![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 11 months ago
Closed 11 months ago
#16309 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.7.1-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202404140648 (2024-04-14 06:48:11 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 0x00007ff844446f80 (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 283 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 1006 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 1169 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, chimerax.surface._surface, chimerax.pdb_lib._load_libs, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, PIL._webp, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct (total: 116)
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{
"uptime" : 67000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 1699,
"osVersion" : {
"train" : "macOS 14.7.1",
"build" : "23H222",
"releaseType" : "User"
},
"captureTime" : "2024-11-14 15:22:06.5909 +0000",
"codeSigningMonitor" : 0,
"incident" : "E27EC1B4-B414-42AE-A874-DF92EF5BFC7C",
"pid" : 65374,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-11-14 12:56:35.4638 +0000",
"procStartAbsTime" : 58561083974000,
"procExitAbsTime" : 67292317375180,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"7FF298D8-9CAA-50B0-B14E-B75862530066","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "29B489BC-839B-868D-A960-82E747B97847",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 9812,
"bridgeVersion" : {"build":"22P1072","train":"9.1"},
"sleepWakeUUID" : "24F4AE09-09B2-45EF-A953-32CA4C716F4F",
"sip" : "enabled",
"vmRegionInfo" : "0x38bb90129ef8 is not in any region. Bytes after previous region: 62371998445305 Bytes before following region: 43174889087240\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n VM_ALLOCATE (reserved) 17142f000-17342f000 [ 32.0M] rw-\/rwx SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5ffe8cbd1000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000038bb90129ef8","rawCodes":[1,62378227179256],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000038bb90129ef8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":65374},
"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\n",
"vmregioninfo" : "0x38bb90129ef8 is not in any region. Bytes after previous region: 62371998445305 Bytes before following region: 43174889087240\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n VM_ALLOCATE (reserved) 17142f000-17342f000 [ 32.0M] rw-\/rwx SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5ffe8cbd1000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"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,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202404140648 (2024-04-14)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by Justin/PGE2
> bound/PGE2-bound-selected/cryosparc_P124_J82_009_volume_map (6).mrc"
Opened cryosparc_P124_J82_009_volume_map (6).mrc as #1, grid size 392,392,392,
pixel 0.732, shown at level 0.0253, step 2, values float32
> volume #1 level 0.06345
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by Justin/PGE2
> bound/PGE2-bound-selected/AF_combined_coot3_P2E.pdb"
AF_combined_coot3_P2E.pdb title:
Alphafold monomer V2.0 prediction for solute carrier organic anion transporter
family member 2A1 (Q00910) [more info...]
Chain information for AF_combined_coot3_P2E.pdb #2
---
Chain | Description | UniProt
A | solute carrier organic anion transporter family member 2A1 | SO2A1_RAT 1-644
Non-standard residues in AF_combined_coot3_P2E.pdb #2
---
P2E — (P2E)
> open "/Users/chitrajoshi/Desktop/SLCO2A1/structure/PDB
> release/P2E/8kgw-2.pdb"
8kgw-2.pdb title:
Molecular mechanism of prostaglandin transporter SLCO2A1 [more info...]
