![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16702 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-15.2-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 0x00000001e9d64240 (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, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.mlp._mlp, chimerax.coulombic._esp, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 60)
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"procRole" : "Background",
"version" : 2,
"userID" : 1383220921,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,4",
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"codeSigningMonitor" : 1,
"incident" : "E341E140-9202-4E25-A044-14AEEEA20ADA",
"pid" : 69533,
"translated" : false,
"cpuType" : "ARM-64",
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"procLaunch" : "2025-01-26 10:46:50.6572 -0500",
"procStartAbsTime" : 698482794253,
"procExitAbsTime" : 913882564541,
"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":"20885E43-D228-5B90-9481-4DF3177184CC","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "39EAB99D-8EB3-5B9B-D120-1E7DFC0F1C25",
"lowPowerMode" : 1,
"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" : 6883,
"sleepWakeUUID" : "44CDBECF-7C19-49A6-8FA6-80685A35EF50",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4370251415\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1047cc000-1047d0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":69533},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4370251415\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1047cc000-1047d0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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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/wangxi/Downloads/ChimeraX/RV-VP1/1cn3.cif
1cn3.cif title:
Interaction of polyomavirus internal protein VP2 with major capsid protein VP1
and implications for participation of VP2 In viral entry [more info...]
Chain information for 1cn3.cif #1
---
Chain | Description | UniProt
A B C D E | COAT PROTEIN VP1 | COA1_POVMP 34-316
F | FRAGMENT OF COAT PROTEIN VP2 | COA2_POVMC 11-29
1cn3.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> sequence chain #1/A#1/B#1/C#1/D#1/E
Alignment identifier is 1
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> style ball
Changed 11261 atom styles
> style sphere
Changed 11261 atom styles
> style stick
Changed 11261 atom styles
> style stick
Changed 11261 atom styles
> style stick
Changed 11261 atom styles
> hide cartoons
> show cartoons
> show atoms
> ui tool show "Selection Inspector"
> color bfactor
11261 atoms, 1444 residues, atom bfactor range 2 to 97.2
> hbonds reveal true
1301 hydrogen bonds found
> ~hbonds
> interfaces ~solvent
7 buried areas: C D 2242, A E 2238, B C 2237, A B 2235, D E 2231, A F 493, E F
470
Alignment identifier is 2
Alignment identifier is 1/F
> hbonds reveal true
1301 hydrogen bonds found
> color bfactor
11261 atoms, 1444 residues, atom bfactor range 2 to 97.2
> mlp
Map values for surface "1cn3.cif_A SES surface": minimum -31.84, mean -4.97,
maximum 22.19
Map values for surface "1cn3.cif_B SES surface": minimum -32.77, mean -4.877,
maximum 23.77
Map values for surface "1cn3.cif_C SES surface": minimum -32.41, mean -4.922,
maximum 22.74
Map values for surface "1cn3.cif_D SES surface": minimum -32.77, mean -4.929,
maximum 22.55
Map values for surface "1cn3.cif_E SES surface": minimum -32.85, mean -4.922,
maximum 23.04
Map values for surface "1cn3.cif_F SES surface": minimum -26.55, mean -4.701,
maximum 21.6
To also show corresponding color key, enter the above mlp command and add key
true
> mlp
Map values for surface "1cn3.cif_A SES surface": minimum -31.84, mean -4.97,
maximum 22.19
Map values for surface "1cn3.cif_B SES surface": minimum -32.77, mean -4.877,
maximum 23.77
Map values for surface "1cn3.cif_C SES surface": minimum -32.41, mean -4.922,
maximum 22.74
Map values for surface "1cn3.cif_D SES surface": minimum -32.77, mean -4.929,
maximum 22.55
