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Opened 2 years ago
Closed 2 years ago
#9839 closed defect (can't reproduce)
Crash in garbage collection during new object allocation
| 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-13.4-arm64-arm-64bit
ChimeraX Version: 1.7.dev202309190305 (2023-09-19 03:05:58 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000002c21cb000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f8b01e00 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 150 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 150 in __iter__
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 945 in _atomspec_attr_filter
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 992 in _atomspec_filter_atom
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 910 in atomspec_filter
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 568 in _filter_parts
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 550 in find_selected_parts
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 561 in find_selected_parts
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 561 in find_selected_parts
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 626 in _add_model_parts
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 606 in find_matches
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 444 in find_matches
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 993 in find_matches
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 990 in evaluate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1080 in evaluate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1100 in evaluate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 1298 in parse
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 890 in parse
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2488 in _parse_arg
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2629 in _process_positional_arguments
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2853 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 38 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/preset_mgr/manager.py", line 88 in execute
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/preset_mgr/builtin.py", line 49 in run_preset
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/preset_mgr/__init__.py", line 44 in run_provider
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1291 in run_provider
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 386 in run_provider
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/preset_mgr/manager.py", line 60 in cb
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/preset_mgr/cmd.py", line 71 in run_preset
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/preset_mgr/cmd.py", line 50 in preset_cmd
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 38 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1215 in
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 912 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1063 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, chimerax.surface._surface, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.dssp._dssp (total: 51)
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"procLaunch" : "2023-09-25 10:29:11.8711 +0200",
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"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"logWritingSignature" : "cd89f35198f4feed87ecb9f90a3d43bd114604d2",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "639124e81d92412bfb4880b3",
"factorPackIds" : {
},
"deploymentId" : 240000012
},
{
"rolloutId" : "60f8ddccefea4203d95cbeef",
"factorPackIds" : {
"NETWORK_SERVICE_PROXY_CONFIG_UPDATE" : "6401414cc679dd6bc5828183"
},
"deploymentId" : 240000025
}
],
"experiments" : [
{
"treatmentId" : "3a3cf641-8471-4e4e-9ad4-81d0ede970fd",
"experimentId" : "64a84dae90d82611a0bd7d3d",
"deploymentId" : 400000010
},
{
"treatmentId" : "6dd670af-0633-45e4-ae5f-122ae4df02be",
"experimentId" : "64406ba83deb637ac8a04419",
"deploymentId" : 900000017
}
]
}
}
===== Log before crash start =====
