![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 17 months ago
Closed 17 months ago
#15387 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000002046ab240 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 157 in asArray
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2828 in set_matrix
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 817 in set_projection_matrix
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 725 in _use_shader
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 801 in _opengl_shader
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 698 in shader
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 818 in _draw_geometry
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 787 in draw_self
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 780 in draw
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1567 in _draw_multiple
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1554 in draw_opaque
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 258 in _draw_scene
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 288 in render
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 113 in _redraw
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 100 in draw_new_frame
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, 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.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lxml._elementpath, lxml.etree, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw (total: 56)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 502,
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"modelCode" : "Mac14,10",
"coalitionID" : 7290,
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"releaseType" : "User"
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"captureTime" : "2024-06-06 10:39:21.3179 -0700",
"codeSigningMonitor" : 1,
"incident" : "EAA9ACF5-F706-473C-9609-1E091F9DC992",
"pid" : 85624,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
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"procLaunch" : "2024-06-05 12:20:22.5845 -0700",
"procStartAbsTime" : 25798611104354,
"procExitAbsTime" : 27721110504939,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"8293FE6F-F548-5303-9CCD-DB3725D73206","thirdParty":true},
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "FA742268-FBD4-F0F3-30A1-33CFEC0719C4",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 1186,
"sleepWakeUUID" : "A6684F4A-8269-4807-AB7E-8729F41AF16F",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140722925272919\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc9bf90000-7ffcc4d40000 [653.7M] r-x\/r-x SM=COW ...ct_id=68b40a9",
"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":85624},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140722925272919\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc9bf90000-7ffcc4d40000 [653.7M] r-x\/r-x SM=COW ...ct_id=68b40a9",
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"faultingThread" : 0,
"threads" : 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]
}
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
> camera ortho
> cofr centerOfView
> mousemode rightMode zoom
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> mousemode alt control leftMode "pick blobs"
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; 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; style ions ball; size
> ballscale 0.2; 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
> alias open_vseries "open browse vseries true"
> 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 #20000 position cofr"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/raop/Documents/Orexin/maps and models/three types of GPCR
> ligands.pdb" format pdb
Summary of feedback from opening /Users/raop/Documents/Orexin/maps and
models/three types of GPCR ligands.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 25
TYR A 39 1 15
Start residue of secondary structure not found: HELIX 2 2 GLN A 44 ARG A 73 1
30
Start residue of secondary structure not found: HELIX 3 3 HIS A 75 MET A 77 1
3
Start residue of secondary structure not found: HELIX 4 4 VAL A 80 CYS A 99 1
20
Start residue of secondary structure not found: HELIX 5 5 LEU A 100 THR A 109
1 10
41 messages similar to the above omitted
End residue of secondary structure not found: HELIX 22 22 CYS B 12 HIS B 21 1
10
End residue of secondary structure not found: HELIX 23 23 ALA B 27 GLY B 29 1
3
