Opened 7 months ago

Closed 7 months ago

#17225 closed defect (can't reproduce)

Crash on exit destroying OpenGL contexts

Reported by: chimerax-bug-report@… 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-15.3.2-x86_64-i386-64bit
ChimeraX Version: 1.10.dev202503262146 (2025-03-26 21:46:50 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 0x00007ff84afc6b00 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 440 in quit
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 805 in closeEvent
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 302 in event
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 339 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 1054 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 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, 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, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, chimerax.alignment_algs._sw, chimerax.pdb._pdbio, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PIL._imagingmath, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 60)


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{
  "uptime" : 7100,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro15,2",
  "coalitionID" : 2722,
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    "build" : "24D81",
    "releaseType" : "User"
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  "captureTime" : "2025-03-27 15:53:36.5400 -0400",
  "codeSigningMonitor" : 0,
  "incident" : "75B3A7E1-B887-443E-9992-32B7A97955E3",
  "pid" : 1995,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-03-27 14:13:40.1445 -0400",
  "procStartAbsTime" : 1166350522627,
  "procExitAbsTime" : 7162610835066,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"F124C8F3-20A4-5DE1-9F07-0AC184CC1883","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "D7647BD3-ABC0-184D-0D50-636FDB066300",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "bootSessionUUID" : "3D97EDBA-DD48-43F3-973E-02DB4674AD89",
  "bridgeVersion" : {"build":"22P3060","train":"9.3"},
  "sip" : "enabled",
  "vmRegionInfo" : "0 is not in any region.  Bytes before following region: 4308041728\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      100c78000-100c7c000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":1995},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
  "vmregioninfo" : "0 is not in any region.  Bytes before following region: 4308041728\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      100c78000-100c7c000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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  "faultingThread" : 0,
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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=1.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG image                           536K       50 \nCG raster data                      44K        4 \nColorSync                          260K       33 \nCoreAnimation                     1264K      118 \nCoreGraphics                        12K        2 \nCoreUI image data                 5128K       39 \nFoundation                          32K        2 \nIOKit                             7940K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                           797.9M      324 \nMALLOC guard page                   48K       12 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMach message                        16K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        188K       47 \nStack                            286.9M       48 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      220.2M      166 \nVM_ALLOCATE (reserved)            32.0M        1         reserved VM address space (unallocated)\n__CTF                               824        1 \n__DATA                            43.7M     1085 \n__DATA_CONST                     102.7M     1012 \n__DATA_DIRTY                      2569K      341 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5176K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       214.8M      154 \n__OBJC_RO                         76.9M        1 \n__OBJC_RW                         2375K        2 \n__TEXT                             1.4G     1101 \n__TPRO_CONST                       272K        2 \ndyld private memory                 80K        2 \nmapped file                      579.5M       94 \nowned unmapped memory             68.2M        1 \nshared memory                     3012K       32 \n===========                     =======  ======= \nTOTAL                              3.8G     4692 \nTOTAL, minus reserved VM space     3.8G     4692 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "logWritingSignature" : "876fdd2010a31ebed43feb87fdba6363a7970e14",
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000464
    },
    {
      "rolloutId" : "6425c75e4327780c10cc4252",
      "factorPackIds" : {
        "SIRI_HOME_AUTOMATION_INTENT_SELECTION_CACHE" : "642600a457e7664b1698eb32"
      },
      "deploymentId" : 240000004
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202503262146 (2025-03-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold predict
> MSVVESKRKENGGSGPVTPDIGGTSLLKRESKVAKSLWLRQQDTITRLEELQRQHEEEIRAKERRQNSYDDLRTPLRSVDGSRRPSVVNDINDYRGRPLHDQLHGAYRATLLSHHTKNLNLRGFLNLFFILLFVINFRMVTDNLMEYGLMIRLPSSFRDILSNWPMLLCFLLMHFCILGAFVIERFVAAWVPHLLDWSECVLIGLNFFLVFIVPYLTVCNSSPSPAASALLLAFSIVWLFKLFSFHHVCLDARRALRDGDNFRELCSNSEEAEHVRRYPYSITLRHLYTFIWMPTMCFQFYYPRVPRIRWLSVIRHVFESAACLALMKIVVDQHIVPVARNSFTITEMQSIPLSTLLVHFLDKITRLSIPNLYVWLLMFVGLFHHWCNILAEVTRFGDRQFYLDWWNASSFGEYWRKWNLPIHHFLNRHINKPLRRARFPRIVATSVVFLISALLHEYMITVPLQLGWTGWVFLGFMAQAPLTYITNLSFFQRNPTVGNCFFWFIFCFSGQPLGILIYWYLWGVKHGTVQQLDPSKIQIM,MSVVESKRKENGGSGPVTPDIGGTSLLKRESKVAKSLWLRQQDTITRLEELQRQHEEEIRAKERRQNSYDDLRTPLRSVDGSRRPSVVNDINDYRGRPLHDQLHGAYRATLLSHHTKNLNLRGFLNLFFILLFVINFRMVTDNLMEYGLMIRLPSSFRDILSNWPMLLCFLLMHFCILGAFVIERFVAAWVPHLLDWSECVLIGLNFFLVFIVPYLTVCNSSPSPAASALLLAFSIVWLFKLFSFHHVCLDARRALRDGDNFRELCSNSEEAEHVRRYPYSITLRHLYTFIWMPTMCFQFYYPRVPRIRWLSVIRHVFESAACLALMKIVVDQHIVPVARNSFTITEMQSIPLSTLLVHFLDKITRLSIPNLYVWLLMFVGLFHHWCNILAEVTRFGDRQFYLDWWNASSFGEYWRKWNLPIHHFLNRHINKPLRRARFPRIVATSVVFLISALLHEYMITVPLQLGWTGWVFLGFMAQAPLTYITNLSFFQRNPTVGNCFFWFIFCFSGQPLGILIYWYLWGVKHGTVQQLDPSKIQIM

