![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 18 months ago
Closed 18 months ago
#15136 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-14.3.1-x86_64-i386-64bit
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
Current thread 0x0000000200f10240 (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/atomic/molobject.py", line 2000 in save_state
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 219 in take_snapshot
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1417 in take_snapshot
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 296 in process
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 273 in discovery
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 636 in save
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 912 in save
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 95 in save
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
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/save_command/cmd.py", line 86 in cmd_save
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/save_command/dialog.py", line 62 in display
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in
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.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, 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.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 (total: 61)
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{
"uptime" : 1800000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,5",
"coalitionID" : 317446,
"osVersion" : {
"train" : "macOS 14.3.1",
"build" : "23D60",
"releaseType" : "User"
},
"captureTime" : "2024-05-08 20:52:28.2193 +0100",
"codeSigningMonitor" : 1,
"incident" : "663A1DD3-2105-49A9-AFE9-620408E3CA05",
"pid" : 68651,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-05-08 20:34:19.8863 +0100",
"procStartAbsTime" : 45082872230364,
"procExitAbsTime" : 45108991328632,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"13C36163-CC03-5074-9FDF-F7545CEC4403","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F9070259-436C-FF97-23D6-B37F3ACB6C68",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 2987,
"sleepWakeUUID" : "7DB353B5-ED37-40B4-B064-4FBFF9203F4D",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140723089456983\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffca5c24000-7ffcce9d4000 [653.7M] r-x\/r-x SM=COW ...t_id=7878c089",
"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":68651},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140723089456983\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffca5c24000-7ffcce9d4000 [653.7M] r-x\/r-x SM=COW ...t_id=7878c089",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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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.
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/JIP3-KLC.cxs"
Log from Tue Feb 20 11:59:33 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Manuscripts/Chaaban-
> JCS-2024/Adaptors/Adaptors/JIP3-linear.pdb"
Chain information for JIP3-linear.pdb #1
---
Chain | Description
B C | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Ammaar/AF/j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb"
Chain information for
j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb #2
---
Chain | Description
A B | No description available
C D | No description available
E F | No description available
> hide #1 models
> close session
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Ammaar/AF/j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb"
> format pdb
Chain information for
j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb #1
---
Chain | Description
A B | No description available
C D | No description available
E F | No description available
> preset custom pretty-chain
Using preset: Custom / Pretty-chain
Preset expands to these ChimeraX commands:
lighting soft
set bgColor white
cartoon style coil width 1.5 thickness 0.8
cartoon style helix xsection round width 3 thickness 0.8
cartoon style strand xsection round width 3 thickness 0.8
cartoon style strand arrowscale 1
cartoon style helix xsection oval sides 10
graphics silhouettes true
graphics silhouettes width 1.5
graphics silhouettes depthJump 0.003
lighting msDepthBias 0.004
lighting shadows true intensity 0.06
lighting depthCueColor #000000
color bychain
> hide atoms
> show cartoons
> select /B/C
3200 atoms, 3262 bonds, 405 residues, 1 model selected
> select /A/B
2510 atoms, 2530 bonds, 328 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #fffb00ff
> select /C/D
