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Opened 6 weeks ago
Closed 5 weeks ago
#18779 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.7.6-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202308300120 (2023-08-30 01:20:01 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000700014453000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700013450000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001244d000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001144a000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700010447000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070000f444000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070000e441000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff854c02a00 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/weakref.py", line 575 in __init__
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1602 in remove_deleted_pointers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 123 in __init__
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 883 in __init__
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ctypes_support.py", line 29 in bonds
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 166 in get_prop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 684 in __init__
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2372 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1433 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1433 in __init__
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/nucleotides/_data.py", line 759 in get_ring
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/nucleotides/_data.py", line 767 in draw_slab
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/nucleotides/_data.py", line 1051 in make_slab
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/nucleotides/_data.py", line 661 in _rebuild_molecule
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/nucleotides/_data.py", line 522 in rebuild
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 138 in invoke
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 237 in _activate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 206 in activate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 382 in activate_trigger
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 54 in draw_new_frame
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 893 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 1044 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, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, 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.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, 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, numpy.linalg.lapack_lite, 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.__nnls, 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._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct (total: 111)
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{
"uptime" : 520000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,1",
"coalitionID" : 32926,
"osVersion" : {
"train" : "macOS 13.7.6",
"build" : "22H625",
"releaseType" : "User"
},
"captureTime" : "2025-09-13 15:28:49.4188 +0530",
"incident" : "3DDEF4F8-9929-4793-9803-81C3B00A1B15",
"pid" : 80763,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-11 19:03:46.6291 +0530",
"procStartAbsTime" : 478698210927935,
"procExitAbsTime" : 524667852272918,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"28244C6E-AEE6-57DA-BB99-CF11903210B3","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "15D25DF0-7659-D181-E945-A179084794A0",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 1046,
"sleepWakeUUID" : "F0148142-5ECC-45C1-9AEB-58CA76BB9512",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737487322967\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff04000-7ffffff05000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":80763},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737487322967\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff04000-7ffffff05000 [ 4K] r-x\/r-x SM=SHM ",
"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 =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.dev202308300120 (2023-08-30)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/jbaral/Downloads/5Y58.cif
5Y58.cif title:
Crystal structure of Ku70/80 and TLC1 [more info...]
Chain information for 5Y58.cif #1
---
Chain | Description | UniProt
A C E | ATP-dependent DNA helicase II subunit 1 | KU70_YEAST 28-602
B D F | ATP-dependent DNA helicase II subunit 2 | KU80_YEAST 2-629
X Y Z | TLC1 |
5Y58.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> hide atoms
> show cartoons
> select /A:28-584
4549 atoms, 4647 bonds, 1 pseudobond, 548 residues, 2 models selected
> select /C:28-584
4549 atoms, 4647 bonds, 1 pseudobond, 548 residues, 2 models selected
> select /B:2-621
4509 atoms, 4583 bonds, 4 pseudobonds, 568 residues, 2 models selected
> select /A:28-584
4549 atoms, 4647 bonds, 1 pseudobond, 548 residues, 2 models selected
