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Opened 9 months ago
Closed 9 months ago
#16976 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-15.3.1-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 0x0000000200af0840 (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.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.mlp._mlp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 120)
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{
"uptime" : 70000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,15",
"coalitionID" : 14828,
"osVersion" : {
"train" : "macOS 15.3.1",
"build" : "24D70",
"releaseType" : "User"
},
"captureTime" : "2025-02-26 20:25:41.6545 -0600",
"codeSigningMonitor" : 1,
"incident" : "78E1A6B4-ADDC-49B0-B69B-E5A4870CD026",
"pid" : 12532,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-26 11:34:51.3645 -0600",
"procStartAbsTime" : 1272913627231,
"procExitAbsTime" : 1689545436989,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"crashReporterKey" : "6719B730-4B00-14D8-AF63-CADBC36C0A0C",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"wakeTime" : 5,
"sleepWakeUUID" : "94600CE1-2CC8-45CB-8B73-3B1002904E42",
"sip" : "enabled",
"vmRegionInfo" : "0x580b8ac2cb08 is not in any region. Bytes after previous region: 96325559569161 Bytes before following region: 8746520360184\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, 0x0000d80b8ac2cb08","rawCodes":[1,237544084261640],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000d80b8ac2cb08 -> 0x0000580b8ac2cb08 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":12532},
"vmregioninfo" : "0x580b8ac2cb08 is not in any region. Bytes after previous region: 96325559569161 Bytes before following region: 8746520360184\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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===== 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/mohamed/Documents/Research/Projects/WSCP/2024_reppert/paper_data_2025/With_water/Q57E/CDC/extended_most_occ_pH8.pdb
> format pdb
Chain information for extended_most_occ_pH8.pdb #1
---
Chain | Description
A | No description available
B | No description available
C D | No description available
Computing secondary structure
> set bgColor white
> color #1 #bfbfbfff
> show nucleic
> hide protein|solvent|H
> surface hidePatches
> style (protein|nucleic|solvent) & @@draw_mode=0 stick
Changed 0 atom styles
> cartoon
> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20
> cartoon style ~(nucleic|strand) xsection round
> cartoon style (nucleic|strand) xsection rectangle
> cartoon style protein modeHelix tube radius 2 sides 24 thickness 0.6
> cartoon style nucleic xsection round width 1.6 thickness 1.6
> nucleotides stubs
> style (protein|nucleic|solvent) & @@draw_mode=0 stick
Changed 0 atom styles
> surface
> color white target s transparency 80
> color :CLA green
> color :CHL green
> color :BCR #FF8C00
> color :XAT #FF8C00
> color :LUT #FF8C00
> color :NEX #FF8C00
> lighting full
> graphics silhouettes true
> transparency 80 target r
> show nucleic
> hide protein|solvent|H
> surface hidePatches
> style (protein|nucleic|solvent) & @@draw_mode=0 stick
Changed 0 atom styles
> ~worm
> cartoon
> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20
> cartoon style ~(nucleic|strand) xsection round
> cartoon style (nucleic|strand) xsection rectangle
> cartoon style protein modeHelix tube radius 2 sides 24 thickness 0.6
> cartoon style nucleic xsection round width 1.6 thickness 1.6
> nucleotides stubs
> select :57,
Expected an objects specifier or a keyword
> select :57
63 atoms, 59 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 63 atom styles
> color sel byhetero
> select :CLA
548 atoms, 556 bonds, 10 pseudobonds, 4 residues, 2 models selected
> show sel atoms
> style sel ball
Changed 548 atom styles
> color sel byhetero
> help help:credits.html
> hide cartoons
> ui mousemode right select
Drag select of 26 atoms, 25 bonds
> select up
28 atoms, 26 bonds, 2 residues, 3 models selected
> select up
32 atoms, 30 bonds, 2 residues, 3 models selected
> mlp sel
Map values for surface "extended_most_occ_pH8.pdb_C SES surface": minimum
-31.54, mean -5.161, maximum 27.03
