![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 22 months ago
Closed 22 months ago
#14522 closed defect (can't reproduce)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.3-arm64-arm-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000002bde0b000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001e4621c40 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py", line 81 in msgpack_deserialize
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 721 in restore
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 1017 in open
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 37 in open
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1977 in _open_dropped_file
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 240 in event
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, 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, chimerax.coulombic._esp (total: 62)
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"codeSigningMonitor" : 1,
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"procLaunch" : "2024-01-31 14:10:41.9015 -0600",
"procStartAbsTime" : 280016417960,
"procExitAbsTime" : 1152359895145,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "79280872-238A-EE79-E148-1CDF8D3710D0",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"sleepWakeUUID" : "2D097B54-EAB5-4BE4-913A-4914520E2241",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 105557948104535\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600120000000-600140000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":16938},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 105557948104535\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600120000000-600140000000 [512.0M] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/20S_Bort_NTer.cxs" format session
opened ChimeraX session
> ui tool show Contacts
> contacts ignoreHiddenModels true dashes 4
1367 contacts
> contacts ignoreHiddenModels true dashes 4
1367 contacts
> select /D:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:9-22
110 atoms, 112 bonds, 44 pseudobonds, 14 residues, 2 models selected
> select clear
> select /E:5
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /E:5-25
170 atoms, 173 bonds, 83 pseudobonds, 21 residues, 2 models selected
> select clear
> select /F:5-6
11 atoms, 10 bonds, 1 pseudobond, 2 residues, 2 models selected
> select /F:5-33
223 atoms, 227 bonds, 115 pseudobonds, 29 residues, 2 models selected
> select clear
> select /G:6-7
9 atoms, 8 bonds, 2 residues, 1 model selected
> select /G:6-23
141 atoms, 144 bonds, 77 pseudobonds, 17 residues, 3 models selected
> select clear
> select /G:6
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /G:6-7
9 atoms, 8 bonds, 2 residues, 1 model selected
> select clear
> view clip false
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/aks3233/Desktop/movie1.mp4
Movie saved to /Users/aks3233/Desktop/movie1.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/aks3233/Desktop/movie2.mp4
Movie saved to /Users/aks3233/Desktop/movie2.mp4
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/2f16_wt_20s_alpha_Nter_BTZ_contacts.cxs" format session
opened ChimeraX session
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/1g0u_opengate_aplha_contacts.cxs" format session
opened ChimeraX session
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/20S_Bort_NTer.cxs" format session
opened ChimeraX session
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/aks3233/Desktop/movie2.mp4
Movie saved to /Users/aks3233/Desktop/movie2.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/aks3233/Desktop/movie3.mp4
Movie saved to /Users/aks3233/Desktop/movie3.mp4
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/2f16_bortezomib.pdb" format pdb
2f16_bortezomib.pdb title:
Crystal structure of the yeast 20S proteasome In complex with bortezomib [more
info...]
Chain information for 2f16_bortezomib.pdb #2
---
Chain | Description | UniProt
1 M | proteasome component PRE4 | PSB4_YEAST -8-211
2 N | proteasome component PRE3 | PSB6_YEAST 1-18
A O | proteasome component Y7 | PSA2_YEAST 4-236
B P | proteasome component Y13 | PSA4_YEAST 4-239
C Q | proteasome component PRE6 | PSA7_YEAST 7-243
D R | proteasome component PUP2 | PSA5_YEAST 9-244
E S | proteasome component PRE5 | PSA1_YEAST 4-233
F T | proteasome component C1 | PSA3_YEAST 5-241
G U | proteasome component C7-α | PSA6_YEAST 6-240
