![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15645 closed defect (duplicate)
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-13.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000030a01f000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001efc6fa80 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/weakref.py", line 576 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1613 in remove_deleted_pointers
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 134 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 807 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ctypes_support.py", line 31 in atoms
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 177 in get_prop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 208 in _update_sel_info
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 39 in check_for_changes
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 77 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3005 in command_trigger
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 144 in __exit__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2899 in run
File "/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 292 in forward_keystroke
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.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.map._map, 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.surface._surface, chimerax.pdb_lib._load_libs, 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, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PIL._imagingmath, chimerax.mlp._mlp (total: 60)
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"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
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],
"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=4.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 4032K 4 \nCG image 1712K 34 \nColorSync 576K 29 \nCoreAnimation 4816K 21 \nCoreGraphics 48K 3 \nCoreUI image data 3440K 26 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.5G 394 \nMALLOC guard page 192K 10 \nMALLOC_MEDIUM (reserved) 808.0M 9 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 608K 38 \nStack 178.4M 39 \nStack Guard 56.0M 1 \nVM_ALLOCATE 519.4M 440 \nVM_ALLOCATE (reserved) 224.0M 4 reserved VM address space (unallocated)\n__AUTH 1933K 360 \n__AUTH_CONST 24.8M 588 \n__CTF 756 1 \n__DATA 21.3M 736 \n__DATA_CONST 37.7M 743 \n__DATA_DIRTY 1983K 229 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 796.9M 154 \n__OBJC_CONST 4752K 325 \n__OBJC_RO 65.4M 1 \n__OBJC_RW 1986K 1 \n__TEXT 807.5M 764 \ndyld private memory 448K 3 \nmapped file 299.4M 58 \nshared memory 3280K 30 \n=========== ======= ======= \nTOTAL 6.5G 5061 \nTOTAL, minus reserved VM space 5.3G 5061 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "62699e1ec1ff2978b47f6c3b",
"factorPackIds" : {
"SIRI_FIND_MY_CONFIGURATION_FILES" : "652805151bce5442b8d752e1"
},
"deploymentId" : 240000031
},
{
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}
],
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{
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"experimentId" : "6639bc6ba73d460582162323",
"deploymentId" : 400000006
}
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/huanggq/Desktop/1/RC-FMO-bc1/PDB/FMO-J6836-coot-1.pdb
Chain information for FMO-J6836-coot-1.pdb #1
---
Chain | Description
B | No description available
D | No description available
I J K | No description available
N P | No description available
Q | No description available
R W | No description available
> hide atoms
> show cartoons
> lighting soft
> lighting full
> lighting soft
> set bgColor white
> hide atoms
> show atoms
> style stick
Changed 14611 atom styles
> hide cartoons
> show cartoons
> hide atoms
> select ::name="BCL"::name="SF4"
1540 atoms, 1620 bonds, 132 pseudobonds, 26 residues, 2 models selected
> show sel atoms
> select add #1
14611 atoms, 14976 bonds, 132 pseudobonds, 1683 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> show #!1 models
> hide cartoons
> show cartoons
> open /Users/huanggq/Downloads/6m32.pdb
6m32.pdb title:
Cryo-em structure of fmo-RC complex from green sulfur bacteria [more info...]
