J,K,B,F,D,C,L,M)
11 1, 4 hydrogen bonds
#1.1, hydrogen bonds, shown, 4 pseudobonds
#1.2, labels, shown, 22 triangles
#1.3, 1, shown, 11 pseudobonds
> save "/Users/admin/Desktop/FGH-allS DNA.cxs"
> ui tool show "Change Chain IDs"
> changechains L H
Chain IDs of 16 residues changed
> changechains M I
Chain IDs of 17 residues changed
Must select one or more chain IDs from the list on the left
> save "/Users/admin/Desktop/FGH-allS DNA.cxs"
——— End of log from Wed May 14 14:35:55 2025 ———
opened ChimeraX session
> set bgColor white
> save "/Users/admin/Desktop/FGH-2S DNA.cxs"
> select clear
> show surfaces
> hide #1.1 models
> hide #1.2 models
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> lighting flat
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting full
> hide #1.10 models
> show #1.10 models
> hide #1.10 models
> show #1.10 models
> hide #1.12 models
> hide #1.13 models
> show atoms
> hide cartoons
> delete h
Missing or invalid "atoms" argument: invalid atoms specifier
> delete atoms h
Expected a keyword
> show #1.12 models
> show #1.13 models
> show cartoons
> hide #1.10 models
> show #1.10 models
> hide #1.12 models
> hide #1.13 models
> hide atoms
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> show surfaces
> hide #1.12 models
> hide #1.13 models
> color #1.12 #f9697cff
> color #1.12 #f97973ff
> undo
[Repeated 8 time(s)]
> color #1.12 lime
> save "/Users/admin/Desktop/FGH all S.tif" width 1344 height 903 supersample
> 3 transparentBackground true
> show #1.1 models
> hide #1.1 models
> show #1.12 models
> show #1.13 models
> color #1.12 #00ff0078
> color #1.13 #00ff007f
> color #1.13 #00ff0080
> color #1.7 #cecaf17c
> color #1.7 #cecaf17d
> color #1.8 #b2d9f77d
> select clear
> hide #1.12 models
> hide #1.13 models
> show #1.12 models
> show #1.13 models
> hide #1.12 models
> hide #1.13 models
> show #1.12 models
> show #1.13 models
> color #1.12 lime
> color #1.13 lime
> color #1.8 #b2d9f7ff
> lighting simple
> lighting soft
> lighting full
> lighting soft
> color #1.7 #cecaf1ff
> save "/Users/admin/Desktop/FGH all S.tif" width 1344 height 903 supersample
> 3 transparentBackground true
> save "/Users/admin/Desktop/FGH all S-1.tif" width 1344 height 903
> supersample 3 transparentBackground true
> select /h/i
1051 atoms, 1133 bonds, 33 residues, 1 model selected
> view sel
> view
> view name 4
> save "/Users/admin/Desktop/FGH all S-2.tif" width 1344 height 903
> supersample 3 transparentBackground true
> view name 4
> select clear
> save "/Users/admin/Desktop/FGH all S-2.tif" width 1344 height 903
> supersample 3 transparentBackground true
> save "/Users/admin/Desktop/FGH all S-1.tif" width 1344 height 903
> supersample 3 transparentBackground true
> view name 6
> view name 5
> view list
Named views: 1, 2, 3, 4, 5, 6
> view 5
> view 6
> save "/Users/admin/Desktop/FGH all S.tif" width 1344 height 903 supersample
> 3 transparentBackground true
> save "/Users/admin/Desktop/FGH-allS DNA.cxs"
——— End of log from Thu May 15 17:19:26 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
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: Mac Studio
Model Identifier: Mac13,1
Model Number: MJMV3LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.101.3
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 3天23小时25分钟
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Redmi 238 NFS:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Redmi 238 NFS:
Resolution: 1080 x 1920
UI Looks like: 1080 x 1920 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: 90
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
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
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-Clipper: 0.24.0
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-ISOLDE: 1.9
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
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
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
more-itertools: 10.3.0
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
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
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
platformdirs: 4.2.2
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
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
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: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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