Map values for surface "extended_most_occ_pH8.pdb_D SES surface": minimum
-27.38, mean -5.36, maximum 26.14
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
274 atoms, 278 bonds, 2 residues, 1 model selected
> mlp sel
mlp: no amino acids specified
Drag select of 185 atoms, 5 pseudobonds, 197 bonds
> select up
196 atoms, 199 bonds, 5 pseudobonds, 4 residues, 4 models selected
> select up
305 atoms, 307 bonds, 5 pseudobonds, 4 residues, 4 models selected
> mlp sel
Map values for surface "extended_most_occ_pH8.pdb_A SES surface": minimum
-27.58, mean -4.913, maximum 26.76
Map values for surface "extended_most_occ_pH8.pdb_B SES surface": minimum
-26.55, mean 8.672e+22, maximum 9.261e+24
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> select clear
> hide surfaces
> ui mousemode right distance
> distance /C:1001@OBD /D:1001@OBD
Distance between /C CLA 1001 OBD and /D CLA 1001 OBD: 5.559Å
> distance /A:1001@OBD /B:1001@OBD
Distance between /A CLA 1001 OBD and /B CLA 1001 OBD: 5.785Å
> distance /D:57@CD /C:57@CD
Distance between /D GLU 57 CD and /C GLU 57 CD: 5.726Å
> distance /B:57@CD /A:57@CD
Distance between /B GLU 57 CD and /A GLU 57 CD: 4.285Å
> show ribons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show cartoons
> ui mousemode right select
> select /A:59
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:54
19 atoms, 18 bonds, 1 residue, 1 model selected
> help help:credits.html
> hide cartoons
> show /A:54,55,56,57,58,59
> style sel ball
Changed 19 atom styles
> color sel byhetero
> show /B:54,55,56,57,58,59
> color sel byhetero
> style sel ball
Changed 19 atom styles
> show /C:54,55,56,57,58,59
> style sel ball
Changed 19 atom styles
> color sel byhetero
> show /D:54,55,56,57,58,59
> style sel ball
Changed 19 atom styles
> color sel byhetero
> select :CLA
548 atoms, 556 bonds, 12 pseudobonds, 4 residues, 3 models selected
> ~select
> :CLA@CAD,CBD,OBD,CHA,CHB,CHC,CHD,C1A,C1B,C1C,C1D,N1A,N1B,N1C,N1D,C2A,C2B,C2C,C2D,C3A,C3B,C3C,C3D,C4A,C4B,C4C,C4D,MG
436 atoms, 372 bonds, 4 residues, 1 model selected
> delete sel
> select :CHL
Nothing selected
> ~select
> :CHL@CAD,CBD,OBD,CHA,CHB,CHC,CHD,C1A,C1B,C1C,C1D,N1A,N1B,N1C,N1D,C2A,C2B,C2C,C2D,C3A,C3B,C3C,C3D,C4A,C4B,C4C,C4D,MG
Nothing selected
> delete sel
> show /D:54,55,56,57,58,59
> style ball
Changed 10651 atom styles
> color byhetero
> ui mousemode right distance
> distance /A:57@N /A:54@O
Distance between /A GLU 57 N and LEU 54 O: 3.368Å
> distance /B:54@O /B:57@N
Distance between /B LEU 54 O and GLU 57 N: 3.356Å
> distance /C:57@N /C:54@O
Distance between /C GLU 57 N and LEU 54 O: 3.366Å
> distance /D:57@N /D:54@O
Distance between /D GLU 57 N and LEU 54 O: 3.351Å
> label height 1.3
> ui mousemode right label
> label #1/A:56
> label /A:56 text {0.chain_id}_{0.name}_{0.number}
> label /B:56 text {0.chain_id}_{0.name}_{0.number}
> label /C:56 text {0.chain_id}_{0.name}_{0.number}
> label /D:56 text {0.chain_id}_{0.name}_{0.number}
> set stick_trancperency
Expected a keyword
> label #1/B:57
> label #1/A:57
> ui mousemode right select
> ui mousemode right label
> label delete residues
> hide #!2 models
> show #!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 #1.1 models
> hide #1.2 models
> hide #1.3 models
> hide #1.4 models
> hide #1.5 models
> hide #1.6 models
> view #2 clip false
> label /C:56 text {0.chain_id}_{0.name}_{0.number}
> label /D:56 text {0.chain_id}_{0.name}_{0.number}
> ui mousemode right distance
> distance /C:54@O /D:54@O
Distance between /C LEU 54 O and /D LEU 54 O: 14.465Å
> ui mousemode right label
> label #1/C:54
> label #1/D:54
> ui mousemode right distance
> distance /B:54@O /A:54@O
Distance between /B LEU 54 O and /A LEU 54 O: 14.532Å
> ui mousemode right select
> transparency -a 0.5
Missing or invalid "percent" argument: Expected a number
> transparency -a 6
Missing or invalid "percent" argument: Expected a number
> transparency a 6
Missing or invalid "percent" argument: Expected a number
> transparency 6 a
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 6 atoms
> transparency 90 atoms
> transparency 90 atoms sele
Expected ',' or a keyword
> transparency 90 atoms :57
Expected ',' or a keyword
> transparency 90 atoms, :57