H V | proteasome component PUP1 | PSB7_YEAST 1-223
I W | proteasome component PUP3 | PSB3_YEAST -8-194
J X | proteasome component C11 | PSB2_YEAST -1-193
K Y | proteasome component PRE2 | PSB5_YEAST 1-211
L Z | multicatalytic endopeptidase complex subunit C5 | PSB1_YEAST -9-194
Non-standard residues in 2f16_bortezomib.pdb #2
---
BO2 —
N-[(1R)-1-(dihydroxyboryl)-3-methylbutyl]-N-(pyrazin-2-ylcarbonyl)-L-phenylalaninamide
(bortezomib)
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 2f16_bortezomib.pdb_A SES surface #1.2: minimum, -9.29,
mean 0.48, maximum 10.01
Coulombic values for 2f16_bortezomib.pdb_B SES surface #1.3: minimum, -11.07,
mean -0.09, maximum 18.03
Coulombic values for 2f16_bortezomib.pdb_C SES surface #1.4: minimum, -10.38,
mean -0.90, maximum 8.83
Coulombic values for 2f16_bortezomib.pdb_D SES surface #1.5: minimum, -7.53,
mean -0.76, maximum 7.73
Coulombic values for 2f16_bortezomib.pdb_E SES surface #1.6: minimum, -10.91,
mean -0.81, maximum 12.06
Coulombic values for 2f16_bortezomib.pdb_F SES surface #1.7: minimum, -10.31,
mean -1.53, maximum 8.16
Coulombic values for 2f16_bortezomib.pdb_G SES surface #1.8: minimum, -7.11,
mean 0.84, maximum 10.57
Coulombic values for 2f16_bortezomib.pdb_1 SES surface #2.1: minimum, -20.44,
mean -1.46, maximum 12.86
Coulombic values for 2f16_bortezomib.pdb_2 SES surface #2.2: minimum, -15.32,
mean -2.29, maximum 8.02
Coulombic values for 2f16_bortezomib.pdb_A SES surface #2.3: minimum, -17.49,
mean -1.78, maximum 10.99
Coulombic values for 2f16_bortezomib.pdb_B SES surface #2.4: minimum, -16.93,
mean -1.80, maximum 19.18
Coulombic values for 2f16_bortezomib.pdb_C SES surface #2.5: minimum, -20.21,
mean -0.89, maximum 16.07
Coulombic values for 2f16_bortezomib.pdb_D SES surface #2.6: minimum, -19.95,
mean -4.41, maximum 8.59
Coulombic values for 2f16_bortezomib.pdb_E SES surface #2.7: minimum, -19.37,
mean -0.36, maximum 14.16
Coulombic values for 2f16_bortezomib.pdb_F SES surface #2.8: minimum, -13.78,
mean -0.72, maximum 13.38
Coulombic values for 2f16_bortezomib.pdb_G SES surface #2.9: minimum, -23.79,
mean -1.81, maximum 11.33
Coulombic values for 2f16_bortezomib.pdb_H SES surface #2.10: minimum, -20.98,
mean -0.85, maximum 13.64
Coulombic values for 2f16_bortezomib.pdb_I SES surface #2.11: minimum, -22.36,
mean -2.89, maximum 11.21
Coulombic values for 2f16_bortezomib.pdb_J SES surface #2.12: minimum, -21.63,
mean -1.62, maximum 11.71
Coulombic values for 2f16_bortezomib.pdb_K SES surface #2.13: minimum, -15.42,
mean -1.25, maximum 12.72
Coulombic values for 2f16_bortezomib.pdb_L SES surface #2.14: minimum, -19.13,
mean -1.76, maximum 9.11
Coulombic values for 2f16_bortezomib.pdb_M SES surface #2.15: minimum, -19.75,
mean -1.48, maximum 10.65
Coulombic values for 2f16_bortezomib.pdb_N SES surface #2.16: minimum, -15.57,
mean -2.33, maximum 8.24
Coulombic values for 2f16_bortezomib.pdb_O SES surface #2.17: minimum, -18.36,
mean -1.78, maximum 11.33
Coulombic values for 2f16_bortezomib.pdb_P SES surface #2.18: minimum, -16.86,
mean -1.81, maximum 17.21
Coulombic values for 2f16_bortezomib.pdb_Q SES surface #2.19: minimum, -17.60,
mean -0.60, maximum 19.90
Coulombic values for 2f16_bortezomib.pdb_R SES surface #2.20: minimum, -21.96,
mean -4.42, maximum 8.65
Coulombic values for 2f16_bortezomib.pdb_S SES surface #2.21: minimum, -19.22,
mean -0.35, maximum 14.22
Coulombic values for 2f16_bortezomib.pdb_T SES surface #2.22: minimum, -13.76,
mean -0.41, maximum 13.86
Coulombic values for 2f16_bortezomib.pdb_U SES surface #2.23: minimum, -18.18,
mean -1.74, maximum 16.67
Coulombic values for 2f16_bortezomib.pdb_V SES surface #2.24: minimum, -23.35,
mean -0.86, maximum 14.07
Coulombic values for 2f16_bortezomib.pdb_W SES surface #2.25: minimum, -39.52,
mean -2.56, maximum 9.73
Coulombic values for 2f16_bortezomib.pdb_X SES surface #2.26: minimum, -21.43,
mean -1.93, maximum 12.01
Coulombic values for 2f16_bortezomib.pdb_Y SES surface #2.27: minimum, -15.75,
mean -1.62, maximum 12.33
Coulombic values for 2f16_bortezomib.pdb_Z SES surface #2.28: minimum, -17.36,
mean -1.75, maximum 8.77
To also show corresponding color key, enter the above coulombic command and
add key true
> save /Users/aks3233/Desktop/image1.png supersample 3
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/1g0u_opengate.pdb" format pdb
1g0u_opengate.pdb title:
A gated channel INTO the proteasome core particle [more info...]