Chain information for 8kgw-2.pdb #3
---
Chain | Description | UniProt
A | solute carrier organic anion transporter family member 2A1 | SO2A1_HUMAN 1-643
Non-standard residues in 8kgw-2.pdb #3
---
P2E — (Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-
cyclopentyl]hept-5-enoic acid (prostaglandin E2)
> hide #!1 models
> set bgColor white
> set bgColor #ffffff00
> color #2 darkgrey
> color #2 #929292ff
> color #2 darkgrey
> color #2 #929292ff
> color #3 #945200ff
> color #3 #9452002c
> color #3 #8b48802c
> color #3 #8b4880ff
> color #3 #8b6a0dff
> select #3/A
4036 atoms, 4144 bonds, 3 pseudobonds, 533 residues, 2 models selected
> ui tool show "Color Actions"
> color sel goldenrod
> color sel dark goldenrod
> color sel wheat
> color sel khaki
> color sel wheat
> color sel beige
> color sel wheat
> color sel tan
> color sel burly wood
> color sel tan
> color sel rosy brown
> color sel tan
> color sel wheat
> color sel tan
> color sel light gray
> color sel silver
> color sel tan
> select clear
> ui tool show Matchmaker
> matchmaker #!3 to #2
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_combined_coot3_P2E.pdb, chain A (#2) with 8kgw-2.pdb, chain A
(#3), sequence alignment score = 2463.3
RMSD between 414 pruned atom pairs is 1.192 angstroms; (across all 526 pairs:
1.849)
> matchmaker #!3 to #2
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_combined_coot3_P2E.pdb, chain A (#2) with 8kgw-2.pdb, chain A
(#3), sequence alignment score = 2463.3
RMSD between 414 pruned atom pairs is 1.192 angstroms; (across all 526 pairs:
1.849)
> hide #!3 models
> select ::name="P2E"
81 atoms, 81 bonds, 2 residues, 2 models selected
> color (#!2 & sel) byelement
> color (#!2 & sel) byhetero
> surface (#!2 & sel)
> transparency (#!2 & sel) 90
> select clear
> transparency #2 80
> select #2/A
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> hide (#!2 & sel) target a
> select ::name="P2E"
81 atoms, 81 bonds, 2 residues, 2 models selected
> show (#!2 & sel) target ab
> color (#!2 & sel) byelement
> undo
> select clear
> save "/Users/chitrajoshi/Desktop/SLCO2A1/Meeting with Phil/Outward open PGE2
> bound RnSLCO2A1.png" width 974 height 803 supersample 4
> save "/Users/chitrajoshi/Desktop/SLCO2A1/Meeting with Phil/Outward open PGE2
> bound RnSLCO2A1 transparent.png" width 974 height 803 supersample 4
> transparentBackground true
> save "/Users/chitrajoshi/Desktop/SLCO2A1/Meeting with Phil/Transparent
> tiff.tif" width 974 height 803 supersample 3 transparentBackground true
> select ::name="P2E"
81 atoms, 81 bonds, 2 residues, 2 models selected
> transparency (#!2 & sel) 70
> select clear
> save /Users/chitrajoshi/Desktop/image1.png supersample 3
> save /Users/chitrajoshi/Desktop/image2.png supersample 3
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> select #2/A
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> cartoon style (#!2 & sel) xsection oval modeHelix default
> cartoon style (#!2 & sel) xsection rectangle modeHelix default
> cartoon style (#!2 & sel & coil) xsection oval
> cartoon style (#!2 & sel) xsection barbell modeHelix default
> cartoon style (#!2 & sel) xsection oval modeHelix default
> cartoon style (#!2 & sel) modeHelix tube sides 20
> select clear
> select #2/A
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> nucleotides sel tube/slab shape muffler
> nucleotides sel tube/slab shape ellipsoid
> nucleotides sel tube/slab shape box
> nucleotides sel slab
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> nucleotides sel tube/slab shape box
> select clear
> save /Users/chitrajoshi/Desktop/image3.png supersample 3
> select #2/A
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> cartoon style (#!2 & sel) xsection oval modeHelix default
> show #!3 models
> hide #!2 models
> select #3/A
4036 atoms, 4144 bonds, 3 pseudobonds, 533 residues, 2 models selected