Chain information for 6m32.pdb #2
---
Chain | Description | UniProt
A a | photosystem P840 reaction center, large subunit | Q8KAY0_CHLTE 1-731
B | photosystem P840 reaction center iron-sulfur protein | Q8KAY1_CHLTE 1-231
D | P840 reaction center 17 kda protein | PSCD_CHLTE 1-143
E F G | bacteriochlorophyll A protein | BCPA_CHLTE 1-366
Non-standard residues in 6m32.pdb #2
---
BCL — bacteriochlorophyll A
CA — calcium ion
F26 —
2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E,19E)-3,7,12,16,20,24-hexamethylpentacosa-1,3,5,7,9,11,13,15,17,19,23-undecaenyl]-1,3,4-trimethyl-
benzene
F39 —
[(2R,3S,4S,5R,6R)-6-[(10E,12E,14E)-2,6,10,14,19,23-hexamethyl-25-(2,3,6-trimethylphenyl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl
dodecanoate
G2O — chlorophyll A ester
GS0 — bacteriochlorophyll A isomer
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
SF4 — iron/sulfur cluster
> hide atoms
> show cartoons
> hide #!1 models
> select add #2/G:221
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/E:172
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #2/F:118
18 atoms, 15 bonds, 3 residues, 1 model selected
> select up
359 atoms, 368 bonds, 46 residues, 1 model selected
> select up
8588 atoms, 8816 bonds, 1081 residues, 1 model selected
> select up
8591 atoms, 8816 bonds, 1081 residues, 1 model selected
> select up
9917 atoms, 10226 bonds, 1102 residues, 1 model selected
> select up
23566 atoms, 24401 bonds, 2590 residues, 1 model selected
> select down
9917 atoms, 10226 bonds, 1102 residues, 1 model selected
> select ~sel & ##selected
13649 atoms, 14175 bonds, 154 pseudobonds, 1488 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> show #!1 models
> ui tool show Matchmaker
> matchmaker #!2 to #1
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 FMO-J6836-coot-1.pdb, chain K (#1) with 6m32.pdb, chain E (#2),
sequence alignment score = 798.5
RMSD between 299 pruned atom pairs is 0.910 angstroms; (across all 352 pairs:
2.011)
> select add #1/I:244
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/I:245
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #1/I:243
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #1/I:242
31 atoms, 28 bonds, 4 residues, 1 model selected
> select add #1/I:241
40 atoms, 36 bonds, 5 residues, 1 model selected
> select add #1/I:246
44 atoms, 39 bonds, 6 residues, 1 model selected
> select add #1/I:247
48 atoms, 42 bonds, 7 residues, 1 model selected
> select add #1/I:240
52 atoms, 45 bonds, 8 residues, 1 model selected
> show sel atoms
> select add #1/R:22
61 atoms, 53 bonds, 9 residues, 1 model selected
> select add #1/R:21
68 atoms, 60 bonds, 10 residues, 1 model selected
> select add #1/R:53
76 atoms, 67 bonds, 11 residues, 1 model selected
> select subtract #1/R:53
68 atoms, 60 bonds, 10 residues, 1 model selected
> select add #1/R:20
75 atoms, 66 bonds, 11 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select add #1/Q:1
84 atoms, 74 bonds, 12 residues, 1 model selected
> show sel atoms
> select add #1/Q:2
92 atoms, 81 bonds, 13 residues, 1 model selected
> select add #2/G:87
100 atoms, 88 bonds, 14 residues, 2 models selected
> select subtract #2/G:87
92 atoms, 81 bonds, 13 residues, 1 model selected
> select add #1/Q:3
99 atoms, 88 bonds, 14 residues, 1 model selected
> show sel atoms
> color sel byhetero
> ui mousemode right distance
> distance #1/I:244@ND2 #1/Q:1@OE2
Distance between FMO-J6836-coot-1.pdb #1/I ASN 244 ND2 and /Q GLU 1 OE2:
7.400Å
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
FMO-J6836-coot-1.pdb #1/Q PRO 97 OXT
FMO-J6836-coot-1.pdb #1/R LYS 65 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for FMO-J6836-coot-1.pdb_I SES surface #1.2: minimum, -19.65,
mean -2.39, maximum 11.95
Coulombic values for FMO-J6836-coot-1.pdb_Q SES surface #1.3: minimum, -16.41,
mean 2.29, maximum 13.73
Coulombic values for FMO-J6836-coot-1.pdb_R SES surface #1.4: minimum, -15.08,
mean -0.16, maximum 9.40
To also show corresponding color key, enter the above coulombic command and
add key true
> select add #1
14611 atoms, 14976 bonds, 133 pseudobonds, 1683 residues, 6 models selected
> select subtract #1
3 models selected
> coulombic
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
6m32.pdb #2/F GLN 366 OXT