Start residue of secondary structure not found: SHEET 1 1 1 MET A 183 SER A
187 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 200 GLU A
204 0
Start residue of secondary structure not found: HELIX 1 1 PRO A 25 TYR A 39 1
15
Start residue of secondary structure not found: HELIX 2 2 GLN A 44 ARG A 73 1
30
Start residue of secondary structure not found: HELIX 3 3 HIS A 75 MET A 77 1
3
8 messages similar to the above omitted
End residue of secondary structure not found: HELIX 12 12 SER A 252 ARG A 256
1 5
Start residue of secondary structure not found: HELIX 13 13 ASN A 257 LYS A
259 1 3
Start residue of secondary structure not found: HELIX 14 14 PRO A 261 GLN A
270 1 10
Start residue of secondary structure not found: HELIX 15 15 GLY A 271 SER A
273 1 3
Start residue of secondary structure not found: HELIX 16 16 PRO A 278 LEU A
312 1 35
Start residue of secondary structure not found: HELIX 17 17 PRO A 313 ARG A
322 1 10
3 messages similar to the above omitted
End residue of secondary structure not found: HELIX 21 21 ASP B 5 CYS B 7 1 3
Start residue of secondary structure not found: HELIX 22 22 CYS B 12 HIS B 21
1 10
Start residue of secondary structure not found: HELIX 23 23 ALA B 27 GLY B 29
1 3
Start residue of secondary structure not found: SHEET 1 1 1 MET A 183 SER A
187 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 200 GLU A
204 0
Start residue of secondary structure not found: HELIX 1 1 PRO A 25 TYR A 39 1
15
8 messages similar to the above omitted
End residue of secondary structure not found: HELIX 10 10 LEU A 210 TYR A 224
1 15
Start residue of secondary structure not found: HELIX 11 11 LEU A 225 TRP A
243 1 19
Start residue of secondary structure not found: HELIX 12 12 SER A 252 ARG A
256 1 5
Start residue of secondary structure not found: HELIX 13 13 ASN A 257 LYS A
259 1 3
Start residue of secondary structure not found: HELIX 14 14 PRO A 261 GLN A
270 1 10
Start residue of secondary structure not found: HELIX 15 15 GLY A 271 SER A
273 1 3
3 messages similar to the above omitted
End residue of secondary structure not found: HELIX 19 19 ARG A 333 LEU A 361
1 29
Start residue of secondary structure not found: HELIX 20 20 GLY A 363 CYS A
376 1 14
Start residue of secondary structure not found: HELIX 21 21 ASP B 5 CYS B 7 1
3
Start residue of secondary structure not found: HELIX 22 22 CYS B 12 HIS B 21
1 10
Start residue of secondary structure not found: HELIX 23 23 ALA B 27 GLY B 29
1 3
Start residue of secondary structure not found: SHEET 1 1 1 MET A 183 SER A
187 0
1 messages similar to the above omitted
Chain information for three types of GPCR ligands.pdb
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
1.3/A 1.3/F | No description available
1.4/A | No description available
1.5/A | No description available
1.1/B | No description available
1.3/B 1.3/C 1.3/D 1.3/J 1.3/N 1.3/O | No description available
1.4/B | No description available
1.4/C | No description available
1.3/E | No description available
1.4/E | No description available
1.3/G | No description available
1.3/H | No description available
1.3/I | No description available
1.3/K | No description available
1.3/L | No description available
1.4/L | No description available
1.3/M | No description available
1.3/P | No description available
1.3/Q | No description available
1.3/R | No description available
1.4/R | No description available
> set bgColor white
> select #1.1/A
2868 atoms, 2948 bonds, 357 residues, 1 model selected
> open 2x6g
2x6g title:
X-ray Structure of Macrophage Inflammatory Protein-1 α (D27A) [more info...]
Chain information for 2x6g #2
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O P Q R | C-C MOTIF CHEMOKINE 3 | CCL3_HUMAN 1-70
2x6g mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
5| author_and_software_defined_assembly
6| author_and_software_defined_assembly
7| author_and_software_defined_assembly
8| author_and_software_defined_assembly
9| author_and_software_defined_assembly
> close #1.1-2#1#1.3-5
> select /A
562 atoms, 532 bonds, 110 residues, 1 model selected
> select ~sel
9029 atoms, 8860 bonds, 2 pseudobonds, 1497 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select /A
562 atoms, 532 bonds, 110 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select /B
542 atoms, 526 bonds, 95 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> hide #!2 models
> show #!2 models
> select add #2
9591 atoms, 9392 bonds, 2 pseudobonds, 1607 residues, 2 models selected