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> mousemode rightMode clip
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode surface cap false; surface style solid; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; transparency 70; cofr centerofview; clip near -10 far 10
> position cofr; color ##~num_residues cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr;
> color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias helix setattr $1 res is_helix true
> alias strand setattr $1 res is_strand true
> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false
> buttonpanel Shortcuts rows 3 columns 4
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #10000 position cofr"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
UCSF ChimeraX version: 1.7.dev202309190305 (2023-09-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/alexandre/Documents/Novalix/TGR5-Krios-
> Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb
Summary of feedback from opening
/Users/alexandre/Documents/Novalix/TGR5-Krios-
Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb
---
warnings | Start residue of secondary structure not found: HELIX 24 24 PHE N
52 ASN N 54 1 3
Start residue of secondary structure not found: HELIX 25 25 GLY N 85 VAL N 87
1 3
Start residue of secondary structure not found: HELIX 26 26 ASN N 97 LYS N 99
1 3
Start residue of secondary structure not found: HELIX 27 27 PRO N 111 ASP N
113 1 3
Start residue of secondary structure not found: SHEET 35 3535 GLN N 26 SER N
30 0
8 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (45 )
Cannot find LINK/SSBOND residue CYS (122 )
Chain information for TGR5-WithFlexDomaine-210623_refined-mod.pdb #1
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
R | No description available
> windowsize 800 800
> set bgColor white
> view matrix camera
> -0.80318,0.34259,-0.48736,-15.845,0.50974,-0.028167,-0.85987,-104.25,-0.30831,-0.93906,-0.15201,73.245
> style stick
Changed 8939 atom styles
> hide atoms
> show cartoons
> color #1 #E7E6E6
> graphics silhouettes true
> color
> #1/R:41-57,75-86,97-99,106-111,128-130,138-141,199-214,233-235,246-249,287-302
> #00B050
> color
> #1/R:266-286,277-286,267-286,269-286,237-245,266-273,274-286,272-286,224-231,66-74
> #FF0000
> color
> #1/R:88-96,87-96,69-74,66-71,88-94,190-198,89-96,159-167,225-232,188-198,155-156,224-232,156-166,64-71,63-71,156-167,64-74,
> 35-40,184-189,155-167,168-173,168-174,112-125,218-223,112-127,175-183,225-231
> #ED7D31
> color
> #1/R:170-174,215-223,176-184,172-183,176-183,170-175,59-68,142-154,280-286,100-104,131-137,142-155,113-125,172-182,237-242,249-262,114-127
> #FFC000
> dssp
> select /A:328
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
172 atoms, 175 bonds, 20 residues, 1 model selected
> select up
1092 atoms, 1118 bonds, 131 residues, 1 model selected
> color #1/A:38-54,39-51,269-275,271-275,276-281 #FF0000
> color #1/A:101-108,168-176,229-239,233-239,238-251,240-245,345-352 #ED7D31
> slect /A
Unknown command: slect /A
> select /A
2756 atoms, 2812 bonds, 3 pseudobonds, 337 residues, 2 models selected
> select /A:11
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:12
5 atoms, 4 bonds, 1 residue, 1 model selected
> color #1/A:68-79,181-190 #FFC000
> color #1/G:29-37 FFC000
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/G:29-37 #FFC000
> color #1 #E7E6E6
> graphics silhouettes true
> color
> #1/R:41-57,75-86,97-99,106-111,128-130,138-141,199-214,233-235,246-249,287-302
> #00B050
> color
> #1/R:266-286,277-286,267-286,269-286,237-245,266-273,274-286,272-286,224-231,66-74
> #FF0000
> color
> #1/R:88-96,87-96,69-74,66-71,88-94,190-198,89-96,159-167,225-232,188-198,155-156,224-232,156-166,64-71,63-71,156-167,64-74,
> 35-40,184-189,155-167,168-173,168-174,112-125,218-223,112-127,175-183,225-231
> #ED7D31
> color #1/A:358-370 #ED7D31
> color
> #1/R:88-96,87-96,69-74,66-71,88-94,190-198,89-96,159-167,225-232,188-198,155-156,224-232,156-166,64-71,63-71,156-167,64-74,
> 35-40,184-189,155-167,168-173,168-174,112-125,218-223,112-127,175-183,225-231
> #ED7D31
> color #1/A:19-25,202-216,358-372 #ED7D31
> color