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  

> matchmaker #5 to #1

No 'to' model specified  
Running AlphaFold prediction  

> save "/Users/jamestyler/Desktop/CimeraX Files/testing alphafold in chimera
> with Tg DGAT.cxs" includeMaps true

> open "/Users/jamestyler/Desktop/CimeraX Files/8esm_DGAT1 with T863
> bound.pdb"

8esm_DGAT1 with T863 bound.pdb title:  
Human triacylglycerol synthesizing enzyme DGAT1 In complex with T863 inhibitor
[more info...]  
  
Chain information for 8esm_DGAT1 with T863 bound.pdb #1  
---  
Chain | Description | UniProt  
A B | diacylglycerol O-acyltransferase 1 | DGAT1_HUMAN 1-488  
  
Non-standard residues in 8esm_DGAT1 with T863 bound.pdb #1  
---  
WS0 —
{(1R,4R)-4-[4-(4-amino-7,7-dimethyl-7H-pyrimido[4,5-B][1,4]oxazin-6-yl)phenyl]cyclohexyl}acetic
acid  
  

> select /A:66-481

3360 atoms, 3467 bonds, 1 pseudobond, 406 residues, 2 models selected  

> show sel surfaces

> ui mousemode right select

> select clear

> ui mousemode right translate

> select ::name="WS0"

58 atoms, 64 bonds, 2 residues, 1 model selected  

> ui tool show Contacts

> contacts sel setAttrs true overlapCutoff 0.4 ignoreHiddenModels true select
> true color #73faf8 reveal true

No contacts  

> contacts sel setAttrs true overlapCutoff 0.20000000000000004
> ignoreHiddenModels true select true color #73faf8 reveal true