Map values for surface "1cn3.cif_E SES surface": minimum -32.85, mean -4.922,
maximum 23.04
Map values for surface "1cn3.cif_F SES surface": minimum -26.55, mean -4.701,
maximum 21.6
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/F GLY 29 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1cn3.cif_A SES surface #1.2: minimum, -20.00, mean -2.15,
maximum 10.59
Coulombic values for 1cn3.cif_B SES surface #1.3: minimum, -17.68, mean -2.14,
maximum 10.47
Coulombic values for 1cn3.cif_C SES surface #1.4: minimum, -15.92, mean -2.16,
maximum 10.57
Coulombic values for 1cn3.cif_D SES surface #1.5: minimum, -20.26, mean -2.17,
maximum 10.62
Coulombic values for 1cn3.cif_E SES surface #1.6: minimum, -16.32, mean -2.15,
maximum 10.27
Coulombic values for 1cn3.cif_F SES surface #1.7: minimum, -10.58, mean -0.11,
maximum 9.53
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic
Coulombic values for 1cn3.cif_A SES surface #1.2: minimum, -20.00, mean -2.15,
maximum 10.59
Coulombic values for 1cn3.cif_B SES surface #1.3: minimum, -17.68, mean -2.14,
maximum 10.47
Coulombic values for 1cn3.cif_C SES surface #1.4: minimum, -15.92, mean -2.16,
maximum 10.57
Coulombic values for 1cn3.cif_D SES surface #1.5: minimum, -20.26, mean -2.17,
maximum 10.62
Coulombic values for 1cn3.cif_E SES surface #1.6: minimum, -16.32, mean -2.15,
maximum 10.27
Coulombic values for 1cn3.cif_F SES surface #1.7: minimum, -10.58, mean -0.11,
maximum 9.53
To also show corresponding color key, enter the above coulombic command and
add key true
> rainbow
> color bypolymer
> color bynucleotide
> color byhetero
> color bychain
> color bypolymer
> rainbow
> style stick
Changed 11261 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style ball
Changed 11261 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> hbonds reveal true
1301 hydrogen bonds found
> ~hbonds
> rainbow
> open /Users/wangxi/Downloads/ChimeraX/RV-VP1/1fpn.cif
Summary of feedback from opening /Users/wangxi/Downloads/ChimeraX/RV-
VP1/1fpn.cif
---
note | Fetching CCD DAO from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/DAO/DAO.cif
1fpn.cif title:
Human rhinovirus serotype 2 (HRV2) [more info...]
Chain information for 1fpn.cif #2
---
Chain | Description | UniProt
1 | COAT PROTEIN VP1 | POLG_HRV2 1-289
2 | COAT PROTEIN VP2 | POLG_HRV2 1-261
3 | COAT PROTEIN VP3 | POLG_HRV2 1-237
4 | COAT PROTEIN VP4 | POLG_HRV2 1-68
Non-standard residues in 1fpn.cif #2
---
DAO — lauric acid
1fpn.cif mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
6| crystal asymmetric unit, crystal frame
> color byhetero
> color bychain
> color bypolymer
> hide #!1 models
> show target m
> hide #!1 models
> close #1
> close #2
> show # target m
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> close #
Expected a models specifier or a keyword
> open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/1fpn-HRV2.pdb
1fpn-HRV2.pdb title:
Human rhinovirus serotype 2 (HRV2) [more info...]
Chain information for 1fpn-HRV2.pdb #1
---
Chain | Description | UniProt
1 | coat protein VP1 | POLG_HRV2 1-289
2 | coat protein VP2 | POLG_HRV2 1-261
3 | coat protein VP3 | POLG_HRV2 1-237
4 | coat protein VP4 | POLG_HRV2 1-68
Non-standard residues in 1fpn-HRV2.pdb #1
---
DAO — lauric acid
> show atoms
> hide atoms
> show cartoons
> hide cartoons
> show cartoons
> style stick
Changed 6316 atom styles
> style sphere
Changed 6316 atom styles
> style sphere
Changed 6316 atom styles
> style ball
Changed 6316 atom styles
> set bgColor white
> set bgColor black
> lighting simple
> lighting soft
> lighting full
> color byhetero
> color bychain
> color bypolymer
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> lighting simple
> ui tool show "Side View"
> transparency 50
> volume showOutlineBox true
No volumes specified
> volume style mesh
No volumes specified
> volume style surface
No volumes specified
> volume style surface
No volumes specified
> volume style surface
No volumes specified
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.