> color (#!2 & sel) #fff2ffff
> color (#!2 & sel) #fff0ffff
> color (#!2 & sel) #ffdcffff
> color (#!2 & sel) #ffc3ffff
> color (#!2 & sel) #ffb5ffff
> color (#!2 & sel) #ffafffff
> color (#!2 & sel) #ffadffff
> color (#!2 & sel) #ffabffff
> color (#!2 & sel) #ffa7ffff
> color (#!2 & sel) #ffa2ffff
> color (#!2 & sel) #ff9cffff
> color (#!2 & sel) #ef9cffff
> color (#!2 & sel) #da9cffff
> color (#!2 & sel) #c99cffff
> color (#!2 & sel) #bf9cffff
> color (#!2 & sel) #ba9cffff
> color (#!2 & sel) #b89cffff
> color (#!2 & sel) #b69cffff
> color (#!2 & sel) #b49cffff
> color (#!2 & sel) #b29cffff
> color (#!2 & sel) #b19cffff
> color (#!2 & sel) #af9cffff
> color (#!2 & sel) #ac9cffff
> color (#!2 & sel) #a99cffff
> color (#!2 & sel) #a79cffff
> color (#!2 & sel) #a59cffff
> color (#!2 & sel) #a49cffff
> color (#!2 & sel) #a09cffff
> color (#!2 & sel) #999cffff
> color (#!2 & sel) #919cffff
> color (#!2 & sel) #8b9cffff
> color (#!2 & sel) #889cffff
> color (#!2 & sel) #859cffff
> color (#!2 & sel) #849cffff
> color (#!2 & sel) #829cffff
> color (#!2 & sel) #809cffff
> color (#!2 & sel) #899cffff
> color (#!2 & sel) #8f9cffff
> color (#!2 & sel) #949cffff
> color (#!2 & sel) #969cffff
> color (#!2 & sel) #968bffff
> color (#!2 & sel) #9673ffff
> color (#!2 & sel) #9665ffff
> color (#!2 & sel) #965cffff
> color (#!2 & sel) #9654ffff
> color (#!2 & sel) #964effff
> color (#!2 & sel) #964affff
> color (#!2 & sel) #9647ffff
> color (#!2 & sel) #9646ffff
> color (#!2 & sel) #9645ffff
> color (#!2 & sel) #9545ffff
> color (#!2 & sel) #8545ffff
> color (#!2 & sel) #7245ffff
> color (#!2 & sel) #6845ffff
> color (#!2 & sel) #6345ffff
> color (#!2 & sel) #6045ffff
> color (#!2 & sel) #5f45ffff
> color (#!2 & sel) #5c45ffff
> color (#!2 & sel) #5845ffff
> color (#!2 & sel) #5445ffff
> color (#!2 & sel) #5445f2ff
> color (#!2 & sel) #5445e8ff
> color (#!2 & sel) #5445e0ff
> color (#!2 & sel) #5445d9ff
> color (#!2 & sel) #5445d4ff
> color (#!2 & sel) #5445d1ff
> color (#!2 & sel) #5445cfff
> color (#!2 & sel) #5445cbff
> color (#!2 & sel) #5445c7ff
> color (#!2 & sel) #5445c4ff
> color (#!2 & sel) #5445c1ff
> color (#!2 & sel) #5445beff
> color (#!2 & sel) #5445bdff
> color (#!2 & sel) #5445baff
> color (#!2 & sel) #5445b8ff
> color (#!2 & sel) #5445b5ff
> color (#!2 & sel) #5445b4ff
> color (#!2 & sel) #5445aeff
> color (#!2 & sel) #5445a8ff
> color (#!2 & sel) #5445a2ff
> color (#!2 & sel) #54459bff
> color (#!2 & sel) #544592ff
> color (#!2 & sel) #54458bff
> color (#!2 & sel) #544586ff
> color (#!2 & sel) #544584ff
> color (#!2 & sel) #544582ff
> color (#!2 & sel) #544580ff
> color (#!2 & sel) #544576ff
> color (#!2 & sel) #544575ff
> color (#!2 & sel) #544574ff
> color (#!2 & sel) #544573ff
> color (#!2 & sel) #544571ff
> color (#!2 & sel) #54456cff
> color (#!2 & sel) #544566ff
> color (#!2 & sel) #544562ff
> color (#!2 & sel) #54455fff
> color (#!2 & sel) #54455eff
> color (#!2 & sel) #54455cff
> color (#!2 & sel) #544559ff
> color (#!2 & sel) #544556ff
> color (#!2 & sel) #544553ff
> color (#!2 & sel) #544551ff
> color (#!2 & sel) #544550ff
> color (#!2 & sel) #54454fff
> color (#!2 & sel) #544551ff
> color (#!2 & sel) #544552ff
> color (#!2 & sel) #544554ff
> color (#!2 & sel) #544556ff
> color (#!2 & sel) #544557ff
> select clear
> open 7o7f
Summary of feedback from opening 7o7f fetched from pdb
---
notes | Fetching compressed mmCIF 7o7f from
http://files.rcsb.org/download/7o7f.cif
Fetching CCD PCA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/PCA/PCA.cif
7o7f title:
Structural basis of the activation of the CC chemokine receptor 5 by a
chemokine agonist [more info...]
Chain information for 7o7f #1
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN
1-354
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_BOVIN 1-340
C | C-C chemokine receptor type 5 | CCR5_HUMAN 1-352
F | Fab antibody fragment light chain |
G | Guanine nucleotide-binding protein G(T) subunit gamma-T1 | GBG1_BOVIN 1-74
H | Fab antibody fragment heavy chain |
I | C-C motif chemokine 5 | CCL5_HUMAN 0-68
> hide #!2 models
> hide #!1 atoms
> hide #!1 cartoons
> show #!1 cartoons
> show #!2 models
> hide #!1 models
> open 7wj5
Summary of feedback from opening 7wj5 fetched from pdb
---
note | Fetching compressed mmCIF 7wj5 from
http://files.rcsb.org/download/7wj5.cif
7wj5 title:
Cryo-EM structure of human somatostatin receptor 2 complex with its agonist
somatostatin delineates the ligand binding specificity [more info...]