No atoms match given atom specifier  

> select add #1

6778 atoms, 6998 bonds, 2 pseudobonds, 814 residues, 3 models selected  

> ui tool show Contacts

> select subtract #1

1 model selected  

> ui mousemode right select

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

29 atoms, 32 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel overlapCutoff 0.2 ignoreHiddenModels true select true color
> #73faf8 reveal true

6 contacts  

> contacts sel setAttrs true attrName overlap_0.2A overlapCutoff 0.2
> ignoreHiddenModels true select true color #73faf8 reveal true

Invalid "attrName" argument: Attribute names can consist only of alphanumeric
characters and underscores  

> ui tool show Contacts

> contacts sel setAttrs true attrName overlap_0_2A overlapCutoff 0.2
> ignoreHiddenModels true select true color #73faf8 reveal true

6 contacts  

> contacts sel setAttrs true attrName overlap_0_2A overlapCutoff 0.2
> ignoreHiddenModels true select true color #73faf8 reveal true

6 contacts  

> select clear

> select /B:501@C11

1 atom, 1 residue, 1 model selected  

> select up

29 atoms, 32 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel overlapCutoff 0.1 ignoreHiddenModels true select true color
> #73faf8 reveal true

12 contacts  

> contacts sel overlapCutoff 0.3 ignoreHiddenModels true select true color
> #73faf8 reveal true

2 contacts  

> select clear

> color sel red

> ui tool show "Color Actions"

> select clear

> select /B:407@CB

1 atom, 1 residue, 1 model selected  

> select up

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color sel red

> undo

> ui tool show "Color Actions"

> color sel red target cs

> select /B:411

6 atoms, 5 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel red target cs

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

29 atoms, 32 bonds, 1 residue, 1 model selected  

> contacts sel overlapCutoff 0.19999999999999998 ignoreHiddenModels true
> select true color #73faf8 reveal true

6 contacts  

> select /B:407

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

7 atoms, 6 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 7 atom styles  

> select /B:411

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

180 atoms, 186 bonds, 22 residues, 1 model selected  

> select down

6 atoms, 5 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 6 atom styles  

> select clear

> select /B:501@C18

1 atom, 1 residue, 1 model selected  

> select up

29 atoms, 32 bonds, 1 residue, 1 model selected  

> select up

3389 atoms, 3499 bonds, 407 residues, 1 model selected  

> select down

29 atoms, 32 bonds, 1 residue, 1 model selected  

> contacts sel overlapCutoff 0.19999999999999998 ignoreHiddenModels true
> select true color #73faf8 reveal true

6 contacts  

> ui tool show "Color Actions"

> color sel orange target cs

> select clear

> select /B:408

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select /B:407@CB

1 atom, 1 residue, 1 model selected  

> select up

7 atoms, 6 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 7 atom styles  

> ui tool show "Color Actions"

> color sel red target cs

> select /B:411

6 atoms, 5 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel red target cs

> select clear

> select /B:411@CB

1 atom, 1 residue, 1 model selected  

> style sel stick

Changed 1 atom style  

> select /B:411@CA

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 6 atom styles  

> select clear

> contacts sel overlapCutoff 0.09999999999999998 ignoreHiddenModels true
> select true color #73faf8 reveal true

No atoms match given atom specifier  

> select /B:501@C11

1 atom, 1 residue, 1 model selected  

> select up

29 atoms, 32 bonds, 1 residue, 1 model selected  

> contacts sel overlapCutoff 0.09999999999999998 ignoreHiddenModels true
> select true color #73faf8 reveal true

12 contacts  

> style sel sphere

Changed 19 atom styles  

> select clear

> select /B:390@CZ

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select up

66 atoms, 67 bonds, 7 residues, 1 model selected  

> select down

12 atoms, 12 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 12 atom styles  

> color sel yellow

> undo

> ui tool show "Color Actions"