6m32.pdb #2/E GLN 366 OXT
6m32.pdb #2/G GLN 366 OXT
FMO-J6836-coot-1.pdb #1/B TRP 166 OXT
FMO-J6836-coot-1.pdb #1/N TYR 94 OXT
FMO-J6836-coot-1.pdb #1/P TYR 94 OXT
FMO-J6836-coot-1.pdb #1/W LYS 65 OXT
FMO-J6836-coot-1.pdb #1/D LEU 60 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for FMO-J6836-coot-1.pdb_B SES surface #1.5: minimum, -17.35,
mean -4.77, maximum 15.63
Coulombic values for FMO-J6836-coot-1.pdb_D SES surface #1.6: minimum, -14.99,
mean -1.92, maximum 9.14
Coulombic values for FMO-J6836-coot-1.pdb_I SES surface #1.2: minimum, -19.65,
mean -2.39, maximum 11.95
Coulombic values for FMO-J6836-coot-1.pdb_J SES surface #1.7: minimum, -21.38,
mean -2.45, maximum 12.26
Coulombic values for FMO-J6836-coot-1.pdb_K SES surface #1.8: minimum, -19.88,
mean -2.35, maximum 12.49
Coulombic values for FMO-J6836-coot-1.pdb_N SES surface #1.9: minimum, -11.49,
mean -0.32, maximum 9.45
Coulombic values for FMO-J6836-coot-1.pdb_P SES surface #1.10: minimum,
-15.27, mean -0.33, maximum 9.91
Coulombic values for FMO-J6836-coot-1.pdb_Q SES surface #1.3: minimum, -16.41,
mean 2.29, maximum 13.73
Coulombic values for FMO-J6836-coot-1.pdb_R SES surface #1.4: minimum, -15.08,
mean -0.16, maximum 9.40
Coulombic values for FMO-J6836-coot-1.pdb_W SES surface #1.11: minimum,
-15.61, mean -0.47, maximum 8.38
Coulombic values for 6m32.pdb_E SES surface #2.3: minimum, -17.29, mean -1.28,
maximum 13.18
Coulombic values for 6m32.pdb_F SES surface #2.4: minimum, -17.39, mean -1.15,
maximum 13.35
Coulombic values for 6m32.pdb_G SES surface #2.5: minimum, -26.67, mean -1.16,
maximum 13.11
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> open /Users/huanggq/Downloads/5lcb.pdb
5lcb.pdb title:
In situ atomic-resolution structure of the baseplate antenna complex In
chlorobaculum tepidum obtained combining solid-state NMR spectroscopy, cryo
electron microscopy and polarization spectroscopy [more info...]
Chain information for 5lcb.pdb #4
---
Chain | Description | UniProt
A B C D E F G H I J K L M N | bacteriochlorophyll C-binding protein |
CSMA_CHLTE 1-59
Non-standard residues in 5lcb.pdb #4
---
BCL — bacteriochlorophyll A
> hide #!1 models
> hide #!4 atoms
> show #!4 cartoons
> coulombic #!4
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 5lcb.pdb_A SES surface #4.2: minimum, -16.61, mean -0.08,
maximum 12.71
Coulombic values for 5lcb.pdb_B SES surface #4.3: minimum, -15.84, mean -0.08,
maximum 12.91
Coulombic values for 5lcb.pdb_C SES surface #4.4: minimum, -14.55, mean -0.02,
maximum 12.67
Coulombic values for 5lcb.pdb_D SES surface #4.5: minimum, -13.55, mean -0.06,
maximum 12.66
Coulombic values for 5lcb.pdb_E SES surface #4.6: minimum, -14.35, mean -0.03,
maximum 12.12
Coulombic values for 5lcb.pdb_F SES surface #4.7: minimum, -14.82, mean -0.05,
maximum 12.53
Coulombic values for 5lcb.pdb_G SES surface #4.8: minimum, -15.67, mean -0.04,
maximum 12.31
Coulombic values for 5lcb.pdb_H SES surface #4.9: minimum, -16.06, mean -0.03,
maximum 12.47
Coulombic values for 5lcb.pdb_I SES surface #4.10: minimum, -14.24, mean
-0.07, maximum 12.68
Coulombic values for 5lcb.pdb_J SES surface #4.11: minimum, -13.98, mean
-0.02, maximum 13.14
Coulombic values for 5lcb.pdb_K SES surface #4.12: minimum, -14.39, mean 0.00,
maximum 13.00
Coulombic values for 5lcb.pdb_L SES surface #4.13: minimum, -15.12, mean
-0.01, maximum 12.92
Coulombic values for 5lcb.pdb_M SES surface #4.14: minimum, -14.69, mean
-0.04, maximum 12.67
Coulombic values for 5lcb.pdb_N SES surface #4.15: minimum, -15.14, mean
-0.03, maximum 13.05
To also show corresponding color key, enter the above coulombic command and
add key true
> show #!4 cartoons
> color #!4 bychain
> show #!4 atoms
> hide #!4 atoms
> hide #!4 cartoons
> show #!4 cartoons
> color #!4 bypolymer
> style #!4 stick
Changed 13860 atom styles
> style #!4 sphere
Changed 13860 atom styles
> style #!4 ball
Changed 13860 atom styles
> color #!4 byhetero
> color #!4 bychain
> close #4
> open /Users/huanggq/Downloads/5lcb.pdb
5lcb.pdb title:
In situ atomic-resolution structure of the baseplate antenna complex In
chlorobaculum tepidum obtained combining solid-state NMR spectroscopy, cryo
electron microscopy and polarization spectroscopy [more info...]