> #1/R:170-174,215-223,176-184,172-183,176-183,170-175,59-68,142-154,280-286,100-104,131-137,142-155,113-125,172-182,237-242,249-262,114-127
> #FFC000
> color #1/A:11-36,19-30,191-197,252-258 #FFC000
> color #1/G: #FFC000
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/B:114-121 #FFC000
> color #1/N:109-125 #FF0000
> color #1/A:19-25,202-216,358-372 #ED7D31
> color #1/N:96-106,95-107,107-115,115-125 #ED7D31
> color #1/B:114-121 #FFC000
> color #1/N:22-34,51-65,109-115,109-134 #FFC000
> color #1/A:1-10 #00B050
> color
> #1/R:41-57,75-86,97-99,106-111,128-130,138-141,199-214,233-235,246-249,287-302
> #00B050
> color #1/A:1-10,159-160,319-321,340-344 #00B050
> select /B
2603 atoms, 2650 bonds, 340 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> close session
> open /Users/alexandre/Documents/Novalix/TGR5-Krios-
> Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb
Summary of feedback from opening
/Users/alexandre/Documents/Novalix/TGR5-Krios-
Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb
---
warnings | Start residue of secondary structure not found: HELIX 18 18 SER B
12 ALA B 34 1 23
Start residue of secondary structure not found: HELIX 19 19 LEU B 40 GLN B 42
1 3
End residue of secondary structure not found: HELIX 20 20 ILE B 43 ASN B 45 1
3
Start residue of secondary structure not found: HELIX 21 21 THR B 138 GLU B
140 1 3
Start residue of secondary structure not found: HELIX 24 24 PHE N 52 ASN N 54
1 3
Start residue of secondary structure not found: HELIX 25 25 GLY N 85 VAL N 87
1 3
Start residue of secondary structure not found: HELIX 26 26 ASN N 97 LYS N 99
1 3
1 messages similar to the above omitted
Start residue of secondary structure not found: SHEET 7 7 7 ARG B 56 ARG B 62
0
Start residue of secondary structure not found: SHEET 8 8 8 ILE B 68 TRP B 73
0
Start residue of secondary structure not found: SHEET 10 1010 LYS B 88 ASP B
93 0
Start residue of secondary structure not found: SHEET 11 1111 ASN B 98 PRO B
104 0
Start residue of secondary structure not found: SHEET 12 1212 VAL B 110 TYR B
115 0
18 messages similar to the above omitted
End residue of secondary structure not found: SHEET 31 3131 ARG B 314 ALA B
319 0
Start residue of secondary structure not found: SHEET 32 3232 VAL B 325 VAL B
330 0
Start residue of secondary structure not found: SHEET 33 3333 VAL B 337 SER B
341 0
Start residue of secondary structure not found: SHEET 34 3434 PHE B 345 ASN B
350 0
Start residue of secondary structure not found: SHEET 35 3535 GLN N 26 SER N
30 0
Start residue of secondary structure not found: SHEET 36 3636 LEU N 41 SER N
48 0
7 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (45 )
Cannot find LINK/SSBOND residue CYS (122 )
Chain information for TGR5-WithFlexDomaine-210623_refined-mod.pdb #1
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
R | No description available
> windowsize 800 800
> set bgColor white
> view matrix camera
> -0.80318,0.34259,-0.48736,-15.845,0.50974,-0.028167,-0.85987,-104.25,-0.30831,-0.93906,-0.15201,73.245
> style stick
Changed 8939 atom styles
> hide atoms
> show cartoons
> color #1 #E7E6E6
> graphics silhouettes true
> color
> #1/R:41-57,75-86,97-99,106-111,128-130,138-141,199-214,233-235,246-249,287-302
> #00B050
> color #1/A:1-10,159-160,319-321,340-344 #00B050
> color
> #1/R:266-286,277-286,267-286,269-286,237-245,266-273,274-286,272-286,224-231,66-74
> #FF0000
> color #1/A:358-370 #FF0000
> color #1/N:109-125 #FF0000
> color
> #1/R:88-96,87-96,69-74,66-71,88-94,190-198,89-96,159-167,225-232,188-198,155-156,224-232,156-166,64-71,63-71,156-167,64-74,
> 35-40,184-189,155-167,168-173,168-174,112-125,218-223,112-127,175-183,225-231
> #ED7D31
> color #1/A:19-25,202-216,358-372 #ED7D31
> color #1/N:96-106,95-107,107-115,115-125 #ED7D31
> color
> #1/R:170-174,215-223,176-184,172-183,176-183,170-175,59-68,142-154,280-286,100-104,131-137,142-155,113-125,172-182,237-242,249-262,114-127
> #FFC000
> color #1/A:11-36,19-30,191-197,252-258 #FFC000
> color #1/B:114-121 #FFC000
> color #1/N:22-34,51-65,109-115,109-134 #FFC000
> dssp
> color #1/B:114-121 #FFC000
> color