Hide dust shortcut requires a displayed map surface
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> color bynucleotide
> show surfaces
> show cartoons
> show atoms
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style stick
Changed 6316 atom styles
> style stick
Changed 6316 atom styles
> style sphere
Changed 6316 atom styles
> style ball
Changed 6316 atom styles
> color bynucleotide
> color byhetero
> color bychain
> color byhetero
> color bychain
> color bypolymer
> rainbow
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/1 SER 133
/2 ARG 12
/4 GLN 7
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1fpn-HRV2.pdb_1 SES surface #1.2: minimum, -13.40, mean
-0.31, maximum 15.27
Coulombic values for 1fpn-HRV2.pdb_2 SES surface #1.3: minimum, -13.04, mean
-0.93, maximum 9.96
Coulombic values for 1fpn-HRV2.pdb_3 SES surface #1.4: minimum, -13.61, mean
-1.20, maximum 8.60
Coulombic values for 1fpn-HRV2.pdb_4 SES surface #1.5: minimum, -5.82, mean
0.95, maximum 8.35
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp
Map values for surface "1fpn-HRV2.pdb_1 SES surface": minimum -28.4, mean
-4.591, maximum 23.44
Map values for surface "1fpn-HRV2.pdb_2 SES surface": minimum -31.93, mean
-5.269, maximum 22.54
Map values for surface "1fpn-HRV2.pdb_3 SES surface": minimum -26.51, mean
-4.189, maximum 21.95
Map values for surface "1fpn-HRV2.pdb_4 SES surface": minimum -22.89, mean
-4.832, maximum 21.79
To also show corresponding color key, enter the above mlp command and add key
true
> mlp
Map values for surface "1fpn-HRV2.pdb_1 SES surface": minimum -28.4, mean
-4.591, maximum 23.44
Map values for surface "1fpn-HRV2.pdb_2 SES surface": minimum -31.93, mean
-5.269, maximum 22.54
Map values for surface "1fpn-HRV2.pdb_3 SES surface": minimum -26.51, mean
-4.189, maximum 21.95
Map values for surface "1fpn-HRV2.pdb_4 SES surface": minimum -22.89, mean
-4.832, maximum 21.79
To also show corresponding color key, enter the above mlp command and add key
true
> color bfactor
6316 atoms, 941 residues, 4 surfaces, atom bfactor range 8.1 to 100
> hbonds reveal true
1092 hydrogen bonds found
> show atoms
> interfaces ~solvent
5 buried areas: 1 3 4025, 1 2 1983, 2 3 1628, 3 4 371, 1 4 354
Alignment identifier is 1/1
Alignment identifier is 1/2
Alignment identifier is 1/3
Alignment identifier is 1/4
> select clear
> ui tool show "Selection Inspector"
> select
> /1:34-35,75-83,94-98,114-131,140-146,168-172,179-182,191-192,215-220,229-247
650 atoms, 663 bonds, 65 pseudobonds, 77 residues, 2 models selected
> select /1:36-40,46-51,62-72,104-112,158-163
301 atoms, 302 bonds, 25 pseudobonds, 37 residues, 2 models selected
> select /1:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /1:34-41
56 atoms, 56 bonds, 3 pseudobonds, 8 residues, 2 models selected
> select /1:28
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /1:28-43
106 atoms, 107 bonds, 5 pseudobonds, 16 residues, 2 models selected
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/wangxi/Desktop/movie1.mp4
Movie saved to /Users/wangxi/Desktop/movie1.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/wangxi/Desktop/movie2.mp4
Movie saved to /Users/wangxi/Desktop/movie2.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/wangxi/Desktop/movie3.mp4
Movie saved to /Users/wangxi/Desktop/movie3.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/wangxi/Desktop/movie4.mp4
Movie saved to /Users/wangxi/Desktop/movie4.mp4
> save /Users/wangxi/Desktop/image1.png supersample 3
> show sel cartoons
> hide sel cartoons
> style sel stick
Changed 106 atom styles
> style sel sphere
Changed 106 atom styles
> style sel ball
Changed 106 atom styles
> color bfactor sel
106 atoms, 16 residues, 1 surfaces, atom bfactor range 64.8 to 98.6
> hbonds sel reveal true
16 hydrogen bonds found
> ~hbonds
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> color bfactor sel
106 atoms, 16 residues, 1 surfaces, atom bfactor range 64.8 to 98.6
