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Opened 12 months ago
Closed 12 months ago
#16336 closed defect (can't reproduce)
Crash closing models
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.8.0-48-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x000078ef8e837e00 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1507 in delete
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 134 in delete
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/models.py", line 1010 in close
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/std_commands/close.py", line 43 in close
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/model_panel/tool.py", line 517 in close
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/model_panel/tool.py", line 92 in
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, psutil._psutil_linux, psutil._psutil_posix, chimerax.atom_search.ast (total: 55)
===== Log before crash start =====
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 244788 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
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
> open
> /home/zahra/Documents/80SPRO_MT/To_send_to_Andrei/60s/open/3941-4073.pdb
Chain information for 3941-4073.pdb #2
---
Chain | Description
A5 | No description available
> open
> /media/zahra/For_paper/RRL_MERGE_60S/4CLASS-3D/1xbin/RRL_50_+-mRNA_merged60s_refined_100_r4.mrc
> /media/zahra/For_paper/RRL_MERGE_60S/4CLASS-3D/1xbin/RRL_50_+-mRNA_merged60s_refined_100_r4_2.9A_B-50.mrc
> /media/zahra/For_paper/RRL_MERGE_60S/4CLASS-3D/1xbin/RRL_50_+-mRNA_merged60s_refined_100_r4_2.9A_B-70.mrc
Opened RRL_50_+-mRNA_merged60s_refined_100_r4.mrc as #3.1, grid size
800,800,800, pixel 0.83, shown at step 1, values float32
Opened RRL_50_+-mRNA_merged60s_refined_100_r4_2.9A_B-50.mrc as #3.2, grid size
800,800,800, pixel 0.83, shown at step 1, values float32
Opened RRL_50_+-mRNA_merged60s_refined_100_r4_2.9A_B-70.mrc as #3.3, grid size
800,800,800, pixel 0.83, shown at step 1, values float32
> volume #3.1 region 0,0,0,799,799,799 step 4
> volume #3.2 region 0,0,0,799,799,799 step 4
> volume #3.3 region 0,0,0,799,799,799 step 4
> transparency #3.1.2 50
> select add #2
2102 atoms, 2300 bonds, 133 residues, 1 model selected
> ui tool show "Fit in Map"
> fitmap #2 inMap #3.1
Fit molecule 3941-4073.pdb (#2) to map
RRL_50_+-mRNA_merged60s_refined_100_r4.mrc (#3.1) using 2102 atoms
average map value = 7.978, steps = 348
shifted from previous position = 29.8
rotated from previous position = 37.5 degrees
atoms outside contour = 585, contour level = 5.7816
Position of 3941-4073.pdb (#2) relative to
RRL_50_+-mRNA_merged60s_refined_100_r4.mrc (#3.1) coordinates:
Matrix rotation and translation
0.85682828 -0.08343678 0.50880605 -103.86684388
-0.10716478 0.93645074 0.33402953 -61.79641376
-0.50434215 -0.34073203 0.79343599 318.22377730
Axis -0.55421348 0.83214638 -0.01948893
Axis point 490.76895973 0.00000000 342.30123407
Rotation angle (degrees) 37.49960778
Shift along axis -0.06109699
> open
> /home/zahra/Documents/80SPRO_MT/To_send_to_Andrei/60s/open/60S_13Nov_vr1.pdb
60S_13Nov_vr1.pdb title:
Alphafold monomer V2.0 prediction for elongation factor 2 (P13639) [more
info...]