> #1/R:266-286,277-286,267-286,269-286,237-245,266-273,274-286,272-286,224-231,66-74
> #FF0000
> color #1/A:358-370 #FF0000
> color #1/N:109-125 #FF0000
> color #1/A:1-10,159-160,319-321,340-344 #00B050
> color #1/B:1-4,169-172,253-255 #00B050
> color #1/G:1-2,40, #00B050
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/G:1-2,40 #00B050
> ui tool show "Show Sequence Viewer"
> sequence chain /N
Alignment identifier is 1/N
> color #1/N:66-67 #00B050
> open /Users/alexandre/Documents/Novalix/TGR5-Krios-
> Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb
Summary of feedback from opening
/Users/alexandre/Documents/Novalix/TGR5-Krios-
Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb
---
warnings | Start residue of secondary structure not found: HELIX 18 18 SER B
12 ALA B 34 1 23
Start residue of secondary structure not found: HELIX 19 19 LEU B 40 GLN B 42
1 3
End residue of secondary structure not found: HELIX 20 20 ILE B 43 ASN B 45 1
3
Start residue of secondary structure not found: HELIX 21 21 THR B 138 GLU B
140 1 3
Start residue of secondary structure not found: HELIX 24 24 PHE N 52 ASN N 54
1 3
Start residue of secondary structure not found: HELIX 25 25 GLY N 85 VAL N 87
1 3
Start residue of secondary structure not found: HELIX 26 26 ASN N 97 LYS N 99
1 3
1 messages similar to the above omitted
Start residue of secondary structure not found: SHEET 7 7 7 ARG B 56 ARG B 62
0
Start residue of secondary structure not found: SHEET 8 8 8 ILE B 68 TRP B 73
0
Start residue of secondary structure not found: SHEET 10 1010 LYS B 88 ASP B
93 0
Start residue of secondary structure not found: SHEET 11 1111 ASN B 98 PRO B
104 0
Start residue of secondary structure not found: SHEET 12 1212 VAL B 110 TYR B
115 0
18 messages similar to the above omitted
End residue of secondary structure not found: SHEET 31 3131 ARG B 314 ALA B
319 0
Start residue of secondary structure not found: SHEET 32 3232 VAL B 325 VAL B
330 0
Start residue of secondary structure not found: SHEET 33 3333 VAL B 337 SER B
341 0
Start residue of secondary structure not found: SHEET 34 3434 PHE B 345 ASN B
350 0
Start residue of secondary structure not found: SHEET 35 3535 GLN N 26 SER N
30 0
Start residue of secondary structure not found: SHEET 36 3636 LEU N 41 SER N
48 0
7 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (45 )
Cannot find LINK/SSBOND residue CYS (122 )
Chain information for TGR5-WithFlexDomaine-210623_refined-mod.pdb #2
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
R | No description available
> windowsize 800 800
> set bgColor white
> view matrix camera
> -0.80318,0.34259,-0.48736,-15.845,0.50974,-0.028167,-0.85987,-104.25,-0.30831,-0.93906,-0.15201,73.245
> style stick
Changed 17878 atom styles
> hide atoms
> show cartoons
> color #1 #E7E6E6
> graphics silhouettes true
> color
> #1/R:41-57,75-86,97-99,106-111,128-130,138-141,199-214,233-235,246-249,287-302
> #00B050
> color #1/A:1-10,159-160,319-321,340-344 #00B050
> color #1/B:1-4,169-172,253-255 #00B050
> color #1/G:1-2,40, #00B050
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/N:66-67 #00B050
> color
> #1/R:266-286,277-286,267-286,269-286,237-245,266-273,274-286,272-286,224-231,66-74
> #FF0000
> color #1/A:358-370 #FF0000
> color #1/N:109-125 #FF0000
> color
> #1/R:88-96,87-96,69-74,66-71,88-94,190-198,89-96,159-167,225-232,188-198,155-156,224-232,156-166,64-71,63-71,156-167,64-74,
> 35-40,184-189,155-167,168-173,168-174,112-125,218-223,112-127,175-183,225-231
> #ED7D31
> color #1/A:19-25,202-216,358-372 #ED7D31
> color #1/N:96-106,95-107,107-115,115-125 #ED7D31
> color
> #1/R:170-174,215-223,176-184,172-183,176-183,170-175,59-68,142-154,280-286,100-104,131-137,142-155,113-125,172-182,237-242,249-262,114-127
> #FFC000
> color #1/A:11-36,19-30,191-197,252-258 #FFC000
> color #1/B:114-121 #FFC000
> color #1/N:22-34,51-65,109-115,109-134 #FFC000
> close session
> open /Users/alexandre/Documents/Novalix/TGR5-Krios-
> Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb
Summary of feedback from opening
/Users/alexandre/Documents/Novalix/TGR5-Krios-
Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb
---
warnings | Start residue of secondary structure not found: HELIX 18 18 SER B
12 ALA B 34 1 23
Start residue of secondary structure not found: HELIX 19 19 LEU B 40 GLN B 42
1 3
End residue of secondary structure not found: HELIX 20 20 ILE B 43 ASN B 45 1
3
Start residue of secondary structure not found: HELIX 21 21 THR B 138 GLU B
140 1 3
Start residue of secondary structure not found: HELIX 24 24 PHE N 52 ASN N 54
1 3
Start residue of secondary structure not found: HELIX 25 25 GLY N 85 VAL N 87
1 3
Start residue of secondary structure not found: HELIX 26 26 ASN N 97 LYS N 99
1 3
1 messages similar to the above omitted
Start residue of secondary structure not found: SHEET 7 7 7 ARG B 56 ARG B 62
0
Start residue of secondary structure not found: SHEET 8 8 8 ILE B 68 TRP B 73
0
Start residue of secondary structure not found: SHEET 10 1010 LYS B 88 ASP B
93 0
Start residue of secondary structure not found: SHEET 11 1111 ASN B 98 PRO B
104 0
Start residue of secondary structure not found: SHEET 12 1212 VAL B 110 TYR B
115 0
18 messages similar to the above omitted
End residue of secondary structure not found: SHEET 31 3131 ARG B 314 ALA B
319 0
Start residue of secondary structure not found: SHEET 32 3232 VAL B 325 VAL B
330 0
Start residue of secondary structure not found: SHEET 33 3333 VAL B 337 SER B
341 0
Start residue of secondary structure not found: SHEET 34 3434 PHE B 345 ASN B
350 0
Start residue of secondary structure not found: SHEET 35 3535 GLN N 26 SER N
30 0
Start residue of secondary structure not found: SHEET 36 3636 LEU N 41 SER N
48 0
7 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (45 )
Cannot find LINK/SSBOND residue CYS (122 )
Chain information for TGR5-WithFlexDomaine-210623_refined-mod.pdb #1
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
R | No description available
> windowsize 800 800
> set bgColor white
> view matrix camera
> -0.80318,0.34259,-0.48736,-15.845,0.50974,-0.028167,-0.85987,-104.25,-0.30831,-0.93906,-0.15201,73.245
> style stick
Changed 8939 atom styles
> hide atoms
> show cartoons
> color #1 #E7E6E6
> graphics silhouettes true
> color
> #1/R:41-57,75-86,97-99,106-111,128-130,138-141,199-214,233-235,246-249,287-302
> #00B050
> color #1/A:1-10,159-160,319-321,340-344 #00B050
> color #1/B:1-4,169-172,253-255 #00B050
> color #1/G:1-2,40, #00B050
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/N:66-67 #00B050
> color
> #1/R:266-286,277-286,267-286,269-286,237-245,266-273,274-286,272-286,224-231,66-74
> #FF0000
> color #1/A:358-370 #FF0000
> color #1/N:109-125 #FF0000
> color
> #1/R:88-96,87-96,69-74,66-71,88-94,190-198,89-96,159-167,225-232,188-198,155-156,224-232,156-166,64-71,63-71,156-167,64-74,
> 35-40,184-189,155-167,168-173,168-174,112-125,218-223,112-127,175-183,225-231
> #ED7D31
> color #1/A:19-25,202-216,358-372 #ED7D31
> color #1/N:96-106,95-107,107-115,115-125 #ED7D31
> color
> #1/R:170-174,215-223,176-184,172-183,176-183,170-175,59-68,142-154,280-286,100-104,131-137,142-155,113-125,172-182,237-242,249-262,114-127
> #FFC000
> color #1/A:11-36,19-30,191-197,252-258 #FFC000
> color #1/B:114-121 #FFC000
> color #1/N:22-34,51-65,109-115,109-134 #FFC000
> dssp
> color #1/A:1-10,159-160,319-321,340-344,372-387 #00B050
> select /B
2603 atoms, 2650 bonds, 340 residues, 1 model selected
> select /B:340
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /N:134
Nothing selected
> show surfaces
> color #1/R #177792 surfaces
> color #1/A #c0cc0e surfaces
> color #1/N #02abd1 surfaces
> color #1/B #79ae2b surfaces
> color #1/G #ebdf00 surfaces
> transparency #1 85 surfaces
> transparency #1 90 surfaces
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> color #1/R blue surfaces
> color #1/A Crim s
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/A crimson surfaces
> color #1/N plum surfaces
> color #1/G violet surfaces
> color #1/G purple surfaces
> color #1/B brown surfaces
> color #1/B sadlebrown s
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/B sadle s
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/B sandybrown surfaces