> cartoon style (#!3 & sel) xsection oval modeHelix default
> hide (#!3 & sel) target a
> select ::name="P2E"
81 atoms, 81 bonds, 2 residues, 2 models selected
> show (#!3 & sel) target ab
> surface (#!3 & sel)
> transparency (#!3 & sel) 70
> color (#!3 & sel) byelement
> undo
> surface hidePatches (#!3 & sel)
> color (#!3 & sel) byelement
> select ::name="CYS"
239 atoms, 205 bonds, 40 residues, 2 models selected
> select ::name="P2E"
81 atoms, 81 bonds, 2 residues, 2 models selected
> surface style #3 solid
> surface (#!3 & sel)
> transparency (#!3 & sel) 70
> color (#!3 & sel) byhetero
> select ::name="P2E"
81 atoms, 81 bonds, 2 residues, 2 models selected
> surface hidePatches (#!3 & sel)
> color (#!3 & sel) byhetero
> show sel & #!3 surfaces
> style sel & #!3 stick
Changed 25 atom styles
> style sel & #!3 sphere
Changed 25 atom styles
> style sel & #!3 ball
Changed 25 atom styles
> surface hidePatches (#!3 & sel)
> style sel & #!3 stick
Changed 25 atom styles
> select #3/A
4036 atoms, 4144 bonds, 3 pseudobonds, 533 residues, 2 models selected
> surface (#!3 & sel)
> transparency (#!3 & sel) 70
> surface hidePatches (#!3 & sel)
> select ligand
81 atoms, 81 bonds, 2 residues, 2 models selected
> surface (#!3 & sel)
> hide #* target a
> show (#!3 & sel) target ab
> ui tool show "Color Actions"
> color (#!3 & sel) byelement
> transparency (#!3 & sel) 70
> ui tool show "Color Actions"
> color sel tan target s
> transparency (#!3 & sel) 70
> select clear
> show #!2 models
> hide #!2 models
> save /Users/chitrajoshi/Desktop/image4.png supersample 3
> show #!2 models
> surface hidePatches #2-3
> select ::name="P2E"
81 atoms, 81 bonds, 2 residues, 2 models selected
> show (#!2-3 & sel) target ab
> select clear
> select #2/A
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> select ::name="P2E"
81 atoms, 81 bonds, 2 residues, 2 models selected
> surface (#!2-3 & sel)
> transparency (#!2-3 & sel) 70
> select clear
> surface hidePatches #2-3
> save /Users/chitrajoshi/Desktop/image5.png supersample 3
> cartoon style #2-3 modeHelix tube sides 20
> cartoon style #2-3 xsection oval modeHelix default
> select strand
233 atoms, 229 bonds, 30 residues, 2 models selected
> select helix
5433 atoms, 5530 bonds, 693 residues, 2 models selected
> cartoon hide (#!2-3 & sel)
> select coil
2606 atoms, 2622 bonds, 4 pseudobonds, 362 residues, 4 models selected
> cartoon hide (#!2-3 & sel)
> undo
> hide #!3 models
> select main
8272 atoms, 8492 bonds, 4 pseudobonds, 1085 residues, 4 models selected
> cartoon hide (#!2 & sel)
> undo
> show #!3 models
> hide #!3 models
> select main
8272 atoms, 8492 bonds, 4 pseudobonds, 1085 residues, 4 models selected
> cartoon hide (#!2 & sel)
> surface (#!2 & sel)
> undo
> surface hidePatches (#!2 & sel)
> cartoon hide (#!2 & sel)
> select ligand
81 atoms, 81 bonds, 2 residues, 2 models selected
> surface (#!2 & sel)
> transparency (#!2 & sel) 80
> surface style #2.2 mesh
> surface (#!2 & sel)
> surface style #2.2 solid
> transparency (#!2 & sel) 90
> ui tool show "Color Actions"
> color sel dark gray target s
> transparency (#!2 & sel) 90
> select clear
> save /Users/chitrajoshi/Desktop/image6.png supersample 3
> save /Users/chitrajoshi/Desktop/image7.png supersample 3
> surface hidePatches #2
> show #!3 models
> hide #!2 models
> select main
8272 atoms, 8492 bonds, 4 pseudobonds, 1085 residues, 4 models selected
> cartoon hide (#!3 & sel)
> show #!2 models
> hide #!2 models
> surface (#!3 & sel)
> surface hidePatches (#!3 & sel)
> select ligand
81 atoms, 81 bonds, 2 residues, 2 models selected
> surface (#!3 & sel)
> transparency (#!3 & sel) 90
> ui tool show "Color Actions"
> color sel tan target s
> transparency (#!3 & sel) 90
> select clear
> save /Users/chitrajoshi/Desktop/image8.png supersample 3