3890 atoms, 3994 bonds, 482 residues, 1 model selected
> color sel #8efa00ff
> color sel #73fa79ff
> select /E/F
4776 atoms, 4866 bonds, 602 residues, 1 model selected
> color sel #ff9300ff
> color sel #ff9941ff
> select /A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /C/D
3890 atoms, 3994 bonds, 482 residues, 1 model selected
> select clear
> select /C
1945 atoms, 1997 bonds, 241 residues, 1 model selected
> select /D
1945 atoms, 1997 bonds, 241 residues, 1 model selected
> hide sel cartoons
> select /F
2388 atoms, 2433 bonds, 301 residues, 1 model selected
> select /E
2388 atoms, 2433 bonds, 301 residues, 1 model selected
> hide sel cartoons
Drag select of 83 residues
> hide sel cartoons
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/chaaban/Desktop/movie1.mp4
Movie saved to /Users/chaaban/Desktop/movie1.mp4
> select /E
2388 atoms, 2433 bonds, 301 residues, 1 model selected
> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/JIP1JIP3KLC.cxs"
> select /E
2388 atoms, 2433 bonds, 301 residues, 1 model selected
> select /F
2388 atoms, 2433 bonds, 301 residues, 1 model selected
> hide sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:55
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:55-59
45 atoms, 46 bonds, 5 residues, 1 model selected
> color sel hot pink
> select clear
> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/JIP1JIP3KLC-J1J3spindly.cxs"
> close session
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Kashish/DDJL.pdb"
Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Kashish/DDJL.pdb
---
warnings | Start residue of secondary structure not found: HELIX 57 57 PRO V 4
ASP V 8 1 5
Start residue of secondary structure not found: HELIX 58 58 PRO V 52 LYS V 58
1 7
Start residue of secondary structure not found: HELIX 117 117 CYS T 742 PHE T
770 1 29
Start residue of secondary structure not found: HELIX 120 120 PRO T 821 ILE T
852 1 32
Start residue of secondary structure not found: HELIX 124 124 LEU T 1099 LYS T
1120 1 22
5 messages similar to the above omitted
End residue of secondary structure not found: HELIX 130 130 GLN T 1274 HIS T
1281 1 8
Start residue of secondary structure not found: HELIX 131 131 ASP T 1282 LEU T
1284 1 3
Start residue of secondary structure not found: HELIX 176 176 CYS S 742 PHE S
770 1 29
Start residue of secondary structure not found: HELIX 178 178 PRO S 821 ILE S
852 1 32
Start residue of secondary structure not found: HELIX 182 182 PRO S 1096 LYS S
1138 1 43
Start residue of secondary structure not found: HELIX 183 183 SER S 1140 PRO S
1142 1 3
20 messages similar to the above omitted
End residue of secondary structure not found: SHEET 157 15715 TYR o 327 CYS o
331 0
Start residue of secondary structure not found: SHEET 158 15815 VAL o 335 PHE
o 340 0
Start residue of secondary structure not found: SHEET 159 15915 LEU o 347 THR
o 352 0
Start residue of secondary structure not found: SHEET 160 16016 ILE o 357 ASP
o 361 0
Start residue of secondary structure not found: SHEET 161 16116 VAL o 384 GLY
o 391 0
Start residue of secondary structure not found: SHEET 162 16216 HIS o 396 SER
o 402 0
14 messages similar to the above omitted
End residue of secondary structure not found: SHEET 177 17717 GLU o 584 GLY o
588 0
Start residue of secondary structure not found: SHEET 178 17817 ILE o 594 VAL
o 599 0
Start residue of secondary structure not found: SHEET 253 25325 LEU h 265 PHE
h 271 0
Start residue of secondary structure not found: SHEET 254 25425 LEU h 285 TRP
h 287 0
Start residue of secondary structure not found: SHEET 255 25525 LEU h 294 TYR
h 299 0
Start residue of secondary structure not found: SHEET 256 25625 GLY h 311 ASN
h 317 0
End residue of secondary structure not found: SHEET 257 25725 TYR h 327 CYS h
331 0
Start residue of secondary structure not found: SHEET 258 25825 VAL h 335 PHE
h 340 0
Start residue of secondary structure not found: SHEET 259 25925 LEU h 347 THR
h 352 0
Start residue of secondary structure not found: SHEET 260 26026 ILE h 357 ASP
h 361 0
Start residue of secondary structure not found: SHEET 261 26126 VAL h 387 GLY
h 391 0
Start residue of secondary structure not found: SHEET 262 26226 HIS h 396 ILE
h 401 0
14 messages similar to the above omitted
End residue of secondary structure not found: SHEET 277 27727 GLU h 584 ASP h
589 0
Start residue of secondary structure not found: SHEET 278 27827 ILE h 594 VAL
h 599 0
Start residue of secondary structure not found: SHEET 489 48948 LEU p 265 PHE
p 271 0
Start residue of secondary structure not found: SHEET 490 49049 LEU p 285 TRP
p 287 0
Start residue of secondary structure not found: SHEET 491 49149 LEU p 294 TYR