Chain information for 60S_13Nov_vr1.pdb #4
---
Chain | Description | UniProt
A | elongation factor 2 | EF2_HUMAN 1-858
A2 | No description available |
A3 | No description available |
A5 | No description available |
E | No description available |
II | No description available |
L5 | No description available |
L6 | No description available |
L7 | No description available |
L8 | No description available |
L9 | No description available |
LA | No description available |
LB | No description available |
LC | No description available |
LD | No description available |
LE | No description available |
LF | No description available |
LG | No description available |
LH | No description available |
LJ | No description available |
LK | No description available |
La | No description available |
Lb | No description available |
Lc | No description available |
Ld | No description available |
Le | No description available |
Lf | No description available |
Lg | No description available |
Lh | No description available |
Lj | No description available |
Lk | No description available |
Ll | No description available |
Ln | No description available |
Lo | No description available |
Lp | No description available |
Lq | No description available |
Lr | No description available |
Ls | No description available |
Lt | No description available |
Lu | No description available |
Lv | No description available |
Lw | No description available |
Lx | No description available |
Ly | No description available |
Z | No description available |
s | No description available |
t | No description available |
Non-standard residues in 60S_13Nov_vr1.pdb #4
---
GDP — (GDP)
> hide #!4 models
> hide #!3.1 models
> select #1/A2:4074
31 atoms, 32 bonds, 1 residue, 1 model selected
> hide #2 models
> select #1/A2:4073
33 atoms, 35 bonds, 1 residue, 1 model selected
> select #1/A2:4074
31 atoms, 32 bonds, 1 residue, 1 model selected
> select add #1/A2:4073
64 atoms, 67 bonds, 2 residues, 1 model selected
> select add #1/A2:4072
95 atoms, 99 bonds, 3 residues, 1 model selected
> select add #1/A2:4071
125 atoms, 130 bonds, 4 residues, 1 model selected
> show #2 models
> hide #2 models
> select add #1/A2:4070
155 atoms, 161 bonds, 5 residues, 1 model selected
> select add #1/A2:4069
185 atoms, 192 bonds, 6 residues, 1 model selected
> select add #1/A2:4068
215 atoms, 223 bonds, 7 residues, 1 model selected
> select add #1/A2:4067
245 atoms, 254 bonds, 8 residues, 1 model selected
Drag select of 3 residues, 2 shapes
> show #2 models
> hide #2 models
> select clear
> select add #1/A2:4070
42 atoms, 31 bonds, 3 residues, 1 model selected
> select add #1/A2:4069
72 atoms, 62 bonds, 4 residues, 1 model selected
> select add #1/A2:4068
102 atoms, 93 bonds, 5 residues, 1 model selected
> select add #1/A2:4067
132 atoms, 124 bonds, 6 residues, 1 model selected
> color sel red
> select add #1/A2:4066
162 atoms, 155 bonds, 7 residues, 1 model selected
> select add #1/A2:4064
209 atoms, 187 bonds, 9 residues, 1 model selected
> select add #1/A2:4063
239 atoms, 218 bonds, 10 residues, 1 model selected
> select add #1/A2:4062
272 atoms, 253 bonds, 11 residues, 1 model selected
> select add #1/A2:4061
306 atoms, 289 bonds, 12 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #2 models
> hide #2 models
> select add #1/A2:4072
23 atoms, 21 bonds, 1 residue, 1 model selected
> select add #1/A2:4071
44 atoms, 40 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #2 models
> hide #2 models
> select add #1/A2:3941
34 atoms, 36 bonds, 1 residue, 1 model selected
> select add #1/A2:3942
67 atoms, 71 bonds, 2 residues, 1 model selected
> select add #1/A2:3943
100 atoms, 106 bonds, 3 residues, 1 model selected
> select add #1/A2:3944
134 atoms, 142 bonds, 4 residues, 1 model selected
> select add #1/A2:3945
167 atoms, 177 bonds, 5 residues, 1 model selected
> select add #1/A2:3946
201 atoms, 213 bonds, 6 residues, 1 model selected
> select add #1/A2:3947
234 atoms, 248 bonds, 7 residues, 1 model selected
> select add #1/A2:3948
265 atoms, 280 bonds, 8 residues, 1 model selected
> select add #1/A2:3949
298 atoms, 315 bonds, 9 residues, 1 model selected
> select add #1/A2:3950
328 atoms, 346 bonds, 10 residues, 1 model selected
> select add #1/A2:3952
361 atoms, 381 bonds, 11 residues, 1 model selected
> select add #1/A2:3951
395 atoms, 417 bonds, 12 residues, 1 model selected
> select add #1/A2:3953
429 atoms, 453 bonds, 13 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #2 models
> select #1/A2:4060
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #1/A2:4059
31 atoms, 32 bonds, 1 residue, 1 model selected
> select add #1/A2:4060
61 atoms, 63 bonds, 2 residues, 1 model selected
> select add #1/A2:4058
91 atoms, 94 bonds, 3 residues, 1 model selected
> select add #1/A2:4057
122 atoms, 126 bonds, 4 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #2 models
> delete atoms sel
> delete bonds sel
> show #2 models
> show #!3.1 models
> select add #2
2102 atoms, 2300 bonds, 133 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.79014,-0.19034,0.58262,-77.024,0.048996,0.96713,0.2495,-79.077,-0.61096,-0.1686,0.7735,289.96
> view matrix models
> #2,0.80249,-0.16923,0.57216,-83.438,0.029911,0.96914,0.24469,-74.135,-0.59591,-0.17925,0.78279,287.36
> ui mousemode right "move picked models"
> view matrix models
> #2,0.80249,-0.16923,0.57216,-84.079,0.029911,0.96914,0.24469,-76.095,-0.59591,-0.17925,0.78279,285.46
> volume #3.1 step 1