Chain information for 5lcb.pdb #4
---
Chain | Description | UniProt
A B C D E F G H I J K L M N | bacteriochlorophyll C-binding protein |
CSMA_CHLTE 1-59
Non-standard residues in 5lcb.pdb #4
---
BCL — bacteriochlorophyll A
> hide #!4 atoms
> show #!4 cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A #4/B #4/C #4/D #4/E #4/F #4/G #4/H #4/I #4/J #4/K #4/L
> #4/M #4/N
Alignment identifier is 1
> select #4/A-N:43-44
462 atoms, 448 bonds, 28 residues, 1 model selected
> select #4/A-N:43-48
1428 atoms, 1428 bonds, 84 residues, 1 model selected
> show sel atoms
> hide sel atoms
> color sel red
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 5lcb.pdb_A SES surface #4.2: minimum, -16.61, mean -0.08,
maximum 12.71
Coulombic values for 5lcb.pdb_B SES surface #4.3: minimum, -15.84, mean -0.08,
maximum 12.91
Coulombic values for 5lcb.pdb_C SES surface #4.4: minimum, -14.55, mean -0.02,
maximum 12.67
Coulombic values for 5lcb.pdb_D SES surface #4.5: minimum, -13.55, mean -0.06,
maximum 12.66
Coulombic values for 5lcb.pdb_E SES surface #4.6: minimum, -14.35, mean -0.03,
maximum 12.12
Coulombic values for 5lcb.pdb_F SES surface #4.7: minimum, -14.82, mean -0.05,
maximum 12.53
Coulombic values for 5lcb.pdb_G SES surface #4.8: minimum, -15.67, mean -0.04,
maximum 12.31
Coulombic values for 5lcb.pdb_H SES surface #4.9: minimum, -16.06, mean -0.03,
maximum 12.47
Coulombic values for 5lcb.pdb_I SES surface #4.10: minimum, -14.24, mean
-0.07, maximum 12.68
Coulombic values for 5lcb.pdb_J SES surface #4.11: minimum, -13.98, mean
-0.02, maximum 13.14
Coulombic values for 5lcb.pdb_K SES surface #4.12: minimum, -14.39, mean 0.00,
maximum 13.00
Coulombic values for 5lcb.pdb_L SES surface #4.13: minimum, -15.12, mean
-0.01, maximum 12.92
Coulombic values for 5lcb.pdb_M SES surface #4.14: minimum, -14.69, mean
-0.04, maximum 12.67
Coulombic values for 5lcb.pdb_N SES surface #4.15: minimum, -15.14, mean
-0.03, maximum 13.05
To also show corresponding color key, enter the above coulombic command and
add key true
> select add #4
13860 atoms, 14000 bonds, 70 pseudobonds, 840 residues, 16 models selected
> select subtract #4
14 models selected
> mlp #!4
Map values for surface "5lcb.pdb_A SES surface": minimum -25.02, mean -2.542,
maximum 22.45
Map values for surface "5lcb.pdb_B SES surface": minimum -26.05, mean -2.631,
maximum 22.98
Map values for surface "5lcb.pdb_C SES surface": minimum -25.94, mean -2.635,
maximum 23.04
Map values for surface "5lcb.pdb_D SES surface": minimum -25.73, mean -2.675,
maximum 23.07
Map values for surface "5lcb.pdb_E SES surface": minimum -26.21, mean -2.567,
maximum 23.3
Map values for surface "5lcb.pdb_F SES surface": minimum -25.97, mean -2.597,
maximum 23.32
Map values for surface "5lcb.pdb_G SES surface": minimum -25.88, mean -2.646,
maximum 23.27
Map values for surface "5lcb.pdb_H SES surface": minimum -26.29, mean -2.601,
maximum 22.99
Map values for surface "5lcb.pdb_I SES surface": minimum -26.03, mean -2.609,
maximum 22.62
Map values for surface "5lcb.pdb_J SES surface": minimum -25.06, mean -2.643,
maximum 22.95
Map values for surface "5lcb.pdb_K SES surface": minimum -25.09, mean -2.675,
maximum 23.01
Map values for surface "5lcb.pdb_L SES surface": minimum -26.36, mean -2.629,
maximum 22.7
Map values for surface "5lcb.pdb_M SES surface": minimum -26.35, mean -2.607,
maximum 22.62
Map values for surface "5lcb.pdb_N SES surface": minimum -25.7, mean -2.6,
maximum 23.85
To also show corresponding color key, enter the above mlp command and add key
true