> color sel yellow target cs

> select /B:375

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel yellow target cs

> select /B:381@CG1

1 atom, 1 residue, 1 model selected  

> color sel yellow target cs

> select clear

> select /B:197

5 atoms, 4 bonds, 1 residue, 1 model selected  

> ui mousemode right translate

> ui mousemode right select

> select /B:501@C13

1 atom, 1 residue, 1 model selected  

> select up

29 atoms, 32 bonds, 1 residue, 1 model selected  

> select up

3389 atoms, 3499 bonds, 407 residues, 1 model selected  

> select down

29 atoms, 32 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 29 atom styles  

> contacts sel overlapCutoff 0.09999999999999998 ignoreHiddenModels true
> select true color #73faf8 reveal true

12 contacts  

> style sel stick

Changed 19 atom styles  

> select clear

Drag select of 4 atoms, 2 residues, 4 bonds  

> select clear

> select /B:501@C11

1 atom, 1 residue, 1 model selected  

> select up

29 atoms, 32 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #8efa00 dashes 6 showDist true twoColors true slopColor
> #ff2600 select true reveal true retainCurrent true

5 hydrogen bonds found  
1 strict hydrogen bonds found  

> ui mousemode right translate

> style sel ball

Changed 7 atom styles  

> hide #1.4.1 models

> ui mousemode right select

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

29 atoms, 32 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #8efa00 dashes 6 showDist true twoColors true slopColor
> #ff2600 select true reveal true retainCurrent true

5 hydrogen bonds found  
1 strict hydrogen bonds found  

> select clear

> hide #1.2 models

> select /A:411

6 atoms, 5 bonds, 1 residue, 1 model selected  

> color sel lime target cs

> select /A:378

8 atoms, 7 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 8 atom styles  

> hide sel cartoons

> show sel cartoons

> hide (#!1 & sel-residues & (protein|nucleic)) target a

> cartoon hide (#!1 & sel-residues)

> show (#!1 & sel-residues & backbone) target ab

> show sel cartoons

> ui mousemode right translate

> cartoon (#!1 & sel)

> show (#!1 & sel) target ab

> hide sel atoms

> ui tool show "Color Actions"

> color sel yellow target cs

> ui mousemode right select

> select /A:374

14 atoms, 15 bonds, 1 residue, 1 model selected  

> color sel yellow target cs

> select /A:377

14 atoms, 15 bonds, 1 residue, 1 model selected  

> color sel yellow target cs

> show #1.4.1 models

> select clear

> ui mousemode right translate

> show #1.2 models

> save "/Users/jamestyler/Desktop/CimeraX Files/8esm_DGAT1 with T863 bound and
> contacts colored.cxs" includeMaps true

> close #1

> open 6pvo format mmcif fromDatabase pdb

6pvo title:  
Cryo-EM structure of mouse TRPV3-Y564A in putative sensitized state at 37
degrees Celsius [more info...]  
  
Chain information for 6pvo #1  
---  
Chain | Description | UniProt  
A B C D | Transient receptor potential cation channel subfamily V member 3 | TRPV3_MOUSE 1-791  
  

> close

> open /Users/jamestyler/Downloads/6vp0.pdb

6vp0.pdb title:  
Human diacylglycerol acyltransferase 1 In complex with oleoyl-coa [more
info...]  
  
Chain information for 6vp0.pdb #1  
---  
Chain | Description | UniProt  
C E | diacylglycerol O-acyltransferase 1 | DGAT1_HUMAN 1-488  
  
Non-standard residues in 6vp0.pdb #1  
---  
3VV —
S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3Λ~5~,5Λ~5~-diphosphaheptadecan-17-yl}
(9Z)-octadec-9-enethioate(non-preferred name) (oleoyl-coa)  
AV0 — lauryl maltose neopentyl glycol (2,2-didecylpropane-1,3-bis-B-D-
maltopyranoside; 2-decyl-2-{[(4-O-α-D-glucopyranosyl-β-D-
glucopyranosyl)oxy]methyl}DODECYL4-O-α-D-glucopyranosyl-β-D-glucopyranoside)  
P5S —
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
(phosphatidyl serine)  
POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl
2-(trimethylammonio)ethyl phosphate (POPC)  
  

