![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 20 months ago
Closed 20 months ago
#14619 closed defect (can't reproduce)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.5.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000117013600 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py", line 81 in msgpack_deserialize
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 721 in restore
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 1017 in open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 37 in open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1979 in _open_dropped_file
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 240 in event
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 61)
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{
"uptime" : 240000,
"procLaunch" : "2024-02-21 15:40:01.3544 +0000",
"procRole" : "Foreground",
"version" : 2,
"userID" : 504,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"procStartAbsTime" : 243501053801233,
"coalitionID" : 47191,
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"build" : "21G83",
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"captureTime" : "2024-02-21 18:18:36.4902 +0000",
"incident" : "3D02A25B-02E5-4CBB-8B13-4B3F41F6EE58",
"bug_type" : "309",
"pid" : 29281,
"procExitAbsTime" : 248867573350359,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"26114317-E94F-5880-8718-22492BDEBA24","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "15AC398D-6EF0-7941-5920-37C63E551743",
"wakeTime" : 3996,
"bridgeVersion" : {"build":"19P6066","train":"6.6"},
"sleepWakeUUID" : "F1B27756-9891-4630-889F-B2ED91F819E8",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737486925655\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffea3000-7fffffea4000 [ 4K] r-x\/r-x SM=ALI ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737486925655\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffea3000-7fffffea4000 [ 4K] r-x\/r-x SM=ALI ",
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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/mandywan/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Sin3B_Project/Writing/Thesis/Thesis_figures/Discussion_figs/Dinuc_struc_tails.pdb
> format pdb
Chain information for Dinuc_struc_tails.pdb #1
---
Chain | Description
A a | No description available
> open 8JHO
8jho title:
Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-
nucleosome [more info...]
Chain information for 8jho #2
---
Chain | Description | UniProt
A E a e | Histone H3 | A0A310TTQ1_XENLA 1-135
B F b f | Histone H4 | A0A8J1LTD2_XENLA 1-102
C G c g | Histone H2A | Q6AZJ8_XENLA 1-129
D H d h | Histone H2B | A0A8J0U496_XENLA 1-122
I | Di-nucleosome template foward |
J | Di-nucleosome template reverse |
K | Transcriptional regulatory protein SIN3 | SIN3_YEAST 1-1536
L | Histone deacetylase RPD3 | RPD3_YEAST 1-433
M O | Chromatin modification-related protein EAF3 | A0A8H4F719_YEASX 1-401
N P | RCO1 isoform 1 | A0A8H4BXB0_YEASX 1-684
Non-standard residues in 8jho #2
---
ML3 — 2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-N,N,N-trimethylethanaminium
ZN — zinc ion
> hide #1 models
> show #1 models
> hide surfaces
> hide cartoons
> hide atoms
> show atoms
> style stick
Changed 42987 atom styles
> nucleotides atoms
> style nucleic stick
Changed 13940 atom styles
> nucleotides atoms
> style nucleic stick
Changed 13940 atom styles
> style stick
Changed 42987 atom styles
> hide atoms
> show cartoons
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> cartoon style nucleic xsection oval width 1.6 thickness 1.6
> color #2/I,J rgb(0.4,0.4,0.4)
> nucleotides ladder
> nucleotides stubs
> show atoms
> undo
> show #2/I,J atoms
> cartoon style #1 thickness 1.6
> ui tool show "Show Sequence Viewer"
> color #1 rgb(1,1,0.5)
> color #1 rgb(1.0,1.0,0.5)
> color #2/K slate blue
> color #2/M,O dark cyan
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> color #2/N,P deep pink
> color #2/L burly wood
> color #A,E,a,e rgb(1.0,1.0,0.5)
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /A,E,a,e rgb(1.0,1.0,0.5)
> color /B,F,b,f rgb(0.65,0.9,0.65)
> color /C,G,c,g rgb(0.0,0.5,1.0)
> color /D,H,d,h rgb(1.0,0.75,0.87)
Drag select of 3 residues, 2 shapes
> save "/Users/mandywan/OneDrive - The Institute of Cancer
> Research/Sin3B_Project/Writing/Thesis/Thesis_figures/Discussion_figs/Dinucleosome_struc2.cxs"
> includeMaps true
> open 36283 fromDatabase emdb
Opened emdb 36283 as #3, grid size 400,400,400, pixel 1.05, shown at level
0.0066, step 2, values float32, fit PDB 8jho
> transparency 70%
Missing or invalid "percent" argument: Expected a number
> transparency 70
> volume #3 step 1
> volume #3 level 0.0066
> volume #3 level 0.007564
> volume #3 level 0.00925
> volume #3 level 0.009009
> open 7HXY
Fetching url http://files.rcsb.org/download/7hxy.cif failed:
HTTP Error 404: Not Found
> open 8HXY
Summary of feedback from opening 8HXY fetched from pdb
---
note | Fetching compressed mmCIF 8hxy from
http://files.rcsb.org/download/8hxy.cif
8hxy title:
Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with
nucleosome [more info...]