> transparency #1 90 surfaces
> transparency #1 95 surfaces
> view matrix camera
> -0.30054,0.20526,0.93142,199.65,-0.95274,-0.10985,-0.28321,92.179,0.044186,-0.97252,0.22857,128.79
> view matrix camera
> -0.80318,0.34259,-0.48736,-15.845,0.50974,-0.028167,-0.85987,-104.25,-0.30831,-0.93906,-0.15201,73.245
> lighting full
> lighting soft
> lighting simple
> windowsize 800 800
> set bgColor white
> view matrix camera
> -0.80318,0.34259,-0.48736,-15.845,0.50974,-0.028167,-0.85987,-104.25,-0.30831,-0.93906,-0.15201,73.245
> style stick
Changed 8939 atom styles
> hide atoms
> show cartoons
> color #1 #E7E6E6
> graphics silhouettes true
> color
> #1/R:41-57,75-86,97-99,106-111,128-130,138-141,199-214,233-235,246-249,287-302
> #00B050
> color #1/A:1-10,159-160,319-321,340-344,372-387 #00B050
> color #1/B:1-4,169-172,253-255 #00B050
> color #1/G:1-2,40, #00B050
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/N:66-67 #00B050
> color
> #1/R:266-286,277-286,267-286,269-286,237-245,266-273,274-286,272-286,224-231,66-74
> #FF0000
> color #1/A:358-370 #FF0000
> color #1/N:109-125 #FF0000
> color
> #1/R:88-96,87-96,69-74,66-71,88-94,190-198,89-96,159-167,225-232,188-198,155-156,224-232,156-166,64-71,63-71,156-167,64-74,
> 35-40,184-189,155-167,168-173,168-174,112-125,218-223,112-127,175-183,225-231
> #ED7D31
> color #1/A:19-25,202-216,358-372 #ED7D31
> color #1/N:96-106,95-107,107-115,115-125 #ED7D31
> color
> #1/R:170-174,215-223,176-184,172-183,176-183,170-175,59-68,142-154,280-286,100-104,131-137,142-155,113-125,172-182,237-242,249-262,114-127
> #FFC000
> color #1/A:11-36,19-30,191-197,252-258 #FFC000
> color #1/B:114-121 #FFC000
> color #1/N:22-34,51-65,109-115,109-134 #FFC000
> save /Users/alexandre/Documents/Novalix/TGR5-Krios-Mai/Figures/Image-1.1.png
> width 1600 supersample 3 transparentBackground true
> view matrix camera
> -0.30054,0.20526,0.93142,199.65,-0.95274,-0.10985,-0.28321,92.179,0.044186,-0.97252,0.22857,128.79
> save /Users/alexandre/Documents/Novalix/TGR5-Krios-Mai/Figures/Image-2.1.png
> width 1600 supersample 3 transparentBackground true
> hide surfaces
> save /Users/alexandre/Documents/Novalix/TGR5-Krios-Mai/Figures/Image-1.2.png
> width 1600 supersample 3 transparentBackground true
> save /Users/alexandre/Documents/Novalix/TGR5-Krios-Mai/Figures/Image-1.3.png
> width 1600 supersample 3 transparentBackground true
> view matrix camera
> -0.80318,0.34259,-0.48736,-15.845,0.50974,-0.028167,-0.85987,-104.25,-0.30831,-0.93906,-0.15201,73.245
> style stick
Changed 8939 atom styles
> save /Users/alexandre/Documents/Novalix/TGR5-Krios-Mai/Figures/Image-1.3.png
> width 1600 supersample 3 transparentBackground true
> turn y -1 90
> save /Users/alexandre/Documents/Novalix/TGR5-Krios-Mai/Figures/Image-1.3.png
> width 1600 supersample 3 transparentBackground true
> show atoms
> hide cartoons
> hide atoms
> open /Users/alexandre/Documents/Novalix/TGR5-Krios-
> Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb
Summary of feedback from opening
/Users/alexandre/Documents/Novalix/TGR5-Krios-
Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb
---
warnings | Start residue of secondary structure not found: HELIX 18 18 SER B
12 ALA B 34 1 23
Start residue of secondary structure not found: HELIX 19 19 LEU B 40 GLN B 42
1 3
End residue of secondary structure not found: HELIX 20 20 ILE B 43 ASN B 45 1
3
Start residue of secondary structure not found: HELIX 21 21 THR B 138 GLU B
140 1 3
Start residue of secondary structure not found: HELIX 24 24 PHE N 52 ASN N 54
1 3
Start residue of secondary structure not found: HELIX 25 25 GLY N 85 VAL N 87
1 3
Start residue of secondary structure not found: HELIX 26 26 ASN N 97 LYS N 99
1 3
1 messages similar to the above omitted
Start residue of secondary structure not found: SHEET 7 7 7 ARG B 56 ARG B 62
0
Start residue of secondary structure not found: SHEET 8 8 8 ILE B 68 TRP B 73
0
Start residue of secondary structure not found: SHEET 10 1010 LYS B 88 ASP B
93 0
Start residue of secondary structure not found: SHEET 11 1111 ASN B 98 PRO B
104 0