Chain information for 7wj5 #3
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN
1-354
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_HUMAN 2-340
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_HUMAN 1-71
E | Gai1 antibody (scfv16) |
R | Soluble cytochrome b562,Somatostatin receptor type 2 | C562_ECOLX -105--1,
SSR2_HUMAN 1-369
S | Somatostatin-14 (SST-14) |
> show #!2-3 cartoons
> hide #!2-3 atoms
> ui mousemode right "translate selected models"
> select #3/S
105 atoms, 110 bonds, 12 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 105 atom styles
> color sel byhetero
> ui tool show "Show Sequence Viewer"
> sequence chain #3/S
Alignment identifier is 3/S
> select clear
> select #3/S:3-10
75 atoms, 78 bonds, 8 residues, 1 model selected
> select clear
> close session
> open "/Users/raop/Documents/Orexin/maps and models/OX1R linker.pdb" format
> pdb
Summary of feedback from opening /Users/raop/Documents/Orexin/maps and
models/OX1R linker.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 25
TYR A 39 1 15
Start residue of secondary structure not found: HELIX 2 2 GLN A 44 ARG A 73 1
30
Start residue of secondary structure not found: HELIX 3 3 HIS A 75 MET A 77 1
3
Start residue of secondary structure not found: HELIX 4 4 VAL A 80 CYS A 99 1
20
Start residue of secondary structure not found: HELIX 5 5 LEU A 100 THR A 109
1 10
45 messages similar to the above omitted
Chain information for OX1R linker.pdb
---
Chain | Description
1.1/A | No description available
1.1/B | No description available
1.3/L | No description available
1.2/R | No description available
1.3/R | No description available
> close session
> open "/Users/raop/Documents/Orexin/maps and models/OX1R.pdb" format pdb
Summary of feedback from opening /Users/raop/Documents/Orexin/maps and
models/OX1R.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 25
TYR A 39 1 15
Start residue of secondary structure not found: HELIX 2 2 GLN A 44 ARG A 73 1
30
Start residue of secondary structure not found: HELIX 3 3 HIS A 75 MET A 77 1
3
Start residue of secondary structure not found: HELIX 4 4 VAL A 80 CYS A 99 1
20
Start residue of secondary structure not found: HELIX 5 5 LEU A 100 THR A 109
1 10
20 messages similar to the above omitted
Chain information for OX1R.pdb
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
1.1/B | No description available
> hide #1.2 models
Drag select of 6 residues
> delete atoms sel
> delete bonds sel
Drag select of 3 residues, 1 pseudobonds
> delete atoms (#!1.1 & sel)
> delete bonds (#!1.1 & sel)
> select clear
Drag select of 1 residues, 1 pseudobonds
> delete atoms (#!1.1 & sel)
> delete bonds (#!1.1 & sel)
> close session
> open "/Users/raop/Documents/Orexin/maps and models/OX1R.pdb" format pdb
Summary of feedback from opening /Users/raop/Documents/Orexin/maps and
models/OX1R.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 25
TYR A 39 1 15
Start residue of secondary structure not found: HELIX 2 2 GLN A 44 ARG A 73 1
30
Start residue of secondary structure not found: HELIX 3 3 HIS A 75 MET A 77 1
3
Start residue of secondary structure not found: HELIX 4 4 VAL A 80 CYS A 99 1
20
Start residue of secondary structure not found: HELIX 5 5 LEU A 100 THR A 109
1 10
20 messages similar to the above omitted
Chain information for OX1R.pdb
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
1.1/B | No description available
> hide #1.2 models
> show #1.2 models
> close #1.2
Drag select of 11 residues
> select subtract /A:377
63 atoms, 10 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 4 residues
> select subtract /A:24
20 atoms, 3 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Color Actions"
> color bychain
> lighting soft
> graphics silhouettes true
> select add /B:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /B:32
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add /B:31
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add /A:119
30 atoms, 26 bonds, 4 residues, 1 model selected
> select subtract /A:119
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add /B:30
32 atoms, 28 bonds, 4 residues, 1 model selected
> select add /B:29
36 atoms, 31 bonds, 5 residues, 1 model selected
> select add /B:28
41 atoms, 35 bonds, 6 residues, 1 model selected
> select add /B:27
46 atoms, 39 bonds, 7 residues, 1 model selected
> select add /B:26
56 atoms, 49 bonds, 8 residues, 1 model selected
> select add /B:25
64 atoms, 56 bonds, 9 residues, 1 model selected
> select add /B:24
68 atoms, 59 bonds, 10 residues, 1 model selected
> color sel lime
> color sel #544557ff
> color sel #544657ff
> color sel #544c57ff
