![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17450 closed defect (duplicate)
Graphics hardware encountered an error and was reset:
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.4.1-x86_64-i386-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. This is an Apple Intel or AMD graphics driver crash that may be related to showing a scene that is complex and uses too much graphics memory. Apple is unlikely to ever fix this since they no longer make computers with Intel or AMD graphics. The crash does not happen with Apple M1,M2,M3... graphics.
Fatal Python error: Aborted
Thread 0x0000700016e1f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff84e291bc0 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 202 in draw
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.9.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-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, PIL._webp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 56)
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"coalitionID" : 9691,
"osVersion" : {
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"build" : "24E263",
"releaseType" : "User"
},
"captureTime" : "2025-04-21 17:18:36.2435 -0400",
"codeSigningMonitor" : 0,
"incident" : "6A48500D-7311-46DD-8E3B-B2A627ACFF7B",
"pid" : 15787,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-21 11:34:57.7856 -0400",
"procStartAbsTime" : 53490872068631,
"procExitAbsTime" : 67599531490711,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"3ADC6D10-30E5-5A82-A664-42F8AFE6C25A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "6F727DB6-9E2B-0BB4-FB27-84442B978D45",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["siriAssetIsNotReady","notOptedIn","unableToFetchAvailability","deviceNotCapable"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"bootSessionUUID" : "3F558B9D-F14E-44C7-AC94-74FF3EC7DE39",
"wakeTime" : 2806,
"bridgeVersion" : {"build":"22P4248","train":"9.4"},
"sleepWakeUUID" : "97B66AAD-760B-45DF-B341-44B10FBA972A",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":15787},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/shukurahanas/Downloads/AF-A0A077FPW4-F1-model_v4.pdb format pdb
Summary of feedback from opening
/Users/shukurahanas/Downloads/AF-A0A077FPW4-F1-model_v4.pdb
---
warning | Ignored bad PDB record found on line 38
DBREF XXXX A 1 220 UNP A0A077FPW4 A0A077FPW4_9RICK 1 220
AF-A0A077FPW4-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for chlamydia protein associating with death
domains (A0A077FPW4) [more info...]
Chain information for AF-A0A077FPW4-F1-model_v4.pdb #1
---
Chain | Description
A | chlamydia protein associating with death domains
Computing secondary structure
> open 1RCW
1rcw title:
Crystal structure of CT610 from Chlamydia trachomatis [more info...]
Chain information for 1rcw #2
---
Chain | Description | UniProt
A B C | CT610 | PQQCL_CHLTR 1-231
Non-standard residues in 1rcw #2
---
FE — Fe (III) ion
1rcw mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_defined_assembly
> select #2/B
1821 atoms, 1789 bonds, 8 pseudobonds, 288 residues, 2 models selected
> ui tool show Toolbar
> hide sel cartoons
> hide sel atoms
> select #2/C
1728 atoms, 1742 bonds, 7 pseudobonds, 241 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> matchmaker #2 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF-A0A077FPW4-F1-model_v4.pdb, chain A (#1) with 1rcw, chain A
(#2), sequence alignment score = 615.6
RMSD between 197 pruned atom pairs is 0.879 angstroms; (across all 212 pairs:
1.324)
> select #1/A: 77
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A: 84
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A: 169
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A: 173
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A: 176
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A: 137
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> set bgColor white
> select #1/A
1763 atoms, 1804 bonds, 220 residues, 1 model selected
> ui tool show "Color Actions"
> color sel hot pink
> color sel cornflower blue
> select #2/A#2/B#2/C
5361 atoms, 5312 bonds, 23 pseudobonds, 815 residues, 2 models selected
> color sel forest green
> color sel cyan
> color sel light sea green
> color sel purple
> color sel hot pink
> color sel magenta
> color sel light gray
> color sel dark gray
> color sel gray
> color sel dark gray
> color sel gray
> color sel light gray
> color sel gray
> color sel dark gray
> color sel dim gray
> color sel orange
> color sel orange red
> color sel gray
> color sel dark gray
> color sel dim gray
> ui tool show "Color Actions"
> color sel light sea green
> color sel gray
> color sel light slate gray
> color sel light salmon
> color sel dark goldenrod
> color sel olive
> color sel tomato
> color sel sienna
> color sel indian red
> color sel sienna
> color sel indian red
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="MSE"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
6949 atoms, 7116 bonds, 860 residues, 2 models selected
> color sel byhetero
> select clear
> select ::name="FE"
6 atoms, 6 residues, 1 model selected
> color sel byhetero
> select ::name="FE"::name="HOH"
175 atoms, 2 pseudobonds, 175 residues, 2 models selected
> select clear
> ui tool show "Side View"
> save "/Users/shukurahanas/Desktop/my protein with 1RCW.tif" width 1984
> height 1137 supersample 3
> open 8VAB
Summary of feedback from opening 8VAB fetched from pdb
---
notes | Fetching compressed mmCIF 8vab from http://files.rcsb.org/download/8vab.cif
Fetching CCD FE2 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/FE2/FE2.cif
8vab title:
Crystal structure of FeII/FeII CtCADD from Chlamydia trachomatis [more
info...]