p 299 0
Start residue of secondary structure not found: SHEET 492 49249 GLY p 311 ASN
p 317 0
End residue of secondary structure not found: SHEET 493 49349 TYR p 327 CYS p
331 0
Start residue of secondary structure not found: SHEET 494 49449 VAL p 335 PHE
p 340 0
Start residue of secondary structure not found: SHEET 495 49549 LEU p 347 THR
p 352 0
Start residue of secondary structure not found: SHEET 496 49649 ILE p 357 ASP
p 361 0
Start residue of secondary structure not found: SHEET 497 49749 VAL p 384 GLY
p 391 0
Start residue of secondary structure not found: SHEET 498 49849 HIS p 396 SER
p 402 0
14 messages similar to the above omitted
End residue of secondary structure not found: SHEET 513 51351 GLU p 584 ASP p
589 0
Start residue of secondary structure not found: SHEET 514 51451 ILE p 594 VAL
p 599 0
Start residue of secondary structure not found: SHEET 530 53053 LEU g 265 PHE
g 271 0
Start residue of secondary structure not found: SHEET 531 53153 LEU g 285 TRP
g 287 0
Start residue of secondary structure not found: SHEET 532 53253 LEU g 294 TYR
g 299 0
Start residue of secondary structure not found: SHEET 533 53353 GLY g 311 ASN
g 317 0
End residue of secondary structure not found: SHEET 534 53453 TYR g 327 CYS g
331 0
Start residue of secondary structure not found: SHEET 535 53553 VAL g 335 PHE
g 340 0
Start residue of secondary structure not found: SHEET 536 53653 LEU g 347 THR
g 352 0
Start residue of secondary structure not found: SHEET 537 53753 ILE g 357 ASP
g 361 0
Start residue of secondary structure not found: SHEET 538 53853 VAL g 384 GLY
g 391 0
Start residue of secondary structure not found: SHEET 539 53953 HIS g 396 SER
g 402 0
14 messages similar to the above omitted
End residue of secondary structure not found: SHEET 554 55455 GLU g 584 ASP g
589 0
Start residue of secondary structure not found: SHEET 555 55555 ILE g 594 VAL
g 599 0
Chain information for DDJL.pdb #1
---
Chain | Description
1 2 | No description available
3 4 | No description available
A B D E F G I | No description available
C | No description available
H | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
W | No description available
X | No description available
Y | No description available
a b d i | No description available
e | No description available
f | No description available
g | No description available
h | No description available
j | No description available
k l v y | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s t w z | No description available
u | No description available
x | No description available
> preset custom pretty-chain
Using preset: Custom / Pretty-chain
Preset expands to these ChimeraX commands:
lighting soft
set bgColor white
cartoon style coil width 1.5 thickness 0.8
cartoon style helix xsection round width 3 thickness 0.8
cartoon style strand xsection round width 3 thickness 0.8
cartoon style strand arrowscale 1
cartoon style helix xsection oval sides 10
graphics silhouettes true
graphics silhouettes width 1.5
graphics silhouettes depthJump 0.003
lighting msDepthBias 0.004
lighting shadows true intensity 0.06
lighting depthCueColor #000000
color bychain
> hide atoms
> show cartoons
> select /x/X
2981 atoms, 2975 bonds, 600 residues, 1 model selected
> ui tool show "Color Actions"
> color sel yellow
> color sel #fffc79ff
> color sel #fffb00ff
> select clear
> select
161768 atoms, 161675 bonds, 32552 residues, 1 model selected
> select /x/X
2981 atoms, 2975 bonds, 600 residues, 1 model selected
> select ~sel
158787 atoms, 158700 bonds, 31952 residues, 1 model selected
> color sel light sea green
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain /X
Alignment identifier is 1/X
> select /X:393
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /X:382
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /X:382-386
25 atoms, 24 bonds, 5 residues, 1 model selected
> color sel hot pink
> select clear
> select /X:518-551
170 atoms, 169 bonds, 34 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light gray
> select /x:518-551
170 atoms, 169 bonds, 34 residues, 1 model selected
> color sel light gray
> select clear
[Repeated 1 time(s)]
> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/DDJL-J3spindly.cxs"
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Ammaar/AF/j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb"
Chain information for
j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb #2
---
Chain | Description
A B | No description available
C D | No description available
E F | No description available
> mmaker #2 to #1/x