> mlp sel
Map values for surface "1fpn-HRV2.pdb_1 SES surface": minimum -28.4, mean
-4.591, maximum 23.44
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Coulombic values for 1fpn-HRV2.pdb_1 SES surface #1.2: minimum, -13.40, mean
-0.31, maximum 15.27
To also show corresponding color key, enter the above coulombic command and
add key true
> rainbow sel
> color sel bypolymer
> color sel bychain
> color sel byhetero
> color sel bynucleotide
> style sel stick
Changed 106 atom styles
> style sel stick
Changed 106 atom styles
> style sel sphere
Changed 106 atom styles
> set bgColor white
> set bgColor black
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> show sel atoms
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> style sel stick
Changed 106 atom styles
> set bgColor white
> color sel byhetero
> style sel ball
Changed 106 atom styles
> color sel bynucleotide
> color sel bychain
> color sel bypolymer
> rainbow sel
> coulombic sel
Coulombic values for 1fpn-HRV2.pdb_1 SES surface #1.2: minimum, -13.40, mean
-0.31, maximum 15.27
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for 1fpn-HRV2.pdb_1 SES surface #1.2: minimum, -13.40, mean
-0.31, maximum 15.27
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for 1fpn-HRV2.pdb_1 SES surface #1.2: minimum, -13.40, mean
-0.31, maximum 15.27
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
Map values for surface "1fpn-HRV2.pdb_1 SES surface": minimum -28.4, mean
-4.591, maximum 23.44
To also show corresponding color key, enter the above mlp command and add key
true
> color bfactor sel
106 atoms, 16 residues, 1 surfaces, atom bfactor range 64.8 to 98.6
> hbonds sel reveal true
16 hydrogen bonds found
> hbonds sel reveal true
16 hydrogen bonds found
> ~hbonds
Destroying pre-existing alignment with identifier 1/1
Alignment identifier is 1/1
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel cartoons
> hide sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> style sel stick
Changed 2168 atom styles
> style sel stick
Changed 2168 atom styles
> style sel sphere
Changed 2168 atom styles
> style sel ball
Changed 2168 atom styles
> select /1:23
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /1:23-43
141 atoms, 143 bonds, 21 residues, 1 model selected
> select /1:23
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /1:23-43
141 atoms, 143 bonds, 21 residues, 1 model selected
> ~hbonds
> show sel surfaces
> show sel cartoons
> show sel atoms
> color sel byhetero
> color sel bychain
> color sel bypolymer
> rainbow sel
> coulombic sel
Coulombic values for 1fpn-HRV2.pdb_1 SES surface #1.2: minimum, -13.40, mean
-0.31, maximum 15.27
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
Map values for surface "1fpn-HRV2.pdb_1 SES surface": minimum -28.4, mean
-4.591, maximum 23.44
To also show corresponding color key, enter the above mlp command and add key
true
> color bfactor sel
141 atoms, 21 residues, 1 surfaces, atom bfactor range 64.8 to 98.6
> color bfactor sel
141 atoms, 21 residues, 1 surfaces, atom bfactor range 64.8 to 98.6
> hbonds sel reveal true
19 hydrogen bonds found
> ~hbonds
Destroying pre-existing alignment with identifier 1/1
Alignment identifier is 1/1
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel slab
> style nucleic & sel stick
Changed 0 atom styles
> color sel bynucleotide
> set bgColor white
> lighting simple
> lighting soft
> volume region all imageMode "full region"
No volumes specified
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> volume style surface
No volumes specified
> volume style surface
No volumes specified
> volume hide
No volumes specified
> volume hide
No volumes specified
> volume showOutlineBox true
No volumes specified
> transparency sel 50
> transparency sel 0
> volume step 1
No volumes specified
> volume planes z style image imageMode "full region"
No volumes specified
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.