> color sel #544f57ff
> color sel #545e57ff
> color sel #546657ff
> color sel #547157ff
> color sel #547c57ff
> color sel #549257ff
> color sel #549c57ff
> color sel #54a457ff
> color sel #54ac57ff
> color sel #54b857ff
> color sel #54bc57ff
> color sel #54c057ff
> color sel #54c357ff
> color sel #54c657ff
> color sel #54c957ff
> color sel #54cc57ff
> color sel #54ce57ff
> select /B:19
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /B:20
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /B:15
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /B:16
19 atoms, 17 bonds, 2 residues, 1 model selected
> select add /B:20
27 atoms, 24 bonds, 3 residues, 1 model selected
> select add /B:19
35 atoms, 31 bonds, 4 residues, 1 model selected
> color sel #54ce57ff
> color sel #54cd57ff
> color sel #54cc57ff
> color sel #54cb57ff
> color sel #54cc57ff
> color sel #54cd57ff
> color sel #54ce57ff
> color sel #54cf57ff
> color sel #54ce57ff
> color sel #54cd57ff
> color sel #54cc57ff
> color sel #54cd57ff
> color sel #54cb57ff
> color sel #54cc57ff
> color sel #54cd57ff
> color sel #54cf57ff
> select clear
> select /B:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel hot pink
> select clear
> select /B:14
6 atoms, 5 bonds, 1 residue, 1 model selected
> color #1.1 #7b688cff
> color #1.1 #7bc28cff
> color #1.1 #b9c28cff
> color #1.1 #b9c2cdff
> select clear
> select /B
248 atoms, 252 bonds, 33 residues, 1 model selected
> color sel cornflower blue
> ui tool show "Color Actions"
> color sel midnight blue
> color sel maroon
> select clear
> select add /B:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /B:32
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add /B:31
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add /B:30
32 atoms, 28 bonds, 4 residues, 1 model selected
> select add /B:29
36 atoms, 31 bonds, 5 residues, 1 model selected
> select add /B:26
46 atoms, 41 bonds, 6 residues, 1 model selected
> select add /B:20
54 atoms, 48 bonds, 7 residues, 1 model selected
> select add /B:19
62 atoms, 55 bonds, 8 residues, 1 model selected
> color sel cornflower blue
> ui tool show "Color Actions"
> color sel dark slate blue
> color sel medium slate blue
> color sel steel blue
> color sel dodger blue
> color sel deep sky blue
> color sel turquoise
> color sel medium turquoise
> select clear
> select /B
248 atoms, 252 bonds, 33 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium turquoise
> select subtract /B:33
239 atoms, 243 bonds, 32 residues, 1 model selected
> select clear
> select /B:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /B:32
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add /B:31
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add /B:30
32 atoms, 28 bonds, 4 residues, 1 model selected
> select add /B:29
36 atoms, 31 bonds, 5 residues, 1 model selected
> select add /B:26
46 atoms, 41 bonds, 6 residues, 1 model selected
> select add /B:20
54 atoms, 48 bonds, 7 residues, 1 model selected
> select add /B:19
62 atoms, 55 bonds, 8 residues, 1 model selected
> ui tool show "Color Actions"
> color sel maroon
> select clear
> ui tool show "Side View"
> ui tool show Matchmaker
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1.1/A
> select /A:25
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:25-40
156 atoms, 162 bonds, 16 residues, 1 model selected
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
> camera ortho
> cofr centerOfView
> mousemode rightMode zoom
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> mousemode alt control leftMode "pick blobs"
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; 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; style ions ball; size
> ballscale 0.2; 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
> alias open_vseries "open browse vseries true"
> 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 #20000 position cofr"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 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: Mac
Model Identifier: Mac14,10
Model Number: Z1740017JLL/A
Chip: Unknown
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 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: 31 days, 1 hour, 15 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 19
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U2723QE:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2723QE:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 17 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 , 17 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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