Missing or invalid "what" argument: Should be one of 'All', 'atoms', 'bonds',
'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or
'surfaces'
> transparency/B 80 target a
Unknown command: transparency/B 80 target a
> transparency/B 80 target atoms
Unknown command: transparency/B 80 target atoms
> transparency/B 80 target r
Unknown command: transparency/B 80 target r
> show cartoons
> transparency 90 cartoons
> ui tool show "Side View"
> transparency 90 atoms
> transparency 40 atoms
> color bychain
> color byhetero
> hide #!2 models
> select clear
> color byhetero
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> color sel byhetero
> style sel ball
Changed 19 atom styles
> style sel sphere
Changed 19 atom styles
> style sel sphere
Changed 19 atom styles
> style sel stick
Changed 19 atom styles
> style sel ball
Changed 19 atom styles
> select /A:55@CD
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 2 models selected
> hide sel atoms
> select /A:56@CD1
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 2 models selected
> hide sel atoms
> select /A:57@CD
1 atom, 1 residue, 1 model selected
> select clear
> select /A:58@CD
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 2 models selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select @@serial_number=8994
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 2 models selected
> hide sel atoms
> select /B:56@CZ
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 2 models selected
> hide sel atoms
> ui mousemode right distance
> distance /A:54@CG /B:54@CG
Distance between /A LEU 54 CG and /B LEU 54 CG: 13.534Å
> distance /A:54@CG /B:54@CG
Distance already exists; modify distance properties with 'distance style'
> show #!2 models
> hide #2.1 models
> close #2
> distance /B:54@CG /A:54@CG
Distance between /B LEU 54 CG and /A LEU 54 CG: 13.534Å
> ui mousemode right select
> select clear
> set bgColor white
> color #1 #bfbfbfff
> show nucleic
> hide protein|solvent|H
> surface hidePatches
> style (protein|nucleic|solvent) & @@draw_mode=0 stick
Changed 0 atom styles
> cartoon
> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20
> cartoon style ~(nucleic|strand) xsection round
> cartoon style (nucleic|strand) xsection rectangle
> cartoon style protein modeHelix tube radius 2 sides 24 thickness 0.6
> cartoon style nucleic xsection round width 1.6 thickness 1.6
> nucleotides stubs
> style (protein|nucleic|solvent) & @@draw_mode=0 stick
Changed 0 atom styles
> surface
> color white target s transparency 80
> color :CLA green
> color :CHL green
> color :BCR #FF8C00
> color :XAT #FF8C00
> color :LUT #FF8C00
> color :NEX #FF8C00
> lighting full
> graphics silhouettes true
> transparency 80 target r
> show nucleic
> hide protein|solvent|H
> surface hidePatches
> style (protein|nucleic|solvent) & @@draw_mode=0 stick
Changed 0 atom styles
> ~worm
> cartoon
> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20
> cartoon style ~(nucleic|strand) xsection round
> cartoon style (nucleic|strand) xsection rectangle
> cartoon style protein modeHelix tube radius 2 sides 24 thickness 0.6
> cartoon style nucleic xsection round width 1.6 thickness 1.6
> nucleotides stubs
> show :54,57
> select :54,57
139 atoms, 131 bonds, 1 pseudobond, 8 residues, 2 models selected
> style sel ball
Changed 139 atom styles
> color sel byhetero
> hbonds sel reveal true
21 hydrogen bonds found
> ~hbonds
> color sel bychain
> select @@serial_number=27558
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 2 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:52@OG1
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 2 models selected
> hide sel atoms
> select /B:52@CB
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 2 models selected
> hide sel atoms
> select /B:1001@C4C
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 32 bonds, 1 residue, 1 model selected
> color sel byhetero
> select /A:1001@N1C
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 32 bonds, 1 residue, 1 model selected
> color sel byhetero
> select @@serial_number=28659
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 2 bonds, 1 residue, 1 model selected
> style sel ball
Changed 3 atom styles
