Opened 7 months ago

Closed 7 months ago

Last modified 7 months ago

#17309 closed defect (can't reproduce)

Some kind of memory/pager failure

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-12.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x000000020280a600 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, chimerax.dssp._dssp, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 64)


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{
  "uptime" : 43000,
  "procLaunch" : "2025-04-07 15:00:46.5640 +1000",
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookAir10,1",
  "procStartAbsTime" : 904771047725,
  "coalitionID" : 1493,
  "osVersion" : {
    "train" : "macOS 12.1",
    "build" : "21C52",
    "releaseType" : "User"
  },
  "captureTime" : "2025-04-07 16:30:38.6011 +1000",
  "incident" : "19E83816-3C7C-4079-812A-AE0F76B0A5B9",
  "bug_type" : "309",
  "pid" : 11975,
  "procExitAbsTime" : 1033511567242,
  "translated" : true,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"6B8556C9-71EB-5517-B328-F73577F2DC82","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "76685193-F55C-E9C2-726A-6C7B93E7C7B4",
  "sleepWakeUUID" : "33B004D4-C842-43CE-91B0-CDF810DC3D97",
  "sip" : "enabled",
  "vmRegionInfo" : "0xff00000169 is not in any region.  Bytes after previous region: 614180323690  Bytes before following region: 104457899605655\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x000000ff00000169","rawCodes":[1,1095216660841],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000ff00000169"},
  "ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
  "vmregioninfo" : "0xff00000169 is not in any region.  Bytes after previous region: 614180323690  Bytes before following region: 104457899605655\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
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  "faultingThread" : 0,
  "threads" : 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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=3.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.1G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework              1152K        9 \nActivity Tracing                   256K        1 \nCG backing stores                 2944K        8 \nCG image                           380K       59 \nColorSync                          240K       28 \nCoreAnimation                      276K       29 \nCoreGraphics                        16K        3 \nCoreServices                       752K        3 \nCoreUI image data                 4372K       44 \nFoundation                          36K        2 \nKernel Alloc Once                    8K        1 \nMALLOC                             1.6G      552 \nMALLOC guard page                  192K       10 \nMALLOC_MEDIUM (reserved)         496.0M        6         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           256.0M        1         reserved VM address space (unallocated)\nMach message                        16K        4 \nOpenGL GLSL                        384K        4 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1380K      342 \nRosetta IndirectBranch            2048K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               840K       84 \nRosetta Thread Context             840K       84 \nSTACK GUARD                         32K        8 \nStack                            156.6M       43 \nStack Guard                       56.1M       35 \nVM_ALLOCATE                      244.2M      529 \nVM_ALLOCATE (reserved)           128.1M       19         reserved VM address space (unallocated)\n__DATA                            39.4M      727 \n__DATA_CONST                      39.6M      399 \n__DATA_DIRTY                      1760K      229 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       739.6M      196 \n__OBJC_RO                         81.8M        1 \n__OBJC_RW                         3136K        2 \n__TEXT                           845.9M      729 \n__UNICODE                          588K        1 \ndyld private memory               1152K        3 \nmapped file                        5.7G     1301 \nshared memory                     3012K       21 \nunshared pmap                     11.0M        9 \n===========                     =======  ======= \nTOTAL                             10.4G     5532 \nTOTAL, minus reserved VM space     9.6G     5532 \n",
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      "factorPackIds" : {

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}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> open /Users/michaelakaoullas/Documents/PhD/Structures/XY6/M4R-ACh-
> XY6_real_space_refined_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_MGK.cxs

opened ChimeraX session  

> open
> /Users/michaelakaoullas/Documents/PhD/Results/CryoEM/M4mGsi_ACh_CVL231/RealSpaceRefine_64/M4RmGsi_AChCVL_refine_34_refine_11_JM_MGK_refine_59_v2_refine_061_v2_refine_62_JM_real_space_refined_064.pdb

Chain information for
M4RmGsi_AChCVL_refine_34_refine_11_JM_MGK_refine_59_v2_refine_061_v2_refine_62_JM_real_space_refined_064.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
N | No description available  
R | No description available  
  

> hide atoms

> show cartoons

> select add #2

8001 atoms, 8172 bonds, 2 pseudobonds, 1029 residues, 2 models selected  

> ui tool show "Color Actions"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color sel light steel blue

> select subtract #2

Nothing selected  

> hide #2.1 models

> dssp

> open
> /Users/michaelakaoullas/Documents/PhD/Results/CryoEM/M4mGsi_xanomeline_MK6884/RealSpaceRefine_46/M4R_mGsi_xano_MK6884_real_space_refined_44_real_space_refined_045-coot-0_real_space_refined_046.pdb

Chain information for
M4R_mGsi_xano_MK6884_real_space_refined_44_real_space_refined_045-coot-0_real_space_refined_046.pdb
#3  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
N | No description available  
R | No description available  
  

> hide #3.1 models

> hide atoms

> show cartoons

> dssp

> select add #3

7982 atoms, 8156 bonds, 2 pseudobonds, 1026 residues, 2 models selected  

> color sel thistle

> select subtract #3

Nothing selected  

> open 7trp

7trp title:  
Human M4 muscarinic acetylcholine receptor complex with Gi1 and the agonist
iperoxo and positive allosteric modulator LY2033298 [more info...]  
  