Chain information for 8hxy #4
---
Chain | Description | UniProt
A E | Histone H3 | A0A310TTQ1_XENLA 1-135
B F | Histone H4 | A0A8J1LTD2_XENLA 1-102
C G | Histone H2A | Q6AZJ8_XENLA 1-129
D H | Histone H2B | A0A8J0U496_XENLA 1-122
I | DNA (352-MER) |
J | DNA (352-MER) |
K | Transcriptional regulatory protein SIN3 | SIN3_YEAST 1-1536
L | Histone deacetylase RPD3 | RPD3_YEAST 1-433
M | Chromatin modification-related protein EAF3 | A0A8H4F719_YEASX 1-401
N P | Transcriptional regulatory protein RCO1 | A0A8H4BXB0_YEASX 1-684
Non-standard residues in 8hxy #4
---
ML3 — 2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-N,N,N-trimethylethanaminium
ZN — zinc ion
> style sel stick
Changed 63 atom styles
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> undo
> cartoon style #4
8hxy #4
\- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow
scale=2
\- strand mode=default xsection=square width=2 height=0.4 arrow=True arrow
scale=2
\- coil xsection=round width=0.4 height=0.4
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
> cartoon #4
> select add #4
26263 atoms, 27486 bonds, 460 pseudobonds, 2725 residues, 4 models selected
> ui tool show "Fit in Map"
> fitmap #4 inMap #3
Fit molecule 8hxy (#4) to map emdb 36283 (#3) using 26263 atoms
average map value = -5.779e-06, steps = 324
shifted from previous position = 55.5
rotated from previous position = 38.9 degrees
atoms outside contour = 26263, contour level = 0.0090094
Position of 8hxy (#4) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.80736002 0.35625844 0.47037190 -134.98102382
-0.22657756 0.92322711 -0.31034546 99.70702296
-0.54482328 0.14398479 0.82609683 95.91162550
Axis 0.36181977 0.80848169 -0.46415925
Axis point 67.84594802 0.00000000 304.94847640
Rotation angle (degrees) 38.89098156
Shift along axis -12.74576899
> select subtract #4
Nothing selected
Average map value = -5.779e-06 for 26263 atoms, 26263 outside contour
> fitmap #4 inMap #3
Fit molecule 8hxy (#4) to map emdb 36283 (#3) using 26263 atoms
average map value = -5.779e-06, steps = 40
shifted from previous position = 0.0119
rotated from previous position = 0.0071 degrees
atoms outside contour = 26263, contour level = 0.0090094
Position of 8hxy (#4) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.80741227 0.35626966 0.47027370 -134.97452409
-0.22657182 0.92320907 -0.31040331 99.72827462
-0.54474823 0.14407267 0.82613100 95.88488871
Axis 0.36196027 0.80839830 -0.46419496
Axis point 67.81678095 0.00000000 304.97599705
Rotation angle (degrees) 38.88786113
Shift along axis -12.74452944
> hide #4
> fitmap #4 inMap #3
Fit molecule 8hxy (#4) to map emdb 36283 (#3) using 26263 atoms
average map value = -5.779e-06, steps = 48
shifted from previous position = 0.0166
rotated from previous position = 0.00735 degrees
atoms outside contour = 26263, contour level = 0.0090094
Position of 8hxy (#4) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.80735451 0.35627455 0.47036915 -134.98527098
-0.22659650 0.92322245 -0.31034551 99.70635686
-0.54482357 0.14397485 0.82609837 95.91438897
Axis 0.36180881 0.80847284 -0.46418320
Axis point 67.84459739 0.00000000 304.95593493
Rotation angle (degrees) 38.89137536
Shift along axis -12.75082748
> fitmap #4 inMap #3
Fit molecule 8hxy (#4) to map emdb 36283 (#3) using 26263 atoms
average map value = -5.779e-06, steps = 40
shifted from previous position = 0.0153
rotated from previous position = 0.00868 degrees
atoms outside contour = 26263, contour level = 0.0090094
Position of 8hxy (#4) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.80742132 0.35626006 0.47026543 -134.97182215
-0.22655219 0.92320864 -0.31041893 99.72552448
-0.54474297 0.14409920 0.82612984 95.88026602
Axis 0.36199650 0.80839348 -0.46417510
Axis point 67.80906704 0.00000000 304.96819286
Rotation angle (degrees) 38.88752089
Shift along axis -12.74709612
> fitmap #4 inMap #3
Fit molecule 8hxy (#4) to map emdb 36283 (#3) using 26263 atoms
average map value = -5.778e-06, steps = 40
shifted from previous position = 0.0152
rotated from previous position = 0.00415 degrees
atoms outside contour = 26263, contour level = 0.0090094