> ui mousemode right "mark maximum"
> style sel ball
Changed 141 atom styles
> style sel ball
Changed 141 atom styles
> rainbow sel
> open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/1fpn-HRV2.pdb
1fpn-HRV2.pdb title:
Human rhinovirus serotype 2 (HRV2) [more info...]
Chain information for 1fpn-HRV2.pdb #2
---
Chain | Description | UniProt
1 | coat protein VP1 | POLG_HRV2 1-289
2 | coat protein VP2 | POLG_HRV2 1-261
3 | coat protein VP3 | POLG_HRV2 1-237
4 | coat protein VP4 | POLG_HRV2 1-68
Non-standard residues in 1fpn-HRV2.pdb #2
---
DAO — lauric acid
> show sel atoms
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/1fpn-HRV2.pdb format pdb
1fpn-HRV2.pdb title:
Human rhinovirus serotype 2 (HRV2) [more info...]
Chain information for 1fpn-HRV2.pdb #3
---
Chain | Description | UniProt
1 | coat protein VP1 | POLG_HRV2 1-289
2 | coat protein VP2 | POLG_HRV2 1-261
3 | coat protein VP3 | POLG_HRV2 1-237
4 | coat protein VP4 | POLG_HRV2 1-68
Non-standard residues in 1fpn-HRV2.pdb #3
---
DAO — lauric acid
> show sel atoms
> hide sel atoms
> open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/1fpn-HRV2.pdb format pdb
1fpn-HRV2.pdb title:
Human rhinovirus serotype 2 (HRV2) [more info...]
Chain information for 1fpn-HRV2.pdb #4
---
Chain | Description | UniProt
1 | coat protein VP1 | POLG_HRV2 1-289
2 | coat protein VP2 | POLG_HRV2 1-261
3 | coat protein VP3 | POLG_HRV2 1-237
4 | coat protein VP4 | POLG_HRV2 1-68
Non-standard residues in 1fpn-HRV2.pdb #4
---
DAO — lauric acid
> open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/1fpn-HRV2.pdb format pdb
1fpn-HRV2.pdb title:
Human rhinovirus serotype 2 (HRV2) [more info...]
Chain information for 1fpn-HRV2.pdb #5
---
Chain | Description | UniProt
1 | coat protein VP1 | POLG_HRV2 1-289
2 | coat protein VP2 | POLG_HRV2 1-261
3 | coat protein VP3 | POLG_HRV2 1-237
4 | coat protein VP4 | POLG_HRV2 1-68
Non-standard residues in 1fpn-HRV2.pdb #5
---
DAO — lauric acid
> transparency sel 50
> volume style image
No volumes specified
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> volume style image
No volumes specified
> transparency sel 0
> volume showOutlineBox true
No volumes specified
> volume step 1
No volumes specified
> volume region all imageMode "full region"
No volumes specified
Color zone shortcut requires 1 displayed atomic model and 1 map, got 5 atomic
models, 0 maps.
> volume hide
No volumes specified
> color sel bynucleotide
> color sel byhetero
> select backbone
15630 atoms, 15605 bonds, 5 pseudobonds, 3905 residues, 10 models selected
> undo
> ui tool show AlphaFold
> select clear
> select #1/1:23
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/1:23-43
141 atoms, 143 bonds, 21 residues, 1 model selected
> ui tool show "Basic Actions"
> ui tool show "Color Key"
> ui mousemode right "color key"
> ui mousemode right "mark maximum"
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/2hwd-HRV1A.pdb
2hwd-HRV1A.pdb title:
A comparison of the ANTI-rhinoviral drug binding pocket In HRV14 and HRV1A
[more info...]