Chain information for 1g0u_opengate.pdb #3
---
Chain | Description | UniProt
1 M | proteasome component PRE4 | PSB4_YEAST -41-211
2 N | proteasome component PRE3 | PSB6_YEAST 1-187
A O | proteasome component Y7 | PSA2_YEAST 4-236
B P | proteasome component Y13 | PSA4_YEAST 3-239
C Q | proteasome component PRE6 | PSA7_YEAST 5-243
D R | proteasome component PUP2 | PSA5_YEAST 1-244
E S | proteasome component PRE5 | PSA1_YEAST 3-233
F T | proteasome component C1 | PSA3_YEAST 1-241
G U | proteasome component C7-α | PSA6_YEAST -3-240
H V | proteasome component PUP1 | PSB7_YEAST 1-223
I W | proteasome component PUP3 | PSB3_YEAST -9-194
J X | proteasome component C11 | PSB2_YEAST -1-193
K Y | proteasome component PRE2 | PSB5_YEAST 1-211
L Z | multicatalytic endopeptidase complex subunit C5 | PSB1_YEAST -28-194
Non-standard residues in 1g0u_opengate.pdb #3
---
MG — magnesium ion
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/1g0u_opengate.pdb" format pdb
1g0u_opengate.pdb title:
A gated channel INTO the proteasome core particle [more info...]
Chain information for 1g0u_opengate.pdb #4
---
Chain | Description | UniProt
1 M | proteasome component PRE4 | PSB4_YEAST -41-211
2 N | proteasome component PRE3 | PSB6_YEAST 1-187
A O | proteasome component Y7 | PSA2_YEAST 4-236
B P | proteasome component Y13 | PSA4_YEAST 3-239
C Q | proteasome component PRE6 | PSA7_YEAST 5-243
D R | proteasome component PUP2 | PSA5_YEAST 1-244
E S | proteasome component PRE5 | PSA1_YEAST 3-233
F T | proteasome component C1 | PSA3_YEAST 1-241
G U | proteasome component C7-α | PSA6_YEAST -3-240
H V | proteasome component PUP1 | PSB7_YEAST 1-223
I W | proteasome component PUP3 | PSB3_YEAST -9-194
J X | proteasome component C11 | PSB2_YEAST -1-193
K Y | proteasome component PRE2 | PSB5_YEAST 1-211
L Z | multicatalytic endopeptidase complex subunit C5 | PSB1_YEAST -28-194
Non-standard residues in 1g0u_opengate.pdb #4
---
MG — magnesium ion
> hide #!2 models
> hide #!1 models
> coulombic #!3-4
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
1g0u_opengate.pdb #3/B THR 13
1g0u_opengate.pdb #3/C ARG 10
1g0u_opengate.pdb #3/D VAL 12
1g0u_opengate.pdb #3/E ASN 7
1g0u_opengate.pdb #3/G ASP 9
1g0u_opengate.pdb #3/P THR 13
1g0u_opengate.pdb #3/Q ARG 10
1g0u_opengate.pdb #3/R VAL 12
1g0u_opengate.pdb #3/S ASN 7
1g0u_opengate.pdb #3/U ASP 9
1g0u_opengate.pdb #4/B THR 13
1g0u_opengate.pdb #4/C ARG 10
1g0u_opengate.pdb #4/D VAL 12
1g0u_opengate.pdb #4/E ASN 7
1g0u_opengate.pdb #4/G ASP 9
1g0u_opengate.pdb #4/P THR 13
1g0u_opengate.pdb #4/Q ARG 10
1g0u_opengate.pdb #4/R VAL 12
1g0u_opengate.pdb #4/S ASN 7
1g0u_opengate.pdb #4/U ASP 9
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1g0u_opengate.pdb_1 SES surface #3.2: minimum, -19.10,
mean -1.46, maximum 10.43
Coulombic values for 1g0u_opengate.pdb_2 SES surface #3.3: minimum, -15.66,
mean -2.21, maximum 10.33