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 DDJL.pdb, chain x (#1) with
j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb, chain A
(#2), sequence alignment score = 351.7
RMSD between 5 pruned atom pairs is 1.401 angstroms; (across all 109 pairs:
75.543)
> mmaker #2 to #1/X
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 DDJL.pdb, chain X (#1) with
j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb, chain A
(#2), sequence alignment score = 535.7
RMSD between 59 pruned atom pairs is 0.840 angstroms; (across all 145 pairs:
83.719)
> hide atoms
> show cartoons
> preset custom pretty
Using preset: Custom / Pretty
Preset expands to these ChimeraX commands:
lighting soft
set bgColor white
cartoon style coil width 1.5 thickness 0.8
cartoon style helix xsection round width 3 thickness 0.8
cartoon style strand xsection round width 3 thickness 0.8
cartoon style strand arrowscale 1
cartoon style helix xsection oval sides 10
graphics silhouettes true
graphics silhouettes width 1.5
graphics silhouettes depthJump 0.003
lighting msDepthBias 0.004
lighting shadows true intensity 0.06
lighting depthCueColor #000000
> hide #!1 models
> select #2/F
2388 atoms, 2433 bonds, 301 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select ~sel & ##selected
8788 atoms, 8957 bonds, 1111 residues, 1 model selected
> select #2/D
1945 atoms, 1997 bonds, 241 residues, 1 model selected
> hide sel cartoons
Drag select of 73 residues
> hide sel cartoons
Drag select of 12 residues
> hide sel cartoons
> select #2/D
1945 atoms, 1997 bonds, 241 residues, 1 model selected
> show sel cartoons
> undo
[Repeated 6 time(s)]
> select #2/C
1945 atoms, 1997 bonds, 241 residues, 1 model selected
> hide sel cartoons
Drag select of 82 residues
> hide sel cartoons
> show #!1 models
> select #2/E
2388 atoms, 2433 bonds, 301 residues, 1 model selected
> color sel orange
> select clear
> select #2/A/B
2510 atoms, 2530 bonds, 328 residues, 1 model selected
> color sel yellow
> select clear
> select ~sel & ##selected
Nothing selected
> select #2/D
1945 atoms, 1997 bonds, 241 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #73fa79ff
> select clear
> hide #!1 models
> show #!1 models
> hide #2 models
> show #2 models
> hide #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> select #2/B:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:56-60
47 atoms, 48 bonds, 5 residues, 1 model selected
> color sel hot pink
> select clear
> show #!1 models
> hide #2 models
> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/DDJL-J3spindly.cxs"
> open 6FUZ
Summary of feedback from opening 6FUZ fetched from pdb
---
notes | Fetching compressed mmCIF 6fuz from
http://files.rcsb.org/download/6fuz.cif
Fetching CCD GOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif
6fuz title:
Crystal structure of the TPR domain of KLC1 in complex with the C-terminal
peptide of JIP1 [more info...]
Chain information for 6fuz #3
---
Chain | Description | UniProt
A | Kinesin light chain 1,Kinesin light chain 1,C-Jun-amino-terminal kinase-
interacting protein 1 | Q5UE59_MOUSE 201-670
N | nanobody |
Non-standard residues in 6fuz #3
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
> open 6EJN
Summary of feedback from opening 6EJN fetched from pdb
---
note | Fetching compressed mmCIF 6ejn from
http://files.rcsb.org/download/6ejn.cif
6ejn title:
The KLC2 TPR domain bound to the JIP3 leucine zipper domain [more info...]
Chain information for 6ejn #4
---
Chain | Description | UniProt
A B | Kinesin light chain 2 | Q91YS4_MOUSE 191-479
C D | C-Jun-amino-terminal kinase-interacting protein 3 | JIP3_MOUSE 417-486
> hide #!3 models
> hide #!4 models
> show #2 models
> hide #!1 models
> mmaker #3 to #2
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 j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain E (#2) with 6fuz, chain A (#3), sequence alignment score = 1402.4
RMSD between 139 pruned atom pairs is 0.979 angstroms; (across all 244 pairs:
3.497)
> mmaker #4 to #2
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 j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain E (#2) with 6ejn, chain B (#4), sequence alignment score = 1306.6
RMSD between 137 pruned atom pairs is 0.816 angstroms; (across all 255 pairs:
5.712)
> show #!3 models
> hide #2 models
> show #2 models
> hide #2 models
> select #3/A
2147 atoms, 2174 bonds, 2 pseudobonds, 274 residues, 2 models selected
> select ~sel & ##selected
873 atoms, 886 bonds, 119 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> preset custom pretty
Using preset: Custom / Pretty
Preset expands to these ChimeraX commands:
lighting soft
set bgColor white