Position of 8hxy (#4) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.80739356 0.35625613 0.47031607 -134.97645811
-0.22656535 0.92321956 -0.31037685 99.70516412
-0.54477865 0.14403895 0.82611682 95.89614245
Axis 0.36190433 0.80843838 -0.46416876
Axis point 67.82497140 0.00000000 304.95208714
Rotation angle (degrees) 38.88888349
Shift along axis -12.75507699
> ui tool show Matchmaker
> matchmaker #!4 to #1
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 Dinuc_struc_tails.pdb, chain A (#1) with 8hxy, chain A (#4),
sequence alignment score = 48.4
RMSD between 10 pruned atom pairs is 0.173 angstroms; (across all 10 pairs:
0.173)
> undo
> redo
> open 35082 fromDatabase emdb
Summary of feedback from opening 35082 fetched from emdb
---
notes | Fetching compressed map 35082 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35082/map/emd_35082.map.gz
Fetching map header 35082 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35082/header/emd-35082.xml
Opened emdb 35082 as #5, grid size 256,256,256, pixel 1.05, shown at level
0.03, step 1, values float32, fit PDB 8hxy
> fitmap #4 inMap #5
Fit molecule 8hxy (#4) to map emdb 35082 (#5) using 26263 atoms
average map value = 0.0008659, steps = 288
shifted from previous position = 66.4
rotated from previous position = 24.1 degrees
atoms outside contour = 26263, contour level = 0.03
Position of 8hxy (#4) relative to emdb 35082 (#5) coordinates:
Matrix rotation and translation
0.18211634 -0.62546900 -0.75869768 427.26680800
-0.91436876 -0.39149278 0.10326262 461.95502534
-0.36161223 0.67492365 -0.64320655 190.94153111
Axis 0.75855799 -0.52690725 -0.38335169
Axis point 0.00000000 354.38060411 263.50739153
Rotation angle (degrees) 157.86391425
Shift along axis 7.50144247
> hide #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> close #5
> volume #3 level 0.007564
> surface #2/
Expected an atoms specifier or a keyword
> surface #2/L
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> color /C,G,c,g royal blue
> color /D,H,d,h (1.0,0.75,0.87)
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /D,H,d,h rgb(1.0,0.75,0.87)
> transparency #2 50
> transparency #2 70
> transparency #2 20
> transparency #2 30
> transparency #2 40
> color #2/L rgb(0.99,0.82,0.65)
> transparency #2 40
> transparency #2 30
> transparency #2 20
> transparency #2 10
> transparency #2 50
> transparency #2 40
> lighting simple
> lighting soft
> lighting full
> transparency #3 40
> transparency #3 50
> transparency #3 70
> transparency #3 30
> transparency #3 40
> transparency #3 30
> transparency #3 50
> surface #2/N,M,L,K
> surface #2/N,M,L,K,O,P
> undo
> surface #2/N,M,L,K
> hide surfaces #2/O,P
Expected ',' or a keyword
> hide surfaces #2/O,P
Expected ',' or a keyword
> ~surface #2/O,P
> ~surface #2/N,M,L,K
> open 35081 fromDatabase emdb
Summary of feedback from opening 35081 fetched from emdb
---
notes | Fetching compressed map 35081 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35081/map/emd_35081.map.gz
Fetching map header 35081 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35081/header/emd-35081.xml
Opened emdb 35081 as #5, grid size 256,256,256, pixel 1.05, shown at level
0.0135, step 1, values float32, fit PDB 8hxx
> fitmap #2 inMap #3
Fit molecule 8jho (#2) to map emdb 36283 (#3) using 42813 atoms
average map value = 0.01303, steps = 84
shifted from previous position = 1.49
rotated from previous position = 1.15 degrees
atoms outside contour = 13151, contour level = 0.0075638
Position of 8jho (#2) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.99981319 -0.01519254 -0.01194854 5.69483194
0.01525831 0.99986883 0.00543239 -3.32790881
0.01186444 -0.00561369 0.99991386 -2.16352830
Axis -0.27475368 -0.59230995 0.75741623
Axis point 268.94024873 349.25268408 0.00000000
Rotation angle (degrees) 1.15182564
Shift along axis -1.23221400
> fitmap #5 inMap #3
Fit map emdb 35081 in map emdb 36283 using 77178 points
correlation = 0.7408, correlation about mean = 0.133, overlap = 2.29
steps = 628, shift = 124, angle = 12.2 degrees
Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.98920703 0.12489032 0.07662806 -14.23972201