> lighting soft
> combine #1#2
Remapping chain ID 'A5' in 3941-4073.pdb #2 to 'A6'
> bond #5/A2:3940@O3'#5/A5:3941@P reasonable false
Must specify two or more atoms
> hide #!3.1 models
> hide #2 models
> hide #!1 models
> bond #5/A2:3940@O3'#5/A6:3941@P reasonable false
Created 1 bond
> bond #5/A2:4073@O3'#5/A2:4074@P reasonable false
Created 2 bonds
> select #5@@serial_number=94668
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #5@@serial_number=94669
1 atom, 1 residue, 1 model selected
> select add #5@@serial_number=94668
2 atoms, 1 residue, 1 model selected
> select add #5@@serial_number=94670
3 atoms, 1 residue, 1 model selected
> select add #5@@serial_number=94688
4 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #5/A2:4073
55 atoms, 60 bonds, 2 residues, 1 model selected
> select #5/A2:4073
55 atoms, 60 bonds, 2 residues, 1 model selected
> select add #5
246007 atoms, 257250 bonds, 22 pseudobonds, 12001 residues, 2 models selected
> select subtract #5
Nothing selected
> select #5/A2:4073
55 atoms, 60 bonds, 2 residues, 1 model selected
> select #5/A2:4073
55 atoms, 60 bonds, 2 residues, 1 model selected
> select #5/A2:4073
55 atoms, 60 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!1 models
> select #1/A2:4073
33 atoms, 35 bonds, 1 residue, 1 model selected
> save /home/zahra/Documents/80SPRO_MT/To_send_to_Andrei/60s/open/rrr.pdb
> models #1 selectedOnly true relModel #3.1
> hide #!1 models
> open /home/zahra/Documents/80SPRO_MT/To_send_to_Andrei/60s/open/rrr.pdb
Summary of feedback from opening
/home/zahra/Documents/80SPRO_MT/To_send_to_Andrei/60s/open/rrr.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU A 14 ALA A 38 1 25
Start residue of secondary structure not found: HELIX 2 2 SER A 44 ILE A 63 1
20
Start residue of secondary structure not found: HELIX 3 3 THR A 136 VAL A 157
1 22
Start residue of secondary structure not found: HELIX 4 4 GLN A 162 PHE A 177
1 16
Start residue of secondary structure not found: HELIX 5 5 THR A 206 ASP A 212
1 7
606 messages similar to the above omitted
rrr.pdb title:
Alphafold monomer V2.0 prediction for ribosomal protein (G1SKZ8) [more
info...]
Non-standard residues in rrr.pdb #6
---
A — (A)
> combine #5 #6
Remapping chain ID 'A2' in rrr.pdb #6 to 'A4'
> hide #6 models
> hide #!5 models
> bond #7/A2:4072@O3'#7/A4:4073@P reasonable false
Created 1 bond
> undo
> hide #!5 models
> hide #!7 models
> show #!7 models
> show #!1 models
> hide #!7 models
> show #2 models
> delete atoms sel
> delete bonds sel
> close #6#5,7
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 60S_13Nov_vr2.pdb
60S_13Nov_vr2.pdb title:
Alphafold monomer V2.0 prediction for ribosomal protein (G1SKZ8) [more
info...]
Chain information for 60S_13Nov_vr2.pdb #1
---
Chain | Description | UniProt
A | ribosomal protein | G1SKZ8_RABIT 1-217
A2 | No description available |
A3 | No description available |
A5 | No description available |
B | No description available |
C | No description available |
D | No description available |
E | No description available |
II | No description available |
L5 | No description available |
L6 | No description available |
L7 | No description available |
L8 | No description available |
L9 | No description available |
LA | No description available |
LB | No description available |
LC | No description available |
LD | No description available |
LE | No description available |
LF | No description available |
LG | No description available |
LH | No description available |
LJ | No description available |
LK | No description available |
La | No description available |
Lb | No description available |
Lc | No description available |
Ld | No description available |
Le | No description available |
Lf | No description available |
Lg | No description available |
Lh | No description available |
Lj | No description available |
Lk | No description available |
Ll | No description available |
Ln | No description available |
Lo | No description available |
Lp | No description available |
Lq | No description available |
Lr | No description available |
Ls | No description available |
Lt | No description available |
Lu | No description available |
Lv | No description available |
Lw | No description available |
Lx | No description available |
Ly | No description available |
Z | No description available |
s | No description available |
t | No description available |
Non-standard residues in 60S_13Nov_vr2.pdb #1
---
GDP — (GDP)
OpenGL version: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA RTX A6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Supermicro
Model: X11DAi-N
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 112 Intel(R) Xeon(R) Gold 6258R CPU @ 2.70GHz
Cache Size: 39424 KB
Memory:
total used free shared buff/cache available
Mem: 187Gi 44Gi 80Gi 478Mi 63Gi 141Gi
Swap: 31Gi 16Gi 15Gi
Graphics:
04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)
DeviceName: Aspeed Video 2500
Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
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: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
distro: 1.9.0
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
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: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 12 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash closing models |
comment:2 by , 12 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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