cartoon style coil width 1.5 thickness 0.8
cartoon style helix xsection round width 3 thickness 0.8
cartoon style strand xsection round width 3 thickness 0.8
cartoon style strand arrowscale 1
cartoon style helix xsection oval sides 10
graphics silhouettes true
graphics silhouettes width 1.5
graphics silhouettes depthJump 0.003
lighting msDepthBias 0.004
lighting shadows true intensity 0.06
lighting depthCueColor #000000
Drag select of 6 atoms, 267 residues, 2 pseudobonds, 5 bonds
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select #3/A:704
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/A:705
14 atoms, 13 bonds, 2 residues, 1 model selected
> select add #3/A:706
23 atoms, 21 bonds, 3 residues, 1 model selected
> select add #3/A:707
31 atoms, 28 bonds, 4 residues, 1 model selected
> select add #3/A:708
39 atoms, 35 bonds, 5 residues, 1 model selected
> select add #3/A:350
48 atoms, 43 bonds, 6 residues, 1 model selected
> select subtract #3/A:350
39 atoms, 35 bonds, 5 residues, 1 model selected
> select add #3/A:709
51 atoms, 47 bonds, 6 residues, 1 model selected
> select add #3/A:710
59 atoms, 54 bonds, 7 residues, 1 model selected
> select add #3/A:711
69 atoms, 63 bonds, 8 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #73fdffff
> color sel #73fa79ff
> select ~sel
181102 atoms, 181334 bonds, 3 pseudobonds, 35008 residues, 6 models selected
> select subtract #4
175895 atoms, 176055 bonds, 1 pseudobond, 34349 residues, 4 models selected
> select subtract #2
164719 atoms, 164665 bonds, 1 pseudobond, 32937 residues, 3 models selected
> select subtract #1
2951 atoms, 2990 bonds, 1 pseudobond, 385 residues, 2 models selected
> color (#!3 & sel) orange
> select clear
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/KCL-JIP1.cxs"
> show #!4 models
> hide #!3 models
> select #4/A/B
4277 atoms, 4351 bonds, 2 pseudobonds, 538 residues, 2 models selected
> color (#!4 & sel) orange
> select #4/C/D
930 atoms, 928 bonds, 121 residues, 1 model selected
> color sel yellow
> select clear
> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/JIP3-KLC.cxs"
——— End of log from Tue Feb 20 11:59:33 2024 ———
opened ChimeraX session
> select #1/X:80-81
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/X:80-432
817 atoms, 815 bonds, 165 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A #4/B
Alignment identifier is 1
> select clear
> select #4/A:191-421/B:193-422
3687 atoms, 3754 bonds, 461 residues, 1 model selected
> select clear
> select #4/A:191-195/B:193-195
64 atoms, 65 bonds, 8 residues, 1 model selected
> select #4/A-B:193-195
48 atoms, 48 bonds, 6 residues, 1 model selected
> select #4/A-B:193-196
58 atoms, 58 bonds, 8 residues, 1 model selected
> select #4/A:191-192
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #4/A:191-194/B:193-194
50 atoms, 49 bonds, 6 residues, 1 model selected
> select clear
> select #4/A-B:477
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #4/A-B:473-477
72 atoms, 70 bonds, 10 residues, 1 model selected
> select clear
> select #4/A-B:473-477
72 atoms, 70 bonds, 10 residues, 1 model selected
> select #4/A-B:236-237
34 atoms, 36 bonds, 4 residues, 1 model selected
> select #4/A-B:236-238
50 atoms, 52 bonds, 6 residues, 1 model selected
> select #4/A:421/B:421-422
21 atoms, 19 bonds, 3 residues, 1 model selected
> select #4/A:414-421/B:414-422
145 atoms, 145 bonds, 17 residues, 1 model selected
> close session
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/JIP3-linear.pdb"
Chain information for JIP3-linear.pdb #1
---
Chain | Description
B C | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain /B /C
Alignment identifier is 1
Drag select of 1 residues
Drag select of 6 residues
> select /B-C:320-321
32 atoms, 30 bonds, 4 residues, 1 model selected
> select /B-C:320-579
4150 atoms, 4196 bonds, 520 residues, 1 model selected
> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_0.cif
Chain information for fold_2024_05_08_20_40_model_0.cif #2
---
Chain | Description
A B | .
C | .
D | .
E | .
F | .
G | .
H I | .
> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_1.cif
Chain information for fold_2024_05_08_20_40_model_1.cif #3
---
Chain | Description
A B | .
C | .
D | .
E | .
F | .
G | .
H I | .
> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_2.cif
Chain information for fold_2024_05_08_20_40_model_2.cif #4
---
Chain | Description
A B | .
C | .
D | .
E | .
F | .
G | .
H I | .
> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_3.cif
Chain information for fold_2024_05_08_20_40_model_3.cif #5
---
Chain | Description
A B | .
C | .
D | .
E | .
F | .
G | .
H I | .
> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_4.cif
Chain information for fold_2024_05_08_20_40_model_4.cif #6
---
Chain | Description
A B | .
C | .
D | .
E | .
F | .
G | .
H I | .
> close session
> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_0.cif
Chain information for fold_2024_05_08_20_40_model_0.cif #1
---
Chain | Description
A B | .
C | .
D | .
E | .
F | .
G | .
H I | .
> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_1.cif
Chain information for fold_2024_05_08_20_40_model_1.cif #2
---
Chain | Description
A B | .
C | .
D | .
E | .
F | .
G | .
H I | .
> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_2.cif
Chain information for fold_2024_05_08_20_40_model_2.cif #3
---
Chain | Description
A B | .
C | .
D | .
E | .
F | .
G | .
H I | .
> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_3.cif
Chain information for fold_2024_05_08_20_40_model_3.cif #4
---
Chain | Description
A B | .
C | .
D | .
E | .
F | .
G | .
H I | .
> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_4.cif
Chain information for fold_2024_05_08_20_40_model_4.cif #5
---
Chain | Description
A B | .
C | .
D | .
E | .
F | .
G | .
H I | .
> preset custom pretty-chain
Using preset: Custom / Pretty-chain
Preset expands to these ChimeraX commands:
lighting soft
set bgColor white
cartoon style coil width 1.5 thickness 0.8
cartoon style helix xsection round width 3 thickness 0.8
cartoon style strand xsection round width 3 thickness 0.8
cartoon style strand arrowscale 1
cartoon style helix xsection oval sides 10
graphics silhouettes true
graphics silhouettes width 1.5
graphics silhouettes depthJump 0.003
lighting msDepthBias 0.004
lighting shadows true intensity 0.06
lighting depthCueColor #000000
color bychain
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #1 atoms
> show #1 cartoons
> show #2 models
> hide #1 models
> show #3 models
> show #4 models
> show #5 models
> hide #2-5 atoms
> show #2-5 cartoons
> hide #5 models
> hide #4 models
> hide #3 models
> select #2/A
1885 atoms, 1936 bonds, 232 residues, 1 model selected
> select #2/A/B
3770 atoms, 3872 bonds, 464 residues, 1 model selected
> show #3 models
> show #4 models
> hide #4 models
> show #5 models
> show #4 models
> show #1 models
> select /A/B
18850 atoms, 19360 bonds, 2320 residues, 5 models selected
> color sel orange red
> select clear
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> select /C
7040 atoms, 7175 bonds, 910 residues, 5 models selected
> select /C/D/E
45710 atoms, 46760 bonds, 5820 residues, 5 models selected
> select /C/D/E/F
52930 atoms, 54095 bonds, 6770 residues, 5 models selected
> select /C/D/E/F/G
68885 atoms, 70335 bonds, 8780 residues, 5 models selected
> select /C/D/E/F
52930 atoms, 54095 bonds, 6770 residues, 5 models selected
> color (#1 & sel) cornflower blue
> show #2 models
> select clear
> show #3 models
> show #4 models
> show #5 models
> select /C/D/E/F
52930 atoms, 54095 bonds, 6770 residues, 5 models selected
> color sel cornflower blue
> select clear
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> select /G/H
26335 atoms, 26735 bonds, 3310 residues, 5 models selected
> select /G
15955 atoms, 16240 bonds, 2010 residues, 5 models selected
> select /h
10380 atoms, 10495 bonds, 1300 residues, 5 models selected
> show #2 models
> show #3 models
> hide #3 models
> show #4 models
> show #3 models
> show #5 models
> select /G
15955 atoms, 16240 bonds, 2010 residues, 5 models selected
> color sel cyan
> select /H/I
20760 atoms, 20990 bonds, 2600 residues, 5 models selected
> color sel hot pink
> color sel yellow
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> select clear
> show #2 models
> hide #1 models
> show #3 models
> hide #2 models
> show #4 models
> hide #3 models
> show #5 models
> hide #4 models
> save /Users/chaaban/Downloads/fold_2024_05_08_20_40/chimerax.cxs
===== 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 (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 M2 Max
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: Mac
Model Identifier: Mac14,5
Model Number: Z17J0018AB/A
Chip: Unknown
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 64 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3.1 (23D60)
Kernel Version: Darwin 23.3.0
Time since boot: 36 days, 10 hours, 8 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL P2717H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
DELL P2722H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
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-Clipper: 0.22.3
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-ISOLDE: 1.7
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 , 18 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 , 18 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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