Coulombic values for 1g0u_opengate.pdb_A SES surface #3.4: minimum, -17.89,
mean -1.93, maximum 11.88
Coulombic values for 1g0u_opengate.pdb_B SES surface #3.5: minimum, -16.46,
mean -2.21, maximum 7.09
Coulombic values for 1g0u_opengate.pdb_C SES surface #3.6: minimum, -17.68,
mean -0.77, maximum 13.44
Coulombic values for 1g0u_opengate.pdb_D SES surface #3.7: minimum, -18.71,
mean -4.53, maximum 12.52
Coulombic values for 1g0u_opengate.pdb_E SES surface #3.8: minimum, -26.92,
mean -1.12, maximum 11.56
Coulombic values for 1g0u_opengate.pdb_F SES surface #3.9: minimum, -15.73,
mean -0.36, maximum 13.39
Coulombic values for 1g0u_opengate.pdb_G SES surface #3.10: minimum, -24.27,
mean -1.90, maximum 10.53
Coulombic values for 1g0u_opengate.pdb_H SES surface #3.11: minimum, -14.89,
mean -0.77, maximum 14.17
Coulombic values for 1g0u_opengate.pdb_I SES surface #3.12: minimum, -21.09,
mean -3.27, maximum 7.63
Coulombic values for 1g0u_opengate.pdb_J SES surface #3.13: minimum, -21.17,
mean -1.67, maximum 12.08
Coulombic values for 1g0u_opengate.pdb_K SES surface #3.14: minimum, -23.99,
mean -1.15, maximum 12.47
Coulombic values for 1g0u_opengate.pdb_L SES surface #3.15: minimum, -16.38,
mean -1.91, maximum 8.89
Coulombic values for 1g0u_opengate.pdb_M SES surface #3.16: minimum, -19.46,
mean -1.75, maximum 10.10
Coulombic values for 1g0u_opengate.pdb_N SES surface #3.17: minimum, -15.80,
mean -2.23, maximum 10.57
Coulombic values for 1g0u_opengate.pdb_O SES surface #3.18: minimum, -18.03,
mean -1.96, maximum 11.77
Coulombic values for 1g0u_opengate.pdb_P SES surface #3.19: minimum, -16.38,
mean -2.23, maximum 7.09
Coulombic values for 1g0u_opengate.pdb_Q SES surface #3.20: minimum, -17.53,
mean -0.78, maximum 15.69
Coulombic values for 1g0u_opengate.pdb_R SES surface #3.21: minimum, -19.30,
mean -4.54, maximum 11.79
Coulombic values for 1g0u_opengate.pdb_S SES surface #3.22: minimum, -26.16,
mean -1.15, maximum 11.51
Coulombic values for 1g0u_opengate.pdb_T SES surface #3.23: minimum, -14.59,
mean -0.33, maximum 13.76
Coulombic values for 1g0u_opengate.pdb_U SES surface #3.24: minimum, -28.08,
mean -1.86, maximum 10.68
Coulombic values for 1g0u_opengate.pdb_V SES surface #3.25: minimum, -14.04,
mean -0.79, maximum 14.02
Coulombic values for 1g0u_opengate.pdb_W SES surface #3.26: minimum, -20.61,
mean -3.26, maximum 7.78
Coulombic values for 1g0u_opengate.pdb_X SES surface #3.27: minimum, -21.13,
mean -1.71, maximum 11.53
Coulombic values for 1g0u_opengate.pdb_Y SES surface #3.28: minimum, -15.75,
mean -1.16, maximum 12.22
Coulombic values for 1g0u_opengate.pdb_Z SES surface #3.29: minimum, -17.67,
mean -1.87, maximum 8.80
Coulombic values for 1g0u_opengate.pdb_1 SES surface #4.2: minimum, -19.10,
mean -1.46, maximum 10.43
Coulombic values for 1g0u_opengate.pdb_2 SES surface #4.3: minimum, -15.66,
mean -2.21, maximum 10.33
Coulombic values for 1g0u_opengate.pdb_A SES surface #4.4: minimum, -17.89,