Start residue of secondary structure not found: SHEET 12 1212 VAL B 110 TYR B
115 0
18 messages similar to the above omitted
End residue of secondary structure not found: SHEET 31 3131 ARG B 314 ALA B
319 0
Start residue of secondary structure not found: SHEET 32 3232 VAL B 325 VAL B
330 0
Start residue of secondary structure not found: SHEET 33 3333 VAL B 337 SER B
341 0
Start residue of secondary structure not found: SHEET 34 3434 PHE B 345 ASN B
350 0
Start residue of secondary structure not found: SHEET 35 3535 GLN N 26 SER N
30 0
Start residue of secondary structure not found: SHEET 36 3636 LEU N 41 SER N
48 0
7 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (45 )
Cannot find LINK/SSBOND residue CYS (122 )
Chain information for TGR5-WithFlexDomaine-210623_refined-mod.pdb #2
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
R | No description available
> hide atoms
> select add #2
8939 atoms, 9136 bonds, 3 pseudobonds, 1140 residues, 2 models selected
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
===== Log before crash end =====
Log:
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> mousemode rightMode clip
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode surface cap false; surface style solid; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; transparency 70; cofr centerofview; clip near -10 far 10
> position cofr; color ##~num_residues cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr;
> color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias helix setattr $1 res is_helix true
> alias strand setattr $1 res is_strand true
> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false
> buttonpanel Shortcuts rows 3 columns 4
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #10000 position cofr"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
UCSF ChimeraX version: 1.7.dev202309190305 (2023-09-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
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: MK193FN/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4 (22F66)
Kernel Version: Darwin 22.5.0
Time since boot: 71 jours, 17 heures et 13 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.0
Babel: 2.12.1
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: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.47.2
ChimeraX-AtomicLibrary: 10.0.8
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: 1.0.3
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.4
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202309190305
ChimeraX-CoreFormats: 1.1
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: 1.1.2
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: 1.2.1
ChimeraX-Log: 1.1.5
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: 1.5.12
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: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
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: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.9.1
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.2
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: 1.31.5
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.2
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.4
contourpy: 1.1.1
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.42.1
funcparserlib: 1.0.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.7.10
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: 5.3.1
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: 2.8.6
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.10.0
prompt-toolkit: 3.0.39
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: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.0
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: 0.6.2
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: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.0.4
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 2 years 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 during new object allocation |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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While evaluating atom spec in preset