> select ::name="POV"

140 atoms, 136 bonds, 4 residues, 1 model selected  

> select add #1

7210 atoms, 7422 bonds, 2 pseudobonds, 820 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select add #1

7210 atoms, 7422 bonds, 2 pseudobonds, 820 residues, 3 models selected  
Alignment identifier is 1  

> ui mousemode right select

> select clear

> select /C-E:404

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select /C-E:404

22 atoms, 20 bonds, 2 residues, 1 model selected  

> style sel sphere

Changed 22 atom styles  

> select clear

> select /C-E:400

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /C-E:400

18 atoms, 16 bonds, 2 residues, 1 model selected  

> style sel sphere

Changed 18 atom styles  

> select clear

> select /C-E:390

24 atoms, 24 bonds, 2 residues, 1 model selected  

> select /C-E:390

24 atoms, 24 bonds, 2 residues, 1 model selected  

> style sel sphere

Changed 24 atom styles  

> select /C-E:382

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select /C-E:382

20 atoms, 20 bonds, 2 residues, 1 model selected  

> style sel sphere

Changed 20 atom styles  

> select /C-E:375

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /C-E:375

18 atoms, 16 bonds, 2 residues, 1 model selected  

> style sel sphere

Changed 18 atom styles  

> select clear

> select /C-E:371

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select /C-E:371

14 atoms, 12 bonds, 2 residues, 1 model selected  

> style sel sphere

Changed 14 atom styles  

> show sel atoms

> select clear

> select /C-E:371

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select /C-E:371

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select /C-E:375

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /C-E:375

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /C-E:382

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select /C-E:382

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select /C-E:371

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select /C-E:375

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /C-E:382

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

67 atoms, 69 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #8efa00 dashes 6 showDist true twoColors true slopColor
> #ff2600 select true reveal true retainCurrent true

7 hydrogen bonds found  
2 strict hydrogen bonds found  

> select clear

> select /E:371@CG2

1 atom, 1 residue, 1 model selected  

> select clear

> select /E:371@CB

1 atom, 1 residue, 1 model selected  

> select up

7 atoms, 6 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 7 atom styles  

> select /E:375@CG

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 9 atom styles  

> select /E:382@NE2

1 atom, 1 residue, 1 model selected  

> select up

10 atoms, 10 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 10 atom styles  

> select /E:400@CD

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 9 atom styles  

> select /E:404@NH1

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 11 atom styles  

> select /E:390@CE2

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 12 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 12 atom styles  

> select clear

> ui mousemode right translate

> save "/Users/jamestyler/Desktop/CimeraX Files/6vp0 DGAT1_Hbonds and paper
> contacts balled.cxs" includeMaps true

> close


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.10.dev202503262146 (2025-03-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-23.0.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.3 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: 2069.80.3.0.0 (iBridge: 22.16.13060.0.0,0)
      OS Loader Version: 582~3311

Software:

    System Software Overview:

      System Version: macOS 15.3.2 (24D81)
      Kernel Version: Darwin 24.3.0
      Time since boot: 2 hours, 18 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: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.2.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.19.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.1
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.13
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    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: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202503262146
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.1
    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: 1.5.3
    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: 2.2
    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: 2.16
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    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-ProfileGrids: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    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: 1.19.1
    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: 2.5.2
    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: 1.45
    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
    coverage: 7.7.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.13
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.56.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    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
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.7
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.5
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 26.3.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 75.8.2
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.13.0
    tzdata: 2025.2
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.13

Change History (2)

comment:1 by pett, 7 months ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on exit destroying OpenGL contexts

comment:2 by pett, 7 months ago

Resolution: → can't reproduce
Status: assigned → closed
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