> show #!1 models
> hide #!1 models
> mlp #!4
Map values for surface "5lcb.pdb_A SES surface": minimum -25.02, mean -2.542,
maximum 22.45
Map values for surface "5lcb.pdb_B SES surface": minimum -26.05, mean -2.631,
maximum 22.98
Map values for surface "5lcb.pdb_C SES surface": minimum -25.94, mean -2.635,
maximum 23.04
Map values for surface "5lcb.pdb_D SES surface": minimum -25.73, mean -2.675,
maximum 23.07
Map values for surface "5lcb.pdb_E SES surface": minimum -26.21, mean -2.567,
maximum 23.3
Map values for surface "5lcb.pdb_F SES surface": minimum -25.97, mean -2.597,
maximum 23.32
Map values for surface "5lcb.pdb_G SES surface": minimum -25.88, mean -2.646,
maximum 23.27
Map values for surface "5lcb.pdb_H SES surface": minimum -26.29, mean -2.601,
maximum 22.99
Map values for surface "5lcb.pdb_I SES surface": minimum -26.03, mean -2.609,
maximum 22.62
Map values for surface "5lcb.pdb_J SES surface": minimum -25.06, mean -2.643,
maximum 22.95
Map values for surface "5lcb.pdb_K SES surface": minimum -25.09, mean -2.675,
maximum 23.01
Map values for surface "5lcb.pdb_L SES surface": minimum -26.36, mean -2.629,
maximum 22.7
Map values for surface "5lcb.pdb_M SES surface": minimum -26.35, mean -2.607,
maximum 22.62
Map values for surface "5lcb.pdb_N SES surface": minimum -25.7, mean -2.6,
maximum 23.85
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic #!4
Coulombic values for 5lcb.pdb_A SES surface #4.2: minimum, -16.61, mean -0.08,
maximum 12.71
Coulombic values for 5lcb.pdb_B SES surface #4.3: minimum, -15.84, mean -0.08,
maximum 12.91
Coulombic values for 5lcb.pdb_C SES surface #4.4: minimum, -14.55, mean -0.02,
maximum 12.67
Coulombic values for 5lcb.pdb_D SES surface #4.5: minimum, -13.55, mean -0.06,
maximum 12.66
Coulombic values for 5lcb.pdb_E SES surface #4.6: minimum, -14.35, mean -0.03,
maximum 12.12
Coulombic values for 5lcb.pdb_F SES surface #4.7: minimum, -14.82, mean -0.05,
maximum 12.53
Coulombic values for 5lcb.pdb_G SES surface #4.8: minimum, -15.67, mean -0.04,
maximum 12.31
Coulombic values for 5lcb.pdb_H SES surface #4.9: minimum, -16.06, mean -0.03,
maximum 12.47
Coulombic values for 5lcb.pdb_I SES surface #4.10: minimum, -14.24, mean
-0.07, maximum 12.68
Coulombic values for 5lcb.pdb_J SES surface #4.11: minimum, -13.98, mean
-0.02, maximum 13.14
Coulombic values for 5lcb.pdb_K SES surface #4.12: minimum, -14.39, mean 0.00,
maximum 13.00
Coulombic values for 5lcb.pdb_L SES surface #4.13: minimum, -15.12, mean
-0.01, maximum 12.92
Coulombic values for 5lcb.pdb_M SES surface #4.14: minimum, -14.69, mean
-0.04, maximum 12.67
Coulombic values for 5lcb.pdb_N SES surface #4.15: minimum, -15.14, mean
-0.03, maximum 13.05
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!4 models
> show #!1 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 20293 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> show #!2 models
> coulombic #!1-2
Coulombic values for FMO-J6836-coot-1.pdb_B SES surface #1.5: minimum, -17.35,
mean -4.77, maximum 15.63
Coulombic values for FMO-J6836-coot-1.pdb_D SES surface #1.6: minimum, -14.99,
mean -1.92, maximum 9.14
Coulombic values for FMO-J6836-coot-1.pdb_I SES surface #1.2: minimum, -19.65,
mean -2.39, maximum 11.95
Coulombic values for FMO-J6836-coot-1.pdb_J SES surface #1.7: minimum, -21.38,
mean -2.45, maximum 12.26
Coulombic values for FMO-J6836-coot-1.pdb_K SES surface #1.8: minimum, -19.88,
mean -2.35, maximum 12.49
Coulombic values for FMO-J6836-coot-1.pdb_N SES surface #1.9: minimum, -11.49,
mean -0.32, maximum 9.45