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> color sel byhetero
> label height 1.3
> ui mousemode right "move label"
> color #2.1 #424242ff models
> color #2.1 #212121ff models
> color #2.1 silver models
> color #2.1 #0096ffff models
> color #2.1 #00fdffff models
> color #2.1 #ffd479ff models
> color #2.1 #941100ff models
> color #2.1 black models
> color #2.1 #212121ff models
> color #2.1 #424242ff models
> color #2.1 black models
> ui mousemode right distance
> distance /A:54@CA /B:54@CA
Distance between /A LEU 54 CA and /B LEU 54 CA: 15.943Å
> hide #1.7 models
> show #1.7 models
> hide #1.7 models
> show #1.7 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 target m
> close #2.1
> close #2
> distance /B:54@CA /A:54@CA
Distance between /B LEU 54 CA and /A LEU 54 CA: 15.943Å
> color #2.1 black models
> label height 1.3
> ui mousemode right select
> select /A:35
16 atoms, 15 bonds, 1 residue, 1 model selected
> select clear
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
31 atoms, 29 bonds, 2 residues, 3 models selected
> style sel ball
Changed 31 atom styles
> color sel byhetero
> select clear
> ui mousemode right "move label"
> color #2 #0433ffff models
> color #2 #011993ff models
> color #2 darkgrey models
> color #2 #d6d6d6ff models
> color #2 #424242ff models
> color #2 black models
> color #2 #ff2600ff models
> color #2 black models
> ui mousemode right label
> label #1/A:54
> label #1/B:54
> label #1/B:57
> label #1/A:57
> label #1/B:1001
> label #1/A:1001
> ui mousemode right "move label"
> label :CLA,54,57 text {0.chain_id}_{0.name}
> label :CLA,54,57 text {0.chain_id}_{0.name}_{0.number}
> label height 1.3
> label height 1
> ui mousemode right label
> label #1/B:1001
> label :54,57 text {0.chain_id}_{0.name}_{0.number}
> label :CLA text {0.chain_id}_{0.name}
> label height 1.3
> label height 1
> ui mousemode right "move label"
> label :54,57 text {0.chain_id}/{0.name}{0.number}
> save CD_pocket.png transparentBackground true
> save /Users/mohamed/Documents/Chimera_working_dir/Q57E_AB_pocket.cxs
> ui mousemode right distance
> hide #!2 models
> show #!2 models
> ui mousemode right label
> ui mousemode right distance
> close #2
> distance /C:54@CA /D:54@CA
Distance between /C LEU 54 CA and /D LEU 54 CA: 16.019Å
> ui mousemode right select
> select /C:52@CG2
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 2 models selected
> color sel byhetero
> style sel ball
Changed 14 atom styles
> hbonds sel reveal true
3 hydrogen bonds found
> ui mousemode right distance
> distance /D:54@CG /C:54@CG
Distance between /D LEU 54 CG and /C LEU 54 CG: 13.284Å
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> show #!2 models
> close #2
> distance /D:54@CG /C:54@CG
Distance between /D LEU 54 CG and /C LEU 54 CG: 13.284Å
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 2 models selected
> hide sel atoms
> select @@serial_number=30833
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 2 bonds, 1 residue, 1 model selected
> color sel byhetero
> select @@serial_number=29627
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 2 bonds, 1 residue, 1 model selected
> color sel byhetero
> select @@serial_number=30521
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 2 bonds, 1 residue, 1 model selected
> color sel byhetero
> ui mousemode right label
> label delete residues
> label #1/D:54
> label #1/D:57
> label #1/C:54
> label #1/C:57
> label #1/C:1001
> label :54,57 text {0.chain_id}_{0.name}_{0.number}
> label :CLA text {0.chain_id}_{0.name}
> label height 1.3
> label height 1
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 2 models selected
> hide sel atoms
> select /C:1001@CHD
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 32 bonds, 1 residue, 1 model selected
> select up
2694 atoms, 2727 bonds, 181 residues, 1 model selected
> select down
28 atoms, 32 bonds, 1 residue, 2 models selected
> style sel ball
Changed 28 atom styles
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 32 bonds, 1 residue, 1 model selected
> color sel byhetero
> color #2 black models
> ~hbonds
> label :54,57 text {0.chain_id}/{0.name}{0.number}
> label :CLA text {0.chain_id}/{0.name}
> label height 1
> ui mousemode right "move label"
> ui mousemode right select