Chain information for 2hwd-HRV1A.pdb #7
---
Chain | Description | UniProt
1 | human rhinovirus 1A coat protein (subunit VP1) | POLG_HRV1A 1-287
2 | human rhinovirus 1A coat protein (subunit VP2) | POLG_HRV1A 1-263
3 | human rhinovirus 1A coat protein (subunit VP3) | POLG_HRV1A 1-238
4 | human rhinovirus 1A coat protein (subunit VP4) | POLG_HRV1A 1-44
Non-standard residues in 2hwd-HRV1A.pdb #7
---
W91 — 5-(3-(2,6-dichloro-4-(4,5-dihydro-2-oxazolyl)phenoxy)propyl)-3-methyl
isoxazole (WIN56291)
> close session
> open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/2hwd-HRV1A.pdb format pdb
2hwd-HRV1A.pdb title:
A comparison of the ANTI-rhinoviral drug binding pocket In HRV14 and HRV1A
[more info...]
Chain information for 2hwd-HRV1A.pdb #1
---
Chain | Description | UniProt
1 | human rhinovirus 1A coat protein (subunit VP1) | POLG_HRV1A 1-287
2 | human rhinovirus 1A coat protein (subunit VP2) | POLG_HRV1A 1-263
3 | human rhinovirus 1A coat protein (subunit VP3) | POLG_HRV1A 1-238
4 | human rhinovirus 1A coat protein (subunit VP4) | POLG_HRV1A 1-44
Non-standard residues in 2hwd-HRV1A.pdb #1
---
W91 — 5-(3-(2,6-dichloro-4-(4,5-dihydro-2-oxazolyl)phenoxy)propyl)-3-methyl
isoxazole (WIN56291)
Alignment identifier is 1/1
Alignment identifier is 1/2
Alignment identifier is 1/3
Alignment identifier is 1/4
> select /1:43-44
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /1:42-44
21 atoms, 20 bonds, 3 residues, 1 model selected
> select /1:28
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /1:28-43
109 atoms, 110 bonds, 16 residues, 1 model selected
> select clear
> select /1:5-287
2262 atoms, 2322 bonds, 283 residues, 1 model selected
> select clear
> select /4
151 atoms, 154 bonds, 19 residues, 1 model selected
> select clear
> select /2
1979 atoms, 2033 bonds, 253 residues, 1 model selected
> select /3:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /3
1831 atoms, 1878 bonds, 238 residues, 1 model selected
> select clear
> select /1:5-287
2262 atoms, 2322 bonds, 283 residues, 1 model selected
> select /1:23
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /1:23-43
149 atoms, 152 bonds, 21 residues, 1 model selected
> view sel
> view
> view orient
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> rainbow sel
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/wangxi/Desktop/movie1.mp4
Movie saved to /Users/wangxi/Desktop/movie1.mp4
> save /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/2hwd-HRV1A-ribbon.cxs
> save /Users/wangxi/Desktop/image2.png supersample 3
> style sel sphere
Changed 149 atom styles
> style sel sphere
Changed 149 atom styles
> style sel stick
Changed 149 atom styles
> style sel ball
Changed 149 atom styles
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> style sel stick
Changed 149 atom styles
> style sel sphere
Changed 149 atom styles
> style sel ball
Changed 149 atom styles
> style sel stick
Changed 149 atom styles
> show sel atoms
> hide sel atoms
> show sel atoms
> show sel cartoons
> save /Users/wangxi/Desktop/image3.png supersample 3
> select clear
> select /1:5-287
2262 atoms, 2322 bonds, 283 residues, 1 model selected
> select clear
> select /1:5-287
2262 atoms, 2322 bonds, 283 residues, 1 model selected
> select /2
1979 atoms, 2033 bonds, 253 residues, 1 model selected
> select /4
151 atoms, 154 bonds, 19 residues, 1 model selected
> select /4
151 atoms, 154 bonds, 19 residues, 1 model selected
> select clear
> select /3
1831 atoms, 1878 bonds, 238 residues, 1 model selected
> select /3:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /3:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select /1:5-287
2262 atoms, 2322 bonds, 283 residues, 1 model selected
> select clear
> select /4
151 atoms, 154 bonds, 19 residues, 1 model selected
> select /3:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /3
1831 atoms, 1878 bonds, 238 residues, 1 model selected
> select clear
> select /1:5-287
2262 atoms, 2322 bonds, 283 residues, 1 model selected