> save /Users/chitrajoshi/Desktop/image9.png supersample 3
> show #!2 models
> hide #!3 models
> select ligand
81 atoms, 81 bonds, 2 residues, 2 models selected
> hide #* target a
> show (#!2 & sel) target ab
> hide (#!2 & sel) target a
> show (#!2 & sel) target ab
> style (#!2 & sel) stick
Changed 56 atom styles
> show (#!2 & sel-residues & sidechain) target ab
> hide (#!2 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!2 & sel-residues)
> show (#!2 & sel-residues & backbone) target ab
> show sel & #!2 atoms
> show #!3 models
> hide #!2 models
> show sel & #!3 atoms
> style sel & #!3 ball
Changed 25 atom styles
> style sel & #!3 stick
Changed 25 atom styles
> show #!2 models
> hide #!3 models
> select main
8272 atoms, 8492 bonds, 4 pseudobonds, 1085 residues, 4 models selected
> cartoon (#!2 & sel)
> select ligand
81 atoms, 81 bonds, 2 residues, 2 models selected
> hide #* target a
> show (#!2 & sel) target ab
> select #2/A
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> show (#!2 & sel) target ab
> hide (#!2 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!2 & sel-residues)
> show (#!2 & sel-residues & backbone) target ab
> undo
> select main
8272 atoms, 8492 bonds, 4 pseudobonds, 1085 residues, 4 models selected
> cartoon (#!2 & sel)
> show (#!2 & sel) target ab
> color (#!2 & sel) byhetero
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> undo
> surface hidePatches (#!2 & sel)
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> surface hidePatches (#!2 & sel)
> preset "molecular surfaces" "chain id coloring (opaque)"
Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> surface hidePatches (#!2 & sel)
> select clear
> view
> ui tool show "Side View"
> select main
8272 atoms, 8492 bonds, 4 pseudobonds, 1085 residues, 4 models selected
> hide (#!2 & sel) target a
> select clear
> save /Users/chitrajoshi/Desktop/image10.png supersample 3
> show #!3 models
> hide #!2 models
> surface hidePatches #3
> cartoon #3
> select ligand
81 atoms, 81 bonds, 2 residues, 2 models selected
> show (#!3 & sel) target ab
> select clear
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> select ligand
81 atoms, 81 bonds, 2 residues, 2 models selected
> ui tool show "Color Actions"
> color sel tan target as
> color sel rosy brown target cs
> color sel tan target cs
> color sel bychain target acs
> color sel byhetero target acs
> color sel tan target acs
> color sel byhetero target acs
> show #!2 models
> hide #!3 models
> select ligand
81 atoms, 81 bonds, 2 residues, 2 models selected
> ui tool show "Color Actions"
> color sel silver target acs
> color sel gray target acs
> color sel dim gray target acs
> color sel gray target acs
> color sel byhetero target acs
> select clear
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> select #3/A
4036 atoms, 4144 bonds, 3 pseudobonds, 533 residues, 2 models selected
> ui tool show "Color Actions"
> color sel tan target acs
> color sel byhetero target acs
> show #!2 models
> hide #!3 models
> select #2/A
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> hide (#!2 & sel) target a
> hide #* target a
> show (#!2 & sel) target ab
> hide (#!2 & sel) target a
> show (#!2 & sel) target ab
> hide (#!2 & sel) target a
> hide #* target a
> show (#!2 & sel) target ab
> hide (#!2 & sel) target a
> select ligand
81 atoms, 81 bonds, 2 residues, 2 models selected
> show (#!2 & sel) target ab
> select clear
> show #!3 models
> select ligand
81 atoms, 81 bonds, 2 residues, 2 models selected
> show (#!2-3 & sel) target ab
> select clear
> save /Users/chitrajoshi/Desktop/image11.png supersample 3
> select ::name="P2E"
81 atoms, 81 bonds, 2 residues, 2 models selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
Already setting window visible!
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
Already setting window visible!