mean -1.93, maximum 11.88
Coulombic values for 1g0u_opengate.pdb_B SES surface #4.5: minimum, -16.46,
mean -2.21, maximum 7.09
Coulombic values for 1g0u_opengate.pdb_C SES surface #4.6: minimum, -17.68,
mean -0.77, maximum 13.44
Coulombic values for 1g0u_opengate.pdb_D SES surface #4.7: minimum, -18.71,
mean -4.53, maximum 12.52
Coulombic values for 1g0u_opengate.pdb_E SES surface #4.8: minimum, -26.92,
mean -1.12, maximum 11.56
Coulombic values for 1g0u_opengate.pdb_F SES surface #4.9: minimum, -15.73,
mean -0.36, maximum 13.39
Coulombic values for 1g0u_opengate.pdb_G SES surface #4.10: minimum, -24.27,
mean -1.90, maximum 10.53
Coulombic values for 1g0u_opengate.pdb_H SES surface #4.11: minimum, -14.89,
mean -0.77, maximum 14.17
Coulombic values for 1g0u_opengate.pdb_I SES surface #4.12: minimum, -21.09,
mean -3.27, maximum 7.63
Coulombic values for 1g0u_opengate.pdb_J SES surface #4.13: minimum, -21.17,
mean -1.67, maximum 12.08
Coulombic values for 1g0u_opengate.pdb_K SES surface #4.14: minimum, -23.99,
mean -1.15, maximum 12.47
Coulombic values for 1g0u_opengate.pdb_L SES surface #4.15: minimum, -16.38,
mean -1.91, maximum 8.89
Coulombic values for 1g0u_opengate.pdb_M SES surface #4.16: minimum, -19.46,
mean -1.75, maximum 10.10
Coulombic values for 1g0u_opengate.pdb_N SES surface #4.17: minimum, -15.80,
mean -2.23, maximum 10.57
Coulombic values for 1g0u_opengate.pdb_O SES surface #4.18: minimum, -18.03,
mean -1.96, maximum 11.77
Coulombic values for 1g0u_opengate.pdb_P SES surface #4.19: minimum, -16.38,
mean -2.23, maximum 7.09
Coulombic values for 1g0u_opengate.pdb_Q SES surface #4.20: minimum, -17.53,
mean -0.78, maximum 15.69
Coulombic values for 1g0u_opengate.pdb_R SES surface #4.21: minimum, -19.30,
mean -4.54, maximum 11.79
Coulombic values for 1g0u_opengate.pdb_S SES surface #4.22: minimum, -26.16,
mean -1.15, maximum 11.51
Coulombic values for 1g0u_opengate.pdb_T SES surface #4.23: minimum, -14.59,
mean -0.33, maximum 13.76
Coulombic values for 1g0u_opengate.pdb_U SES surface #4.24: minimum, -28.08,
mean -1.86, maximum 10.68
Coulombic values for 1g0u_opengate.pdb_V SES surface #4.25: minimum, -14.04,
mean -0.79, maximum 14.02
Coulombic values for 1g0u_opengate.pdb_W SES surface #4.26: minimum, -20.61,
mean -3.26, maximum 7.78
Coulombic values for 1g0u_opengate.pdb_X SES surface #4.27: minimum, -21.13,
mean -1.71, maximum 11.53
Coulombic values for 1g0u_opengate.pdb_Y SES surface #4.28: minimum, -15.75,
mean -1.16, maximum 12.22
Coulombic values for 1g0u_opengate.pdb_Z SES surface #4.29: minimum, -17.67,
mean -1.87, maximum 8.80
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> view clip false
> save /Users/aks3233/Desktop/image2.png supersample 3
> hide #!3 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/1ryp_WT.pdb" format pdb
1ryp_WT.pdb title:
Crystal structure of the 20S proteasome from yeast At 2.4 angstroms resolution
[more info...]