-0.11171858 0.98124879 -0.15706611 59.98940524
-0.09480723 0.14681012 0.98461077 115.50987072
Axis 0.72083386 0.40666677 -0.56126703
Axis point 0.00000000 -532.50448220 576.78120646
Rotation angle (degrees) 12.16812733
Shift along axis -50.70065828
> fitmap #5 inMap #3
Fit map emdb 35081 in map emdb 36283 using 77178 points
correlation = 0.7409, correlation about mean = 0.133, overlap = 2.29
steps = 44, shift = 0.0172, angle = 0.00855 degrees
Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.98922680 0.12476281 0.07658057 -14.23385105
-0.11160550 0.98127227 -0.15699984 59.96184917
-0.09473413 0.14676164 0.98462504 115.49857769
Axis 0.72101794 0.40663804 -0.56105136
Axis point 0.00000000 -532.81392555 576.74552571
Rotation angle (degrees) 12.16030948
Shift along axis -50.68072740
> fitmap #5 inMap #3
Fit map emdb 35081 in map emdb 36283 using 77178 points
correlation = 0.7409, correlation about mean = 0.133, overlap = 2.29
steps = 40, shift = 0.00512, angle = 0.0116 degrees
Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.98925306 0.12456976 0.07655558 -14.20980922
-0.11142405 0.98130346 -0.15693374 59.91995306
-0.09467346 0.14671705 0.98463752 115.49234470
Axis 0.72131112 0.40674820 -0.56059447
Axis point -0.00000000 -533.38445172 576.56621718
Rotation angle (degrees) 12.15079427
Shift along axis -50.62173088
> open 35082 fromDatabase emdb
Opened emdb 35082 as #6, grid size 256,256,256, pixel 1.05, shown at level
0.03, step 1, values float32, fit PDB 8hxy
> fitmap #6 inMap #3
Fit map emdb 35082 in map emdb 36283 using 137879 points
correlation = 0.04101, correlation about mean = 0.0363, overlap = 0.1579
steps = 408, shift = 65.8, angle = 34.3 degrees
Position of emdb 35082 (#6) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.83002691 0.11306315 0.54614289 -127.05113795
-0.16595560 0.98494900 0.04831368 40.10259507
-0.53246039 -0.13073712 0.83629764 119.92242510
Axis -0.15867614 0.95586619 -0.24726848
Axis point 154.85301937 0.00000000 272.44851364
Rotation angle (degrees) 34.34689659
Shift along axis 28.83966372
> hide #!5 models
> close #5
> close #6
> open 35081 fromDatabase emdb
Opened emdb 35081 as #5, grid size 256,256,256, pixel 1.05, shown at level
0.0135, step 1, values float32, fit PDB 8hxx
> volume #5 level 0.01492
> volume #5 level 0.0135
> volume #5 level 0.01528
> fitmap #5 inMap #3
Fit map emdb 35081 in map emdb 36283 using 66947 points
correlation = 0.7501, correlation about mean = 0.1202, overlap = 2.153
steps = 676, shift = 124, angle = 12.1 degrees
Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.98939564 0.12015212 0.08160718 -14.18603821
-0.10620192 0.98173516 -0.15785193 59.27347054
-0.09908288 0.14751118 0.98408487 115.95656871
Axis 0.72555185 0.42932496 -0.53782394
Axis point 0.00000000 -552.69586595 567.85192373
Rotation angle (degrees) 12.14784968
Shift along axis -47.20934497
> fitmap #5 inMap #3 metric correlation
Fit map emdb 35081 in map emdb 36283 using 66947 points
correlation = 0.8144, correlation about mean = 0.1298, overlap = 1.857
steps = 136, shift = 6.95, angle = 19.2 degrees
Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.95131278 0.20632824 -0.22898176 11.80469811
-0.25694936 0.94118296 -0.21943486 97.18243585
0.17023812 0.26758791 0.94837529 62.23418195
Axis 0.62295947 -0.51064922 -0.59258660
Axis point 0.00000000 -7.02044215 260.56361502
Rotation angle (degrees) 23.01016501
Shift along axis -79.15142910
> fitmap #5 inMap #3 metric correlation
Fit map emdb 35081 in map emdb 36283 using 66947 points
correlation = 0.8144, correlation about mean = 0.1298, overlap = 1.857
steps = 40, shift = 0.00643, angle = 0.00133 degrees
Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.95131514 0.20630820 -0.22899003 11.81311889
-0.25693391 0.94118449 -0.21944641 97.18111392
0.17024827 0.26759800 0.94837062 62.22747418
Axis 0.62298566 -0.51067158 -0.59253979
Axis point 0.00000000 -7.02867722 260.56344632
Rotation angle (degrees) 23.01022287
Shift along axis -79.14048369
> fitmap #5 inMap #3 metric correlation
Fit map emdb 35081 in map emdb 36283 using 66947 points
correlation = 0.8144, correlation about mean = 0.1298, overlap = 1.857