> select clear
> save CD_pocket.png transparentBackground true
> ui mousemode right "move label"
> ui mousemode right distance
> distance /A:54@CG /B:54@CG
Distance between /A LEU 54 CG and /B LEU 54 CG: 13.534Å
> distance /B:54@CD1 /A:54@CD1
Distance between /B LEU 54 CD1 and /A LEU 54 CD1: 11.511Å
> close #2
> distance /B:54@CG /B:54@CD1
Distance between /B LEU 54 CG and CD1: 1.520Å
> close #2
> distance /B:54@CD1 /A:54@CD1
Distance between /B LEU 54 CD1 and /A LEU 54 CD1: 11.511Å
> distance /C:54@CD1 /D:54@CD1
Distance between /C LEU 54 CD1 and /D LEU 54 CD1: 11.186Å
> color #2 black models
> color #2.1 black models
> ui mousemode right select
> select clear
> ui mousemode right "move label"
> ui mousemode right distance
> HIDE CARTOON
Unknown command: HIDE CARTOON
> hide cartoons
> distance /D:57@CA /C:57@CA
Distance between /D GLU 57 CA and /C GLU 57 CA: 6.840Å
> distance /A:57@CA /B:57@CA
Distance between /A GLU 57 CA and /B GLU 57 CA: 6.693Å
> open
> /Users/mohamed/Documents/Research/Projects/WSCP/Alpha_fold/WSCP_Q57E_rank_001.pdb
Chain information for WSCP_Q57E_rank_001.pdb #3
---
Chain | Description
A | No description available
B | No description available
C D | No description available
Computing secondary structure
> hide #!1 models
> hide #!2 models
> show #!1 models
> show cartoons
> hide #!1 models
> show #!1 models
> ui mousemode right select
> select #1/A:54
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide #3 models
> show #3 models
> hide #!1 models
> select #3/C:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel ball
Changed 8 atom styles
> show sel atoms
> show #!1 models
> matchmaker #3 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_most_occ_pH8.pdb, chain D (#1) with
WSCP_Q57E_rank_001.pdb, chain C (#3), sequence alignment score = 843.5
RMSD between 164 pruned atom pairs is 0.615 angstroms; (across all 177 pairs:
1.018)
> ui mousemode right label
> label delete residues
> label #3/A:53
> ui mousemode right select
> select #3/A:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel ball
Changed 8 atom styles
> show sel atoms
> color sel byhetero
> select #3/D:52
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 8 atom styles
> color sel byhetero
> hide #!1 models
> ui mousemode right distance
> distance #3/A:53@CG #3/D:52@CB
Distance between WSCP_Q57E_rank_001.pdb #3/A LEU 53 CG and /D LEU 52 CB:
12.968Å
> show #!2 models
> close #2
> distance #3/A:53@CG #3/D:52@CB
Distance between WSCP_Q57E_rank_001.pdb #3/A LEU 53 CG and /D LEU 52 CB:
12.968Å
> show #!1 models
> hide #!1 models
> show #!1 models
> ui mousemode right rotate
> ui mousemode right select
> select #3/C:52
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 8 atom styles
> select #3/B:51
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 8 atom styles
> hide #!1 models
> ui mousemode right distance
> distance #3/C:52@CG #3/B:51@CG
Distance between WSCP_Q57E_rank_001.pdb #3/C LEU 52 CG and /B LEU 51 CG:
12.927Å
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> ui mousemode right label
> label #1/D:54
> label delete residues
> ui mousemode right distance
> distance #1/D:54@CG #1/C:54@CG
Distance between extended_most_occ_pH8.pdb #1/D LEU 54 CG and /C LEU 54 CG:
13.284Å
> show #3 models
> hide #3 models
> distance #1/B:54@CD1 #1/A:54@CG
Distance between extended_most_occ_pH8.pdb #1/B LEU 54 CD1 and /A LEU 54 CG:
12.502Å
> show #3 models
> hide #!1 models
> hide #3 models
> show #!1 models
> select :cys
48 atoms, 40 bonds, 8 residues, 1 model selected
> show #!1 atoms
> undo
> ui mousemode right select
> select clear
> select :cys
48 atoms, 40 bonds, 8 residues, 1 model selected
> show #!1 atoms
> hide #!1 atoms
> undo
Alignment identifier is 3/A
Alignment identifier is 3/B
Alignment identifier is 1
> select #3/A:44
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:44
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:30
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:30-64
248 atoms, 254 bonds, 35 residues, 1 model selected
> view sel
> select #3/A:85
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:72-85
108 atoms, 108 bonds, 14 residues, 1 model selected
> view orient
> view
> select #3/A:23-61