Chain information for 7trp #4  
---  
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  
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 2-71  
H | Antibody fragment scFv16 |   
R | Muscarinic acetylcholine receptor M4 | ACM4_HUMAN 1-387 388-479  
  
Non-standard residues in 7trp #4  
---  
IUE — 3-amino-5-chloro-N-
cyclopropyl-6-methoxy-4-methylthieno[2,3-b]pyridine-2-carboxamide  
IXO — 4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium
(Iperoxo)  
  

> hide atoms

> show cartoons

> hide #4.1 models

> dssp

> select add #4

8681 atoms, 8869 bonds, 3 pseudobonds, 1124 residues, 2 models selected  

> color sel gray

> color sel light gray

> color sel gainsboro

> color sel tan

> color sel burly wood

> color sel tan

> select clear

> open 7trs

7trs title:  
Human M4 muscarinic acetylcholine receptor complex with Gi1 and the endogenous
agonist acetylcholine [more info...]  
  
Chain information for 7trs #5  
---  
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  
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 2-71  
H | Antibody fragment scFv16 |   
R | Muscarinic acetylcholine receptor M4 | ACM4_HUMAN 1-387 388-479  
  
Non-standard residues in 7trs #5  
---  
ACH — acetylcholine  
  

> hide atoms

> show cartoons

> select add #5

8571 atoms, 8757 bonds, 3 pseudobonds, 1122 residues, 2 models selected  

> hide #5.1 models

> dssp

> color sel misty rose

> color sel wheat

> color sel silver

> color sel dim gray

> color sel gray

> color sel gainsboro

> select clear

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #!2-5 to #1/R pairing bs

Parameters  
---  
Chain pairing | bs  
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 M4R-ACh-
XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb,
chain R (#1) with
M4RmGsi_AChCVL_refine_34_refine_11_JM_MGK_refine_59_v2_refine_061_v2_refine_62_JM_real_space_refined_064.pdb,
chain R (#2), sequence alignment score = 1395.3  
RMSD between 266 pruned atom pairs is 0.635 angstroms; (across all 270 pairs:
0.706)  
  
Matchmaker M4R-ACh-
XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb,
chain R (#1) with
M4R_mGsi_xano_MK6884_real_space_refined_44_real_space_refined_045-coot-0_real_space_refined_046.pdb,
chain R (#3), sequence alignment score = 1395.9  
RMSD between 263 pruned atom pairs is 0.607 angstroms; (across all 268 pairs:
0.698)  
  
Matchmaker M4R-ACh-
XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb,
chain R (#1) with 7trp, chain R (#4), sequence alignment score = 1381.2  
RMSD between 267 pruned atom pairs is 0.475 angstroms; (across all 267 pairs:
0.475)  
  
Matchmaker M4R-ACh-
XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb,
chain R (#1) with 7trs, chain R (#5), sequence alignment score = 1400.4  
RMSD between 270 pruned atom pairs is 0.497 angstroms; (across all 270 pairs:
0.497)  
  

> select /a-h, n

31199 atoms, 31804 bonds, 8 pseudobonds, 4063 residues, 10 models selected  

> hide sel cartoons

> select clear

> select /r:413

70 atoms, 75 bonds, 5 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 70 atom styles  

> color sel byhetero

> select clear

> cartoon style width 1.3 thickness 0.3

> select /R:413:412:415

140 atoms, 145 bonds, 15 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 140 atom styles  

> color sel byhetero

> select /R:129:130:131

155 atoms, 155 bonds, 15 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 155 atom styles  

> color sel byhetero

> select /R:449:450:453:451:452

190 atoms, 195 bonds, 25 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 190 atom styles  

> color sel byhetero

> select /R:207:120:409

125 atoms, 120 bonds, 15 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 125 atom styles  

> color sel byhetero

> open 5dsg

5dsg title:  
Structure of the M4 muscarinic acetylcholine receptor (M4-mT4L) bound to
tiotropium [more info...]  
  