Chain information for 1ryp_WT.pdb #5
---
Chain | Description | UniProt
1 M | 20S proteasome | PSB1_YEAST -9-213
2 N | 20S proteasome | PSB4_YEAST -8-225
A O | 20S proteasome | PSA6_YEAST 10-252
B P | 20S proteasome | PSA2_YEAST 1-250
C Q | 20S proteasome | PSA4_YEAST 2-245
D R | 20S proteasome | PSA7_YEAST 3-243
E S | 20S proteasome | PSA5_YEAST 9-250
F T | 20S proteasome | PSA1_YEAST 2-234
G U | 20S proteasome | PSA3_YEAST 4-247
H V | 20S proteasome | PSB6_YEAST -9-196
I W | 20S proteasome | PSB7_YEAST 1-222
J X | 20S proteasome | PSB3_YEAST -8-196
K Y | 20S proteasome | PSB2_YEAST -1-197
L Z | 20S proteasome | PSB5_YEAST 1-212
Non-standard residues in 1ryp_WT.pdb #5
---
MG — magnesium ion
> show #!4 models
> hide #!2 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> coulombic #!5
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1ryp_WT.pdb_1 SES surface #5.2: minimum, -16.10, mean
-1.71, maximum 9.53
Coulombic values for 1ryp_WT.pdb_2 SES surface #5.3: minimum, -39.88, mean
-1.53, maximum 10.23
Coulombic values for 1ryp_WT.pdb_A SES surface #5.4: minimum, -22.37, mean
-1.90, maximum 10.80
Coulombic values for 1ryp_WT.pdb_B SES surface #5.5: minimum, -17.03, mean
-1.84, maximum 11.29
Coulombic values for 1ryp_WT.pdb_C SES surface #5.6: minimum, -21.97, mean
-1.88, maximum 17.40
Coulombic values for 1ryp_WT.pdb_D SES surface #5.7: minimum, -17.69, mean
-0.90, maximum 14.30
Coulombic values for 1ryp_WT.pdb_E SES surface #5.8: minimum, -18.52, mean
-4.41, maximum 12.49
Coulombic values for 1ryp_WT.pdb_F SES surface #5.9: minimum, -19.52, mean
-0.72, maximum 12.59
Coulombic values for 1ryp_WT.pdb_G SES surface #5.10: minimum, -13.69, mean
-0.22, maximum 14.03
Coulombic values for 1ryp_WT.pdb_H SES surface #5.11: minimum, -14.46, mean
-1.86, maximum 11.04
Coulombic values for 1ryp_WT.pdb_I SES surface #5.12: minimum, -14.45, mean
-0.79, maximum 15.20
Coulombic values for 1ryp_WT.pdb_J SES surface #5.13: minimum, -30.39, mean
-2.75, maximum 23.71
Coulombic values for 1ryp_WT.pdb_K SES surface #5.14: minimum, -20.04, mean
-1.71, maximum 11.31
Coulombic values for 1ryp_WT.pdb_L SES surface #5.15: minimum, -15.78, mean
-1.07, maximum 13.35
Coulombic values for 1ryp_WT.pdb_M SES surface #5.16: minimum, -18.55, mean
-1.75, maximum 8.68
Coulombic values for 1ryp_WT.pdb_N SES surface #5.17: minimum, -24.20, mean
-1.55, maximum 10.63
Coulombic values for 1ryp_WT.pdb_O SES surface #5.18: minimum, -26.94, mean
-1.91, maximum 11.27
Coulombic values for 1ryp_WT.pdb_P SES surface #5.19: minimum, -16.96, mean
-1.84, maximum 10.97
Coulombic values for 1ryp_WT.pdb_Q SES surface #5.20: minimum, -15.56, mean
-1.85, maximum 18.10
Coulombic values for 1ryp_WT.pdb_R SES surface #5.21: minimum, -17.97, mean
-0.87, maximum 13.64
Coulombic values for 1ryp_WT.pdb_S SES surface #5.22: minimum, -19.61, mean
-4.44, maximum 13.77
Coulombic values for 1ryp_WT.pdb_T SES surface #5.23: minimum, -20.60, mean
-0.70, maximum 12.52
Coulombic values for 1ryp_WT.pdb_U SES surface #5.24: minimum, -13.31, mean
-0.18, maximum 14.03
Coulombic values for 1ryp_WT.pdb_V SES surface #5.25: minimum, -15.29, mean
-2.15, maximum 10.68
Coulombic values for 1ryp_WT.pdb_W SES surface #5.26: minimum, -14.05, mean
-0.81, maximum 26.04
Coulombic values for 1ryp_WT.pdb_X SES surface #5.27: minimum, -35.85, mean
-2.68, maximum 10.77
Coulombic values for 1ryp_WT.pdb_Y SES surface #5.28: minimum, -19.92, mean
-1.71, maximum 11.57
Coulombic values for 1ryp_WT.pdb_Z SES surface #5.29: minimum, -15.47, mean
-1.11, maximum 12.72
To also show corresponding color key, enter the above coulombic command and
add key true
> save /Users/aks3233/Desktop/image3.png supersample 3
> hide #!5 models
> show #!5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!3 models
> show #!2 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/20S_Bort_NTer.cxs" format session
opened ChimeraX session
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/2f16_bortezomib.pdb" format pdb
2f16_bortezomib.pdb title:
Crystal structure of the yeast 20S proteasome In complex with bortezomib [more
info...]