278 atoms, 285 bonds, 39 residues, 1 model selected
> select #3/A:23-52
209 atoms, 212 bonds, 30 residues, 1 model selected
> select #3/A:66
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:66-102
277 atoms, 284 bonds, 37 residues, 1 model selected
> select #3/A:85
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:77-85
70 atoms, 70 bonds, 9 residues, 1 model selected
> show #3 models
> hide #!1 models
> select #3/A:74
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:47-74
201 atoms, 205 bonds, 28 residues, 1 model selected
> select #3/A:66-110
345 atoms, 353 bonds, 45 residues, 1 model selected
> select #3/A:79-110
254 atoms, 261 bonds, 32 residues, 1 model selected
> show #!1 models
> hide #3 models
Alignment identifier is 3/A
> select #3/A:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:62-72
74 atoms, 74 bonds, 11 residues, 1 model selected
> select #3/A:117-118
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/A:117-128
102 atoms, 104 bonds, 12 residues, 1 model selected
> select #3/A:34
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:34-172
1065 atoms, 1092 bonds, 139 residues, 1 model selected
> select add #3
5353 atoms, 5480 bonds, 2 pseudobonds, 699 residues, 2 models selected
> select add #1
16004 atoms, 16262 bonds, 16 pseudobonds, 1412 residues, 5 models selected
> select add #2
16004 atoms, 16262 bonds, 16 pseudobonds, 1412 residues, 10 models selected
> select #3/A:84-85
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #3/A:85-121
286 atoms, 295 bonds, 37 residues, 1 model selected
> select #3/A:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:21-77
409 atoms, 418 bonds, 57 residues, 1 model selected
> select #3/A:40-98
443 atoms, 456 bonds, 59 residues, 1 model selected
> select #3/A:40-92
394 atoms, 405 bonds, 53 residues, 1 model selected
> select #3/A:107-168
485 atoms, 497 bonds, 62 residues, 1 model selected
> select #3/A:40-168
988 atoms, 1014 bonds, 129 residues, 1 model selected
> select #1/D:45
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel ball
Changed 10 atom styles
> show sel atoms
> color sel byhetero
> select #1/A:45
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 10 atom styles
> color sel byhetero
> show #3 models
> hide #3 models
> show #3 models
> select #1/D:57@CA
1 atom, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 1 atom style
> color sel byhetero
> hide #!1 models
> select #3/C:55
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> color sel byhetero
> close #2
> show #!1 models
> hide #!1 models
> select #3/B:54
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> color sel byhetero
> ui mousemode right distance
> distance #3/B:54@CD #3/C:55@CD
Distance between WSCP_Q57E_rank_001.pdb #3/B GLU 54 CD and /C GLU 55 CD:
5.378Å
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #3 models
> show #3 models
> ui mousemode right select
> select #3/D:55
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> select #3/A:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> hide #!1 models
> ui mousemode right distance
> distance #3/D:55@CD #3/A:56@CD
Distance between WSCP_Q57E_rank_001.pdb #3/D GLU 55 CD and /A GLU 56 CD:
5.384Å
> show #!1 models
> hide #3 models
> ui tool show "Side View"
> hide cartoons
> distance #1/B:57@CD #1/A:57@CD
Distance between extended_most_occ_pH8.pdb #1/B GLU 57 CD and /A GLU 57 CD:
4.285Å
> show #3 models
> hide #!1 models
> show #!1 models
> hide #3 models
> show cartoons
> distance #1/D:57@CD #1/D:57@OE2
Distance between extended_most_occ_pH8.pdb #1/D GLU 57 CD and OE2: 1.249Å
> distance #1/D:57@OE2 #1/C:57@CD
Distance between extended_most_occ_pH8.pdb #1/D GLU 57 OE2 and /C GLU 57 CD:
5.026Å
> hide cartoons
===== 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 - 89.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,15
Model Number: MQKW3LL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 1 day, 22 hours, 35 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2880 x 1864 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LS27D36xG:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 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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