steps = 48, shift = 0.00512, angle = 0.00617 degrees
Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.95132248 0.20635803 -0.22891464 11.79566434
-0.25697085 0.94116310 -0.21949487 97.19898510
0.17015148 0.26763479 0.94837761 62.23909035
Axis 0.62308146 -0.51044049 -0.59263818
Axis point 0.00000000 -7.01223637 260.64504895
Rotation angle (degrees) 23.01074024
Shift along axis -79.14989857
Correlation = 0.8144, Correlation about mean = 0.1298, Overlap = 1.857
> fitmap #5 inMap #3 metric cam
Fit map emdb 35081 in map emdb 36283 using 66947 points
correlation = 0.7826, correlation about mean = 0.1769, overlap = 1.83
steps = 156, shift = 9.68, angle = 15.7 degrees
Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.96600153 0.16994144 -0.19483569 10.67086071
-0.24444876 0.84574362 -0.47430215 132.80677431
0.08417746 0.50580394 0.85853161 53.47424980
Axis 0.89094092 -0.25362992 -0.37669104
Axis point 0.00000000 -0.94289344 256.61144526
Rotation angle (degrees) 33.36974963
Shift along axis -44.31993584
> fitmap #2 inMap #5
Fit molecule 8jho (#2) to map emdb 35081 (#5) using 42813 atoms
average map value = 0.002236, steps = 808
shifted from previous position = 65.2
rotated from previous position = 20.3 degrees
atoms outside contour = 41844, contour level = 0.015275
Position of 8jho (#2) relative to emdb 35081 (#5) coordinates:
Matrix rotation and translation
0.99723440 0.05928757 0.04481678 -84.00347569
-0.07153422 0.92926586 0.36241939 -127.92858091
-0.02015973 -0.36462301 0.93093697 -71.63525434
Axis -0.98040889 0.08762013 -0.17641179
Axis point 0.00000000 -218.54305667 330.58789023
Rotation angle (degrees) 21.76405662
Shift along axis 83.78593966
> fitmap #2 inMap #3
Fit molecule 8jho (#2) to map emdb 36283 (#3) using 42813 atoms
average map value = 0.01303, steps = 472
shifted from previous position = 65.2
rotated from previous position = 20.3 degrees
atoms outside contour = 13154, contour level = 0.0075638
Position of 8jho (#2) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.99981479 -0.01515479 -0.01186217 5.68056937
0.01521933 0.99986976 0.00536897 -3.31142014
0.01177926 -0.00554851 0.99991523 -2.15083773
Axis -0.27287765 -0.59090732 0.75918794
Axis point 268.18095539 349.47915962 -0.00000000
Rotation angle (degrees) 1.14624124
Shift along axis -1.22624808
> fitmap #5 inMap #3
Fit map emdb 35081 in map emdb 36283 using 66947 points
correlation = 0.7501, correlation about mean = 0.1202, overlap = 2.153
steps = 192, shift = 9.64, angle = 25.7 degrees
Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.98938462 0.12021951 0.08164160 -14.20138256
-0.10625304 0.98171267 -0.15795734 59.30490700
-0.09913815 0.14760589 0.98406510 115.95518391
Axis 0.72560073 0.42928567 -0.53778936
Axis point 0.00000000 -552.30010817 567.68201061
Rotation angle (degrees) 12.15510087
Shift along axis -47.20525068
> fitmap #5 inMap #3
Fit map emdb 35081 in map emdb 36283 using 66947 points
correlation = 0.7501, correlation about mean = 0.1203, overlap = 2.153
steps = 44, shift = 0.00958, angle = 0.00986 degrees
Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.98940099 0.12011757 0.08159325 -14.18101529
-0.10617263 0.98174301 -0.15782282 59.26271540
-0.09906090 0.14748708 0.98409070 115.95508528
Axis 0.72557774 0.42932978 -0.53778517
Axis point 0.00000000 -552.82488963 567.86588218
Rotation angle (degrees) 12.14526063
Shift along axis -47.20510550
> select add #5
2 models selected
Drag select of 5 emdb 35081
> ui mousemode right "translate selected models"
> ui mousemode right "move picked models"
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.9894,0.12012,0.081593,121.86,-0.10617,0.98174,-0.15782,96.351,-0.099061,0.14749,0.98409,28.646
> select add #4
26263 atoms, 27486 bonds, 460 pseudobonds, 2725 residues, 6 models selected
> show #!4 models
> select subtract #4
2 models selected
> hide #!4 models
> open 8HXX
Summary of feedback from opening 8HXX fetched from pdb
---
note | Fetching compressed mmCIF 8hxx from
http://files.rcsb.org/download/8hxx.cif
8hxx title:
Cryo-EM structure of the histone deacetylase complex Rpd3S [more info...]