Chain information for 5dsg #6  
---  
Chain | Description | UniProt  
A B | Muscarinic acetylcholine receptor M4,Endolysin,Endolysin,Muscarinic acetylcholine receptor M4 | ACM4_HUMAN 22-226 390-478, ENLYS_BPT4 1002-1011 1018-1118  
  
Non-standard residues in 5dsg #6  
---  
0HK —
(1R,2R,4S,5S,7S)-7-{[hydroxy(dithiophen-2-yl)acetyl]oxy}-9,9-dimethyl-3-oxa-9-azoniatricyclo[3.3.1.0~2,4~]nonane
(Tiotropium)  
EDT — {[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)  
P6G — hexaethylene glycol (polyethylene glycol PEG400)  
PG6 — 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane  
  
5dsg mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| software_defined_assembly  
  

> select add #5

8671 atoms, 8853 bonds, 3 pseudobonds, 1134 residues, 6 models selected  

> select subtract #5

100 atoms, 96 bonds, 12 residues, 4 models selected  

> select add #4

8756 atoms, 8941 bonds, 3 pseudobonds, 1133 residues, 5 models selected  

> select subtract #4

75 atoms, 72 bonds, 9 residues, 3 models selected  

> select add #3

8032 atoms, 8204 bonds, 2 pseudobonds, 1032 residues, 4 models selected  

> select subtract #3

50 atoms, 48 bonds, 6 residues, 2 models selected  

> select add #2

8026 atoms, 8196 bonds, 2 pseudobonds, 1032 residues, 3 models selected  

> select subtract #2

25 atoms, 24 bonds, 3 residues, 1 model selected  

> select add #1

8731 atoms, 8921 bonds, 3 pseudobonds, 1131 residues, 2 models selected  

> select subtract #1

Nothing selected  

> select add #6

6516 atoms, 6636 bonds, 3 pseudobonds, 834 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #6/A

3254 atoms, 3309 bonds, 2 pseudobonds, 418 residues, 2 models selected  

> delete atoms (#!6 & sel)

> delete bonds (#!6 & sel)

> select #6 /B

3262 atoms, 3327 bonds, 1 pseudobond, 416 residues, 2 models selected  

> select clear

> hide #6.1 models

> select add #6

3262 atoms, 3327 bonds, 1 pseudobond, 416 residues, 2 models selected  

> color sel olive

> color sel olive drab

> color sel forest green

> color sel dark red

> color sel dark goldenrod

> color sel dim gray

> color sel gray

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #!2-6 to #1/R pairing bs

Parameters  
---  
Chain pairing | bs  
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 M4R-ACh-
XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb,
chain R (#1) with
M4RmGsi_AChCVL_refine_34_refine_11_JM_MGK_refine_59_v2_refine_061_v2_refine_62_JM_real_space_refined_064.pdb,
chain R (#2), sequence alignment score = 1395.3  
RMSD between 266 pruned atom pairs is 0.635 angstroms; (across all 270 pairs:
0.706)  
  
Matchmaker M4R-ACh-
XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb,
chain R (#1) with
M4R_mGsi_xano_MK6884_real_space_refined_44_real_space_refined_045-coot-0_real_space_refined_046.pdb,
chain R (#3), sequence alignment score = 1395.9  
RMSD between 263 pruned atom pairs is 0.607 angstroms; (across all 268 pairs:
0.698)  
  
Matchmaker M4R-ACh-
XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb,
chain R (#1) with 7trp, chain R (#4), sequence alignment score = 1381.2  
RMSD between 267 pruned atom pairs is 0.475 angstroms; (across all 267 pairs:
0.475)  
  
Matchmaker M4R-ACh-
XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb,
chain R (#1) with 7trs, chain R (#5), sequence alignment score = 1400.4  
RMSD between 270 pruned atom pairs is 0.497 angstroms; (across all 270 pairs:
0.497)  
  
Matchmaker M4R-ACh-
XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb,
chain R (#1) with 5dsg, chain B (#6), sequence alignment score = 1285.3  
RMSD between 212 pruned atom pairs is 0.853 angstroms; (across all 274 pairs:
2.423)  
  

> select subtract #6

Nothing selected  

> select add #5

8571 atoms, 8757 bonds, 3 pseudobonds, 1122 residues, 2 models selected  

> color sel lavender blush

> color sel light coral

> color sel medium purple

> color sel rosy brown

> select subtract #5

Nothing selected  

> select add #6

3262 atoms, 3327 bonds, 1 pseudobond, 416 residues, 2 models selected  

> color sel gray

> color sel silver

> color sel light gray

> color sel gainsboro

> color sel light gray

> select clear

> select /R:413:412:415:129:130:131:449:450:453:451:452:207:120:409

610 atoms, 615 bonds, 70 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 610 atom styles  

> color sel byhetero

> select #6 /b:413:412:415:129:130:131:449:450:453:451:452:207:120:409

122 atoms, 123 bonds, 14 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 122 atom styles  

> color sel byhetero

> select clear

> cartoon style width 1.3 thickness 0.3 transparenc 60 cartoons

Expected a keyword  

> cartoon style width 1.3 thickness 0.3

> lighting soft multiShadow 128

> transparency 60 cartoons

> select /R:395

45 atoms, 40 bonds, 5 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 45 atom styles  