> select
> #2/A:27-29,31-42,47-63,67-93,97-121,164-184,187-198,204-212,221-231,257-276,309-323,325-339,345-356,360-369,379-388,396-415,443-445,512-532,534-542,546-548,550-557,569-579,599-634
2613 atoms, 2656 bonds, 330 residues, 1 model selected
> select #2/A:27
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:27-42
127 atoms, 129 bonds, 16 residues, 1 model selected
> select #2/A:27
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:27-63
303 atoms, 309 bonds, 37 residues, 1 model selected
> select clear
> select #2/A:599
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:579-580
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #2/A:569-580
87 atoms, 88 bonds, 12 residues, 1 model selected
> select #2/A:580-581
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/A:545-580
281 atoms, 287 bonds, 36 residues, 1 model selected
> select #2/A:599
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:599-634
311 atoms, 317 bonds, 36 residues, 1 model selected
> select #2/A:542-543
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #2/A:511-543
254 atoms, 259 bonds, 33 residues, 1 model selected
> select #2/A:546
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:546-579
267 atoms, 273 bonds, 34 residues, 1 model selected
> select #2/A:542
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:512-542
241 atoms, 246 bonds, 31 residues, 1 model selected
> select #2/A:504
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:497-504
46 atoms, 45 bonds, 8 residues, 1 model selected
> select #2/A:508
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:450-508
409 atoms, 419 bonds, 59 residues, 1 model selected
> select
> #2/A:27-29,31-42,47-63,67-93,97-121,164-184,187-198,204-212,221-231,257-276,309-323,325-339,345-356,360-369,379-388,396-415,443-445,512-532,534-542,546-548,550-557,569-579,599-634
2613 atoms, 2656 bonds, 330 residues, 1 model selected
> select #2/A:415
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:396-415
150 atoms, 152 bonds, 20 residues, 1 model selected
> select #2/A:446
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:396-446
378 atoms, 388 bonds, 51 residues, 1 model selected
> select #2/A:388-389
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #2/A:378-388
83 atoms, 83 bonds, 11 residues, 1 model selected
> select #2/A:389
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:360-389
218 atoms, 222 bonds, 30 residues, 1 model selected
> select
> #3/A:30-64,66-91,96-122,169-184,186-198,203-215,217-230,256-278,307-312,314-333,338-346,348-357,360-390,396-411,414-419,468-473,511-515,521-530,533-564,567-579,598-629
2820 atoms, 2874 bonds, 363 residues, 1 model selected
> select #3/A:629
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:610-629
159 atoms, 162 bonds, 20 residues, 1 model selected
> select clear
> select #3/A:597-629
270 atoms, 275 bonds, 33 residues, 1 model selected
> select #3/A:579
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:533-579
375 atoms, 384 bonds, 47 residues, 1 model selected
> select #3/A:579-580
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/A:567-580
97 atoms, 99 bonds, 14 residues, 1 model selected
> select #3/A:580
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:551-580
230 atoms, 236 bonds, 30 residues, 1 model selected
> select #3/A:550
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:532-550
157 atoms, 159 bonds, 19 residues, 1 model selected
> select #3/A:550
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:521-550
238 atoms, 241 bonds, 30 residues, 1 model selected
> open
> /Users/chitrajoshi/Downloads/cryosparc_P73_J74_class_00_final_volume.mrc
Opened cryosparc_P73_J74_class_00_final_volume.mrc as #4, grid size
256,256,256, pixel 0.975, shown at level 0.213, step 1, values float32
> hide #!2 models
> hide #!3 models
> view
> volume #4 level 0.3638
> volume #4 level 0.3578
> surface dust #4 size 9.75
> volume #4 color #ffd996
> volume #4 level 0.3487
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202404140648 (2024-04-14)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-22.5.12
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
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 Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.11072.0.0,0)
OS Loader Version: 580.140.1~51
Software:
System Software Overview:
System Version: macOS 14.7.1 (23H222)
Kernel Version: Darwin 23.6.0
Time since boot: 3 days, 6 hours, 12 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56.1
ChimeraX-AtomicLibrary: 14.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202404140648
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
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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
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
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
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: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
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: 2.1
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: 1.0
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: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
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: 1.37.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4
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: 1.1.3
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: 3.13.3
fonttools: 4.51.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
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: 0.1.6
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.0.1
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: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
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: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.2.0
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: 2.0.0
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
traitlets: 5.14.2
typing-extensions: 4.11.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 11 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 11 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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