Chain information for 8hxx #6
---
Chain | Description | UniProt
E | Histone H3 | A0A310TTQ1_XENLA 1-135
K | Transcriptional regulatory protein SIN3 | SIN3_YEAST 1-1536
L | Histone deacetylase RPD3 | RPD3_YEAST 1-433
M O | Chromatin modification-related protein EAF3 | A0A8H4F719_YEASX 1-401
N P | RCO1 isoform 1 | A0A8H4BXB0_YEASX 1-684
Non-standard residues in 8hxx #6
---
ZN — zinc ion
> hide surfaces #6
Expected ',' or a keyword
> ~surface #6
> show #1#!2,6 cartoons
> ~surface #6
> cartoon #6
> ui tool show "Fit in Map"
> fitmap #6 inMap #3
Fit molecule 8hxx (#6) to map emdb 36283 (#3) using 14873 atoms
average map value = 0.007384, steps = 1324
shifted from previous position = 192
rotated from previous position = 84.9 degrees
atoms outside contour = 8440, contour level = 0.0075638
Position of 8hxx (#6) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.09978045 0.90768477 0.40761774 38.43434035
-0.96868019 0.18223183 -0.16867202 322.90482788
-0.22738194 -0.37802106 0.89743943 267.95201370
Axis -0.10509844 0.31878567 -0.94198196
Axis point 220.22121701 193.84102671 0.00000000
Rotation angle (degrees) 84.85216422
Shift along axis -153.50792245
> fitmap #6 inMap #5
Fit molecule 8hxx (#6) to map emdb 35081 (#5) using 14873 atoms
average map value = -0.0007173, steps = 88
shifted from previous position = 1.17
rotated from previous position = 4.43 degrees
atoms outside contour = 14873, contour level = 0.015275
Position of 8hxx (#6) relative to emdb 35081 (#5) coordinates:
Matrix rotation and translation
0.23343365 0.91014681 0.34225943 -131.97554074
-0.96245141 0.26641879 -0.05204139 248.64620284
-0.13854965 -0.31725986 0.93816319 203.78654595
Axis -0.13590868 0.24638603 -0.95959510
Axis point 100.10439965 246.69161615 0.00000000
Rotation angle (degrees) 77.34923611
Shift along axis -116.35299942
> view matrix models
> #5,0.9894,0.12012,0.081593,124.47,-0.10617,0.98174,-0.15782,55.166,-0.099061,0.14749,0.98409,52.618
> view matrix models
> #5,0.9894,0.12012,0.081593,159.95,-0.10617,0.98174,-0.15782,-42.27,-0.099061,0.14749,0.98409,106.38
> view matrix models
> #5,0.9894,0.12012,0.081593,173.46,-0.10617,0.98174,-0.15782,-59.056,-0.099061,0.14749,0.98409,114.9
> ui mousemode right select
> select #6/N:92@ND2
1 atom, 1 residue, 1 model selected
> select add #6
14873 atoms, 15195 bonds, 36 pseudobonds, 1824 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.10405,0.90662,0.40893,28.485,-0.9478,0.21499,-0.23549,387.98,-0.30142,-0.36308,0.88166,248.38
> view matrix models
> #6,0.10405,0.90662,0.40893,18.191,-0.9478,0.21499,-0.23549,473.12,-0.30142,-0.36308,0.88166,188.87
> hide sel atoms
> ui tool show Matchmaker
> matchmaker #!2 to #6
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 8hxx, chain K (#6) with 8jho, chain K (#2), sequence alignment
score = 6474.3
RMSD between 549 pruned atom pairs is 0.199 angstroms; (across all 549 pairs:
0.199)
> fitmap #2 inMap #3
Fit molecule 8jho (#2) to map emdb 36283 (#3) using 42813 atoms
average map value = 0.0001283, steps = 784
shifted from previous position = 96.9
rotated from previous position = 30.9 degrees
atoms outside contour = 42813, contour level = 0.0075638
Position of 8jho (#2) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.72834200 -0.34573474 -0.59159565 97.43009351
-0.68149783 -0.27570900 -0.67789767 726.41678596
0.07126453 0.89691250 -0.43642792 89.56609192
Axis 0.90438437 -0.38066835 -0.19282253
Axis point 0.00000000 367.61128453 264.28163066
Rotation angle (degrees) 119.46537244
Shift along axis -205.67998503