Chain information for 2f16_bortezomib.pdb #2
---
Chain | Description | UniProt
1 M | proteasome component PRE4 | PSB4_YEAST -8-211
2 N | proteasome component PRE3 | PSB6_YEAST 1-18
A O | proteasome component Y7 | PSA2_YEAST 4-236
B P | proteasome component Y13 | PSA4_YEAST 4-239
C Q | proteasome component PRE6 | PSA7_YEAST 7-243
D R | proteasome component PUP2 | PSA5_YEAST 9-244
E S | proteasome component PRE5 | PSA1_YEAST 4-233
F T | proteasome component C1 | PSA3_YEAST 5-241
G U | proteasome component C7-α | PSA6_YEAST 6-240
H V | proteasome component PUP1 | PSB7_YEAST 1-223
I W | proteasome component PUP3 | PSB3_YEAST -8-194
J X | proteasome component C11 | PSB2_YEAST -1-193
K Y | proteasome component PRE2 | PSB5_YEAST 1-211
L Z | multicatalytic endopeptidase complex subunit C5 | PSB1_YEAST -9-194
Non-standard residues in 2f16_bortezomib.pdb #2
---
BO2 —
N-[(1R)-1-(dihydroxyboryl)-3-methylbutyl]-N-(pyrazin-2-ylcarbonyl)-L-phenylalaninamide
(bortezomib)
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/20S_Bort_NTer.cxs" format session
opened ChimeraX session
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/1ryp_20s_wt_alpha_CONTACTS.cxs" format session
opened ChimeraX session
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/aks3233/Desktop/movie2.mp4
Movie saved to /Users/aks3233/Desktop/movie2.mp4
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/1g0u_opengate_aplha_contacts.cxs" format session
opened ChimeraX session
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/aks3233/Desktop/movie1.mp4
Movie saved to /Users/aks3233/Desktop/movie1.mp4
> select clear
> select /G:21-31
94 atoms, 96 bonds, 35 pseudobonds, 11 residues, 2 models selected
> select /G:9
5 atoms, 4 bonds, 1 residue, 1 model selected
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/20S_Bort_NTer.cxs" format session
opened ChimeraX session
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/1g0u_opengate_aplha_contacts.cxs" format session
opened ChimeraX session
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/20S_Bort_NTer.cxs" format session
opened ChimeraX session
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/20S_Bort_NTer.cxs" format session
opened ChimeraX session
> select /A:21-34
103 atoms, 103 bonds, 14 residues, 1 model selected
> select /A:4
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:4-5
15 atoms, 14 bonds, 2 residues, 1 model selected
> select clear
> select /A:4-5
15 atoms, 14 bonds, 2 residues, 1 model selected
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/1g0u_opengate_aplha_contacts.cxs" format session
opened ChimeraX session
> select clear
> select /A:8
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:14
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:13-14
14 atoms, 13 bonds, 2 residues, 1 model selected
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/20S_Bort_NTer.cxs" format session
opened ChimeraX session
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/2f16_wt_20s_alpha_Nter_BTZ_contacts.cxs" format session
opened ChimeraX session
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/1ryp_20s_wt_alpha_CONTACTS.cxs" format session
opened ChimeraX session
> open "/Users/aks3233/Desktop/Projects/Indiana_mass/20S
> structure/20S_Bort_NTer.cxs" format session
opened ChimeraX session
> open /Users/aks3233/Desktop/1ryp_wt_alphaonly.cxs
> set bgColor #ffffff00
opened ChimeraX session
> open /Users/aks3233/Desktop/1ryp_wt_alphaonly.cxs
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: MK183LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3 (23D56)
Kernel Version: Darwin 23.3.0
Time since boot: 1 day, 6 hours, 10 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2417H:
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: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 22 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 22 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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Hi Amit,
--Eric