Chain information for 8vab #3
---
Chain | Description | UniProt
A | 4-aminobenzoate synthase | CADD_CHLTR 1-220
Non-standard residues in 8vab #3
---
FE2 — Fe (II) ion
8vab mmCIF Assemblies
---
1| author_and_software_defined_assembly
> matchmaker #3 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF-A0A077FPW4-F1-model_v4.pdb, chain A (#1) with 8vab, chain A
(#3), sequence alignment score = 617.5
RMSD between 196 pruned atom pairs is 0.847 angstroms; (across all 213 pairs:
1.313)
> hide #!2 models
> save "/Users/shukurahanas/Desktop/MY PROTEİN WİTH 8VAB.tif" width 1984
> height 1137 supersample 3
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> save "/Users/shukurahanas/Desktop/MY PROTEİN WİTH 1RCW.tif" width 1984
> height 1137 supersample 3
> open 1OTV
Summary of feedback from opening 1OTV fetched from pdb
---
note | Fetching compressed mmCIF 1otv from http://files.rcsb.org/download/1otv.cif
1otv title:
PqqC, Pyrroloquinolinquinone Synthase C [more info...]
Chain information for 1otv #4
---
Chain | Description | UniProt
A B | Coenzyme PQQ synthesis protein C | PQQC_KLEPN 1-259
1otv mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> matchmaker #4 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF-A0A077FPW4-F1-model_v4.pdb, chain A (#1) with 1otv, chain B
(#4), sequence alignment score = 363.6
RMSD between 131 pruned atom pairs is 1.167 angstroms; (across all 219 pairs:
3.243)
> hide #!2 models
> hide #4 models
> show #4 models
> hide #1 models
> close #4
> show #1 models
> show #!2 models
> show #!3 models
> hide #!2 models
> open 1OTW
Summary of feedback from opening 1OTW fetched from pdb
---
notes | Fetching compressed mmCIF 1otw from http://files.rcsb.org/download/1otw.cif
Fetching CCD PEO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/PEO/PEO.cif
Fetching CCD PQQ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Q/PQQ/PQQ.cif
1otw title:
Crystal structure of PqqC in complex with PQQ and a putative H2O2 [more
info...]
Chain information for 1otw #4
---
Chain | Description | UniProt
A B | Coenzyme PQQ synthesis protein C | PQQC_KLEPN 0-254
Non-standard residues in 1otw #4
---
PEO — hydrogen peroxide
PQQ — pyrroloquinoline quinone
> matchmaker #4 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF-A0A077FPW4-F1-model_v4.pdb, chain A (#1) with 1otw, chain A
(#4), sequence alignment score = 432.5
RMSD between 157 pruned atom pairs is 1.086 angstroms; (across all 220 pairs:
2.461)
> hide #!3 models
> select #4/B
2129 atoms, 2154 bonds, 290 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide #4 models
> close #4
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> open /Users/shukurahanas/Downloads/clustalw.aln
Summary of feedback from opening /Users/shukurahanas/Downloads/clustalw.aln
---
notes | Alignment identifier is clustalw.aln
Associated AF-A0A077FPW4-F1-model_v4.pdb chain A to A0A077FPW4 with 0
mismatches
Associated 1rcw chain A to O84616 with 0 mismatches
Associated 1rcw chain B to O84616 with 0 mismatches
Associated 1rcw chain C to O84616 with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment clustalw.aln
Opened 3 sequences from clustalw.aln
> open 2VK8
Summary of feedback from opening 2VK8 fetched from pdb
---
notes | Fetching compressed mmCIF 2vk8 from http://files.rcsb.org/download/2vk8.cif
Fetching CCD 2OP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/2OP/2OP.cif
Fetching CCD TPP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/TPP/TPP.cif
2vk8 title:
Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase
variant E477Q in complex with its substrate [more info...]