> undo
> fitmap #2 inMap #3
Fit molecule 8jho (#2) to map emdb 36283 (#3) using 42813 atoms
average map value = 0.0001283, steps = 76
shifted from previous position = 0.0488
rotated from previous position = 0.0505 degrees
atoms outside contour = 42813, contour level = 0.0075638
Position of 8jho (#2) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.72784539 -0.34625506 -0.59190245 97.75586173
-0.68197094 -0.27510514 -0.67766717 726.37739434
0.07181028 0.89689720 -0.43636990 89.39943104
Axis 0.90419473 -0.38113752 -0.19278509
Axis point 0.00000000 367.73688204 264.25423815
Rotation angle (degrees) 119.45993471
Shift along axis -205.69421913
> fitmap #2 inMap #3
Fit molecule 8jho (#2) to map emdb 36283 (#3) using 42813 atoms
average map value = 0.0001283, steps = 100
shifted from previous position = 0.0103
rotated from previous position = 0.00923 degrees
atoms outside contour = 42813, contour level = 0.0075638
Position of 8jho (#2) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.72792795 -0.34616908 -0.59185123 97.70017775
-0.68189432 -0.27523035 -0.67769344 726.38710680
0.07170109 0.89689198 -0.43639859 89.43861713
Axis 0.90422774 -0.38105421 -0.19279492
Axis point 0.00000000 367.71402087 264.25938814
Rotation angle (degrees) 119.46228226
Shift along axis -205.69296922
> fitmap #2 inMap #3
Fit molecule 8jho (#2) to map emdb 36283 (#3) using 42813 atoms
average map value = 0.0001283, steps = 104
shifted from previous position = 0.0227
rotated from previous position = 0.0246 degrees
atoms outside contour = 42813, contour level = 0.0075638
Position of 8jho (#2) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.72817642 -0.34590544 -0.59169970 97.53792390
-0.68165589 -0.27550674 -0.67782098 726.40298652
0.07144470 0.89690884 -0.43640599 89.50967529
Axis 0.90432102 -0.38082433 -0.19281161
Axis point 0.00000000 367.65295955 264.27238549
Rotation angle (degrees) 119.46344435
Shift along axis -205.68483847
> close #5
> hide #!6 models
> fitmap #2 inMap #3
Fit molecule 8jho (#2) to map emdb 36283 (#3) using 42813 atoms
average map value = 0.0001283, steps = 96
shifted from previous position = 0.0376
rotated from previous position = 0.0322 degrees
atoms outside contour = 42813, contour level = 0.0075638
Position of 8jho (#2) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.72785905 -0.34628785 -0.59186648 97.74913213
-0.68195792 -0.27517534 -0.67765177 726.39972736
0.07179551 0.89686301 -0.43644260 89.42971413
Axis 0.90420416 -0.38112436 -0.19276687
Axis point 0.00000000 367.73677550 264.25461763
Rotation angle (degrees) 119.46418729
Shift along axis -205.70254289
Opened 8jho map 5 as #5, grid size 124,118,186, pixel 1.67, shown at level
0.101, step 1, values float32
> fitmap #2 inMap #3 resolution 5
Fit map 8jho map 5 in map emdb 36283 using 156378 points
correlation = 0.3254, correlation about mean = -0.00831, overlap = 5.777
steps = 68, shift = 0.472, angle = 0.523 degrees
Position of 8jho map 5 (#5) relative to emdb 36283 (#3) coordinates:
Matrix rotation and translation
0.73203849 -0.34017073 -0.59025717 94.63424804
-0.67819095 -0.28168408 -0.67875703 726.98647447
0.06462722 0.89718334 -0.43690430 91.26196499
Axis 0.90584462 -0.37642509 -0.19429276
Axis point 0.00000000 366.66005673 264.64136770
Rotation angle (degrees) 119.55606255
Shift along axis -205.66356583
Average map value = 0.0001285 for 32643 atoms, 42813 outside contour
> open 8JHO
8jho title:
Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-
nucleosome [more info...]