> lighting simple
> lighting soft
> lighting simple
> set bgColor white
> lighting simple
> set bgColor white
> set bgColor black
> set bgColor white
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> hide sel atoms
> show sel atoms
> style sel stick
Changed 2262 atom styles
> style sel sphere
Changed 2262 atom styles
> style sel sphere
Changed 2262 atom styles
> style sel stick
Changed 2262 atom styles
> style sel ball
Changed 2262 atom styles
> style sel ball
Changed 2262 atom styles
> style sel stick
Changed 2262 atom styles
> show sel cartoons
> hide sel atoms
> show sel atoms
> hide sel atoms
> select /1:23
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /1:23-30
60 atoms, 61 bonds, 8 residues, 1 model selected
> select /1:28
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /1:28-43
109 atoms, 110 bonds, 16 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 109 atom styles
> style sel stick
Changed 109 atom styles
> show sel cartoons
> show sel atoms
> select clear
> select /2
1979 atoms, 2033 bonds, 253 residues, 1 model selected
> hide sel cartoons
> select /3:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /3
1831 atoms, 1878 bonds, 238 residues, 1 model selected
> hide sel cartoons
> select clear
> select /2
1979 atoms, 2033 bonds, 253 residues, 1 model selected
> hide sel cartoons
> select clear
> select /4
151 atoms, 154 bonds, 19 residues, 1 model selected
> hide sel cartoons
> select clear
> select /1:5-287
2262 atoms, 2322 bonds, 283 residues, 1 model selected
> select /1:28
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /1:28-43
109 atoms, 110 bonds, 16 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel atoms
> hide sel atoms
> show sel atoms
> save /Users/wangxi/Desktop/image4.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/wangxi/Desktop/movie2.mp4
Movie saved to /Users/wangxi/Desktop/movie2.mp4
> select clear
> select /2
1979 atoms, 2033 bonds, 253 residues, 1 model selected
> select clear
> select /2
1979 atoms, 2033 bonds, 253 residues, 1 model selected
> select /2:263
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /2
1979 atoms, 2033 bonds, 253 residues, 1 model selected
> lighting simple
> lighting soft
> lighting simple
> set bgColor white
> lighting full
> lighting simple
> show sel atoms
> show sel cartoons
> show sel atoms
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> save /Users/wangxi/Desktop/image1.png supersample 3
> hide sel cartoons
> select /3:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /3
1831 atoms, 1878 bonds, 238 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select clear
> select /2
1979 atoms, 2033 bonds, 253 residues, 1 model selected
> show sel cartoons
> select /3:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /3
1831 atoms, 1878 bonds, 238 residues, 1 model selected
> save /Users/wangxi/Desktop/image1.png supersample 3
> select clear
> select /4
151 atoms, 154 bonds, 19 residues, 1 model selected
> select /4:44
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /4
151 atoms, 154 bonds, 19 residues, 1 model selected
> select /4
151 atoms, 154 bonds, 19 residues, 1 model selected
> show sel cartoons
> save /Users/wangxi/Desktop/image1.png supersample 3
> open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/6sk5-RV-B5.pdb
6sk5-RV-B5.pdb title:
Cryo-em structure of rhinovirus-B5 complexed to antiviral obr-5-340 [more
info...]
Chain information for 6sk5-RV-B5.pdb #2
---
Chain | Description | UniProt
A | rhinovirus B5 VP1 | Q7T659_9ENTO 1-288
B | rhinovirus B5 VP2 | B9V433_9ENTO 8-259
C | rhinovirus B5 VP3 | B9V433_9ENTO 1-230
D | rhinovirus B5 VP4 | Q80SQ3_9ENTO 1-69
Non-standard residues in 6sk5-RV-B5.pdb #2
---
LGQ —
6-phenyl-~{N}3-[4-(trifluoromethyl)phenyl]-1~{H}-pyrazolo[3,4-D]pyrimidine-3,4-diamine
> open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/6sk5-RV-B5.pdb format pdb
6sk5-RV-B5.pdb title:
Cryo-em structure of rhinovirus-B5 complexed to antiviral obr-5-340 [more
info...]