> color sel byhetero

> select #6 /B:395

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

> show sel atoms

> color sel byhetero

> select clear

> select add #6

3262 atoms, 3327 bonds, 1 pseudobond, 416 residues, 2 models selected  

> color sel gray

> color (#!6 & sel) byhetero

> select clear

> select #6 /B:394-1017

719 atoms, 738 bonds, 1 pseudobond, 91 residues, 2 models selected  

> select clear

> select #6 /B:1017-1118

788 atoms, 802 bonds, 102 residues, 1 model selected  

> hide sel cartoons

> select #6/B:1010

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

> select up

73 atoms, 73 bonds, 9 residues, 1 model selected  

> select up

1663 atoms, 1705 bonds, 213 residues, 1 model selected  

> select down

73 atoms, 73 bonds, 9 residues, 1 model selected  

> hide sel cartoons

> select #6/B:1011

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

> hide sel cartoons

> select clear

> select #6 /B:415

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

> select #6 /B:451

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

> hide sel atoms

> select /r:451

25 atoms, 20 bonds, 5 residues, 5 models selected  

> hide sel atoms

> select clear

> select ::name="ACH"

30 atoms, 27 bonds, 3 residues, 3 models selected  

> show sel atoms

> color sel byhetero

> select ::name="XNO"

19 atoms, 20 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel byhetero

> select ::name="IXO"

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

> show sel atoms

> color sel byhetero

> select clear

> ui tool show "Side View"

> transparency 80 cartoons

> view

> select /3:452

Nothing selected  

> select /r:452

30 atoms, 25 bonds, 5 residues, 5 models selected  

> hide sel atoms

> select #6 /B:452

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

> hide sel atoms

> select clear

> save "/Users/michaelakaoullas/Documents/PhD/Milestones/36
> Month/CVL_XanMK_XY6_7trp_7trs_5dsg.png" width 2000 height 1189 supersample 4

> save "/Users/michaelakaoullas/Documents/PhD/Milestones/36
> Month/CVL_XanMK_XY6_7trp_7trs_5dsg.cxs" includeMaps true

> select #6 /b:413:412:415:129:130:131:449:450:453:451:452:207:120:409

122 atoms, 123 bonds, 14 residues, 1 model selected  

> hide sel atoms

> select /r:413:412:415:129:130:131:449:450:453:451:452:207:120:409

610 atoms, 615 bonds, 70 residues, 5 models selected  

> hide sel atoms

> select /r:413:412:415:129:130:131:449:450:453:451:452:207:120:409:395

655 atoms, 655 bonds, 75 residues, 5 models selected  

> hide sel atoms

> select #6 /b:413:412:415:129:130:131:449:450:453:451:452:207:120:409:395

131 atoms, 131 bonds, 15 residues, 1 model selected  

> hide sel atoms

> select clear

> select add #1

8731 atoms, 8921 bonds, 3 pseudobonds, 1131 residues, 2 models selected  

> select add #2

16732 atoms, 17093 bonds, 5 pseudobonds, 2160 residues, 4 models selected  

> select add #3

24714 atoms, 25249 bonds, 7 pseudobonds, 3186 residues, 6 models selected  

> select add #4

33395 atoms, 34118 bonds, 10 pseudobonds, 4310 residues, 8 models selected  

> select add #5

41966 atoms, 42875 bonds, 13 pseudobonds, 5432 residues, 10 models selected  

> show sel cartoons

> select clear

> transparency 0 cartoons

> select g

Expected an objects specifier or a keyword  

> select /h

5337 atoms, 5475 bonds, 3 pseudobonds, 704 residues, 6 models selected  

> hide sel cartoons

> select /n

1948 atoms, 1992 bonds, 256 residues, 2 models selected  

> hide sel cartoons

> select clear

> select /b

16173 atoms, 16473 bonds, 1 pseudobond, 2110 residues, 7 models selected  

> hide sel cartoons

> select /g

2091 atoms, 2121 bonds, 282 residues, 5 models selected  

> hide sel cartoons


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

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache: 8 MB
      Memory: 8 GB

Software:

    System Software Overview:

      System Version: macOS 12.1 (21C52)
      Kernel Version: Darwin 21.2.0
      Time since boot: 2 days 5:10

Graphics/Displays:

    Apple G13G:

      Chipset Model: Apple G13G
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        PHL 241S9:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (3)

comment:1 by Eric Pettersen, 7 months ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Some kind of memory/pager failure

comment:2 by Eric Pettersen, 7 months ago

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

comment:3 by Tom Goddard, 7 months ago

Unfortunately running Intel ChimeraX on Mac ARM machine with only 8 GB of memory.

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