Chain information for 8jho #7
---
Chain | Description | UniProt
A E a e | Histone H3 | A0A310TTQ1_XENLA 1-135
B F b f | Histone H4 | A0A8J1LTD2_XENLA 1-102
C G c g | Histone H2A | Q6AZJ8_XENLA 1-129
D H d h | Histone H2B | A0A8J0U496_XENLA 1-122
I | Di-nucleosome template foward |
J | Di-nucleosome template reverse |
K | Transcriptional regulatory protein SIN3 | SIN3_YEAST 1-1536
L | Histone deacetylase RPD3 | RPD3_YEAST 1-433
M O | Chromatin modification-related protein EAF3 | A0A8H4F719_YEASX 1-401
N P | RCO1 isoform 1 | A0A8H4BXB0_YEASX 1-684
Non-standard residues in 8jho #7
---
ML3 — 2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-N,N,N-trimethylethanaminium
ZN — zinc ion
> hide #!2 models
> hide #1#!7 atoms
> show #1#!7 atoms
> show #1#!7 cartoons
> hide #1#!7 atoms
> color #2/L rgb(0.99,0.82,0.65)
> color /C,G,c,g royal blue
> cartoon style nucleic xsection oval width 1.6 thickness 1.6
> color #2/I,J rgb(0.4,0.4,0.4)
> show #2/I,J atoms
> cartoon style #1 thickness 1.6
> color #1 rgb(1,1,0.5)
> color #1 rgb(1.0,1.0,0.5)
> color #2/K slate blue
> color #2/M,O dark cyan
> color #2/N,P deep pink
> color #2/L burly wood
> color /A,E,a,e rgb(1.0,1.0,0.5)
> color /B,F,b,f rgb(0.65,0.9,0.65)
> color /C,G,c,g rgb(0.0,0.5,1.0)
> color /D,H,d,h rgb(1.0,0.75,0.87)
> color #/D,H,d,h rgb(1.0,0.75,0.87)
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #7/D,H,d,h rgb(1.0,0.75,0.87)
> color #7/C,G,c,g rgb(0.0,0.5,1.0)
> color #7/B,F,b,f rgb(0.65,0.9,0.65)
> color #7/A,E,a,e rgb(1.0,1.0,0.5)
> color #7/L burly wood
> color #7/N,P deep pink
> color #7/M,O dark cyan
> cartoon style 71 thickness 1.6
Expected an atoms specifier or a keyword
> cartoon style #7/1 thickness 1.6
> color #7/I,J rgb(0.4,0.4,0.4)
> color #7/K slate blue
> nucleotides #1#!7 stubs
> nucleotides stubs
> show #1#!7 atoms
> hide #1#!7 atoms
> show #7/I,J atoms
> save "/Users/mandywan/OneDrive - The Institute of Cancer
> Research/Sin3B_Project/Writing/Thesis/Thesis_figures/Discussion_figs/Dinucleosome_struc2.cxs"
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting full
> set bgColor white
> transparency 50
> transparency 40
> transparency 70
> transparency 80
> transparency 90
> transparency 80
> close #5
> volume #3 level 0.007443
> save "/Users/mandywan/OneDrive - The Institute of Cancer
> Research/Sin3B_Project/Writing/Thesis/Thesis_figures/Discussion_figs/Dinucleosome_struc.png"
> width 1038 height 932 supersample 3 transparentBackground true
> lighting simple
> lighting soft
> lighting full
> lighting simple
> save "/Users/mandywan/OneDrive - The Institute of Cancer
> Research/Sin3B_Project/Writing/Thesis/Thesis_figures/Discussion_figs/Dinucleosome_struc2.png"
> width 1038 height 932 supersample 3 transparentBackground true
> open /Users/mandywan/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Sin3B_Project/Writing/Thesis/Thesis_figures/Discussion_figs/Dinucleosome_struc2.cxs
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.8.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16066.0.0,0)
OS Loader Version: 540.120.3~19
Software:
System Software Overview:
System Version: macOS 12.5.1 (21G83)
Kernel Version: Darwin 21.6.0
Time since boot: 4 days 5:58
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 Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL U2717D:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: J0XYN7CL625S
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 5.04
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 20 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 20 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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