Chain information for 6sk5-RV-B5.pdb #3
---
Chain | Description | UniProt
A | rhinovirus B5 VP1 | Q7T659_9ENTO 1-288
B | rhinovirus B5 VP2 | B9V433_9ENTO 8-259
C | rhinovirus B5 VP3 | B9V433_9ENTO 1-230
D | rhinovirus B5 VP4 | Q80SQ3_9ENTO 1-69
Non-standard residues in 6sk5-RV-B5.pdb #3
---
LGQ —
6-phenyl-~{N}3-[4-(trifluoromethyl)phenyl]-1~{H}-pyrazolo[3,4-D]pyrimidine-3,4-diamine
> open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/6sk5-RV-B5.pdb
6sk5-RV-B5.pdb title:
Cryo-em structure of rhinovirus-B5 complexed to antiviral obr-5-340 [more
info...]
Chain information for 6sk5-RV-B5.pdb #4
---
Chain | Description | UniProt
A | rhinovirus B5 VP1 | Q7T659_9ENTO 1-288
B | rhinovirus B5 VP2 | B9V433_9ENTO 8-259
C | rhinovirus B5 VP3 | B9V433_9ENTO 1-230
D | rhinovirus B5 VP4 | Q80SQ3_9ENTO 1-69
Non-standard residues in 6sk5-RV-B5.pdb #4
---
LGQ —
6-phenyl-~{N}3-[4-(trifluoromethyl)phenyl]-1~{H}-pyrazolo[3,4-D]pyrimidine-3,4-diamine
> close session
> open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/6sk5-RV-B5.pdb format pdb
6sk5-RV-B5.pdb title:
Cryo-em structure of rhinovirus-B5 complexed to antiviral obr-5-340 [more
info...]
Chain information for 6sk5-RV-B5.pdb #1
---
Chain | Description | UniProt
A | rhinovirus B5 VP1 | Q7T659_9ENTO 1-288
B | rhinovirus B5 VP2 | B9V433_9ENTO 8-259
C | rhinovirus B5 VP3 | B9V433_9ENTO 1-230
D | rhinovirus B5 VP4 | Q80SQ3_9ENTO 1-69
Non-standard residues in 6sk5-RV-B5.pdb #1
---
LGQ —
6-phenyl-~{N}3-[4-(trifluoromethyl)phenyl]-1~{H}-pyrazolo[3,4-D]pyrimidine-3,4-diamine
Alignment identifier is 1/D
Alignment identifier is 1/B
Alignment identifier is 1/A
Alignment identifier is 1/C
> select clear
> select /A:16-288
4340 atoms, 4399 bonds, 273 residues, 1 model selected
> select /A:23-24
23 atoms, 22 bonds, 2 residues, 1 model selected
> select /A:23-30
126 atoms, 126 bonds, 8 residues, 1 model selected
> select /A:31
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:31-38
113 atoms, 113 bonds, 8 residues, 1 model selected
> select /A:41-42
24 atoms, 23 bonds, 2 residues, 1 model selected
> select /A:41-47
99 atoms, 100 bonds, 7 residues, 1 model selected
> select /B:8
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B
3826 atoms, 3870 bonds, 252 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /C:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /C
3583 atoms, 3631 bonds, 230 residues, 1 model selected
> hide sel cartoons
> select clear
> select /D
589 atoms, 595 bonds, 40 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide sel cartoons
> select clear
> select /A:16-288
4340 atoms, 4399 bonds, 273 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select /C:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /C
3583 atoms, 3631 bonds, 230 residues, 1 model selected
> hide sel cartoons
> select clear
> select /A:16-104
1384 atoms, 1396 bonds, 89 residues, 1 model selected
> lighting soft
> lighting simple
===== 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 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: MacBook Pro
Model Identifier: MacBookPro18,4
Model Number: Z15K0010BLL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 11881.61.3
OS Loader Version: 11881.61.3
Software:
System Software Overview:
System Version: macOS 15.2 (24C101)
Kernel Version: Darwin 24.2.0
Time since boot: 1 day, 21 hours, 38 minutes
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:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL U2718Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
DELL U2718Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra 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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