Chain information for 2vk8 #4
---
Chain | Description | UniProt
A B C D | PYRUVATE DECARBOXYLASE ISOZYME 1 | PDC1_YEAST 1-563
Non-standard residues in 2vk8 #4
---
2OP — (2S)-2-hydroxypropanoic acid
MG — magnesium ion
TPP — thiamine diphosphate
2vk8 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> hide #1 models
> select :20P
Nothing selected
> select :2OP
24 atoms, 20 bonds, 4 residues, 1 model selected
> show sel atoms
> select #4/A#4/B#4/C#4/D
19242 atoms, 17787 bonds, 24 pseudobonds, 4078 residues, 2 models selected
> color (#!4 & sel) purple
> select :2OP
24 atoms, 20 bonds, 4 residues, 1 model selected
> color sel byhetero
> hide #!4 models
> show #!4 models
> close #4
> show #1 models
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/sideview/tool.py", line 113, in _redraw
self.render()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/sideview/tool.py", line 288, in render
self.view.draw()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw
self._draw_scene(camera, drawings)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 239, in _draw_scene
camera.draw_background(vnum, r)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/camera.py", line 195, in draw_background
render.draw_background()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
Error processing trigger "frame drawn":
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Unsupported scale factor (0.000000) detected on Display0
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #1 models
> select ::name="HOH"
201 atoms, 201 residues, 2 models selected
> color (#!2 & sel) byhetero
> select clear
> select #2/A: 82-87
48 atoms, 49 bonds, 6 residues, 1 model selected
> color sel byhetero
> select #2/A: 82-87
48 atoms, 49 bonds, 6 residues, 1 model selected
> color #2/A: 82-87 blue
> color #2/A: 82-87 orange
> select #2/B
1821 atoms, 1789 bonds, 8 pseudobonds, 288 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select #2/B
1821 atoms, 1789 bonds, 8 pseudobonds, 288 residues, 2 models selected
> hide sel cartoons
> show #1 models
> color #1/A: 82-87 blue
> undo
> color #1/A: 78-84 blue
> undo
> color #1/A: 78-83 blue
> color #2/A: 59-85 blue
> color #2/A: 59-85 orange
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> save "/Users/shukurahanas/Desktop/active site of blue and salmon.tif" width
> 1951 height 1263 supersample 3
> hide #!2 models
> show #!2 models
> hide #1 models
> select add #2
5361 atoms, 5312 bonds, 23 pseudobonds, 815 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2
5361 atoms, 5312 bonds, 23 pseudobonds, 815 residues, 2 models selected
> select subtract #2
Nothing selected
> ui mousemode right label
> label delete residues
> select clear
> show #1 models
> hide #1 models
> select #2/A: 81
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> undo
> color sel byhetero
> show #1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #2/A
1812 atoms, 1781 bonds, 8 pseudobonds, 286 residues, 2 models selected
> select add #2
5361 atoms, 5312 bonds, 23 pseudobonds, 815 residues, 2 models selected
> select subtract #2
Nothing selected
> ui mousemode right zoom
> ui mousemode right select
> select clear
> hide #1 models
> ui mousemode right distance
> ui mousemode right label
> label delete residues
> select #2/A: 178
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!2 models
> show #!2 models
> select add #2
5361 atoms, 5312 bonds, 23 pseudobonds, 815 residues, 2 models selected
> select subtract #2
Nothing selected
> select #2/A: 178
8 atoms, 7 bonds, 1 residue, 1 model selected
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-23.0.26
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 2075.101.2.0.0 (iBridge: 22.16.14248.0.0,0)
OS Loader Version: 583~900
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 2 days, 4 hours, 59 minutes
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: On
Mirror Status: Hardware Mirror
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2724DEB:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 59.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 1CQRJ04
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
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: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset: |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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