Coulombic values for FMO-J6836-coot-1.pdb_P SES surface #1.10: minimum,
-15.27, mean -0.33, maximum 9.91
Coulombic values for FMO-J6836-coot-1.pdb_Q SES surface #1.3: minimum, -16.41,
mean 2.29, maximum 13.73
Coulombic values for FMO-J6836-coot-1.pdb_R SES surface #1.4: minimum, -15.08,
mean -0.16, maximum 9.40
Coulombic values for FMO-J6836-coot-1.pdb_W SES surface #1.11: minimum,
-15.61, mean -0.47, maximum 8.38
Coulombic values for 6m32.pdb_E SES surface #2.3: minimum, -17.29, mean -1.28,
maximum 13.18
Coulombic values for 6m32.pdb_F SES surface #2.4: minimum, -17.39, mean -1.15,
maximum 13.35
Coulombic values for 6m32.pdb_G SES surface #2.5: minimum, -26.67, mean -1.16,
maximum 13.11
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #3.1 models
> show #3.1 models
> hide #!1 models
> open /Users/huanggq/Desktop/1/RC-FMO-bc1/PDB/typeI-J815-RC-FMO-
> bc1-240621.pdb
Chain information for typeI-J815-RC-FMO-bc1-240621.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E e | No description available
F f | No description available
G | No description available
H h | No description available
I J K | No description available
L M | No description available
N P | No description available
O | No description available
Q | No description available
R W | No description available
T U | No description available
a | No description available
c | No description available
g | No description available
> hide #!5 atoms
> show #!5 cartoons
Drag select of 317 residues
> select up
3838 atoms, 3917 bonds, 479 residues, 1 model selected
> select up
10345 atoms, 10582 bonds, 1317 residues, 1 model selected
> select up
11869 atoms, 12202 bonds, 1341 residues, 1 model selected
> select up
45509 atoms, 46776 bonds, 5270 residues, 1 model selected
> select down
11869 atoms, 12202 bonds, 1341 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 13 residues
> select add #5/N:82
93 atoms, 6 bonds, 14 residues, 1 model selected
> select up
226 atoms, 222 bonds, 31 residues, 1 model selected
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83
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: MK193CH/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 8419.60.44
OS Loader Version: 8419.60.44
Software:
System Software Overview:
System Version: macOS 13.1 (22C65)
Kernel Version: Darwin 22.2.0
Time since boot: 1天9小时46分钟
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
Installed Packages:
alabaster: 0.7.16
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: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 1.7.1
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: 2.6.1
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: 1.5.14
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: 1.0.4
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: 1.12.4
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: 1.33.3
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: 0.2.1
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: 4.47.2
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: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
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: 10.2.0
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: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
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: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 15 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 , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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