> select /E:28-584
4549 atoms, 4647 bonds, 1 pseudobond, 548 residues, 2 models selected
> select /X:286-315
641 atoms, 717 bonds, 26 pseudobonds, 30 residues, 2 models selected
> sequence chain #1/X#1/Y#1/Z
Alignment identifier is 1
> select a,b
Expected an objects specifier or a keyword
> select #1/a,b
9184 atoms, 9230 bonds, 5 pseudobonds, 1242 residues, 2 models selected
> select ~sel
20136 atoms, 20526 bonds, 89 pseudobonds, 2491 residues, 3 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> set bgColor white
> select clear
> select ~sel & ##selected
Nothing selected
> select #1/a:359-509
1245 atoms, 1277 bonds, 151 residues, 1 model selected
> select #1/b:359-509
1180 atoms, 1198 bonds, 151 residues, 1 model selected
> sequence chain #1/A#1/C#1/E
Alignment identifier is 1/A
> sequence chain #1/A#1/C#1/E
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select /B:2-621
4509 atoms, 4583 bonds, 4 pseudobonds, 568 residues, 2 models selected
> select
> /A:39-44,46-50,53-73,104-120,124-130,141-153,177-199,217-225,252-261,276-279,345-355,372-374,396-411,451-455,470-487,495-499,501-516,527-558,564-584
2035 atoms, 2050 bonds, 242 residues, 1 model selected
> select /A:201-202
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /A:201-584
3122 atoms, 3194 bonds, 1 pseudobond, 375 residues, 2 models selected
> color #1 #797979ff
> select #1/b
4575 atoms, 4583 bonds, 4 pseudobonds, 634 residues, 2 models selected
> hide sel cartoons
> select /A:264
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:264-584
2680 atoms, 2741 bonds, 321 residues, 1 model selected
> select /A:264
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:28-264
1878 atoms, 1914 bonds, 1 pseudobond, 228 residues, 2 models selected
> hide sel cartoons
> undo
> hide sel atoms
> hide sel cartoons
> hide #1/a ribbons
> shoe #1/b ribbon
Unknown command: shoe #1/b ribbon
> show #1/b ribbons
> sequence chain #1/a
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> sequence chain #1/b
Alignment identifier is 1/B
> select /B:207
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:207-621
3010 atoms, 3063 bonds, 2 pseudobonds, 379 residues, 2 models selected
> select /B:206-207
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /B:2-207
1508 atoms, 1528 bonds, 2 pseudobonds, 190 residues, 2 models selected
> select /B:206
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:2-206
1499 atoms, 1519 bonds, 2 pseudobonds, 189 residues, 2 models selected
> hide sel cartoons
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/a:28-264
1878 atoms, 1914 bonds, 1 pseudobond, 228 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> select clear
> show cartoons
> select #1/a:28-264
1878 atoms, 1914 bonds, 1 pseudobond, 228 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
Drag select of 13 residues
> select clear
> select /B:207
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:207-621
3010 atoms, 3063 bonds, 2 pseudobonds, 379 residues, 2 models selected
> sequence chain #1/a
Alignment identifier is 1/A
> select /A:265
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:265-584
2671 atoms, 2732 bonds, 320 residues, 1 model selected
> hide sel cartoons
> open 1jey
1jey title:
Crystal Structure of the Ku heterodimer bound to DNA [more info...]
Chain information for 1jey #2
---
Chain | Description | UniProt
A | Ku70 | KU70_HUMAN 1-609
B | Ku80 | KU86_HUMAN 1-565
C | DNA
(5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3') |
D | DNA (34-MER) |
> select add #1
5807 atoms, 5795 bonds, 2 pseudobonds, 825 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> sequence chain #2/a
Alignment identifier is 2/A
> select #2/b
4351 atoms, 4329 bonds, 1 pseudobond, 639 residues, 2 models selected
> hide sel
> ribbon
> hide sel cartoons
> select #2/A:34-270
1842 atoms, 1870 bonds, 1 pseudobond, 229 residues, 2 models selected
> select #2/a:253-534
2286 atoms, 2335 bonds, 282 residues, 1 model selected
> select #2/A:253
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:253-534
2286 atoms, 2335 bonds, 282 residues, 1 model selected
> sequence chain #1/b
Alignment identifier is 1/B
> select clear
> hide #!2 cartoons
> show #2/b ribbons
> select #1/B:207-282
581 atoms, 587 bonds, 76 residues, 1 model selected
> select #1/B:242-243
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/B:207-243
276 atoms, 278 bonds, 37 residues, 1 model selected
> set bgColor black
> show #!2 atoms
> hide #!2 atoms
> select #1/B:208
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:208-457
1863 atoms, 1892 bonds, 1 pseudobond, 239 residues, 2 models selected
> sequence chain #1/b
Alignment identifier is 1/B
> sequence chain #2/b
Alignment identifier is 2/B
> select #2/B:243
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:243-545
2450 atoms, 2504 bonds, 303 residues, 1 model selected
> open /Users/jbaral/Downloads/5Y58.cif
5Y58.cif title:
Crystal structure of Ku70/80 and TLC1 [more info...]
Chain information for 5Y58.cif #3
---
Chain | Description | UniProt
A C E | ATP-dependent DNA helicase II subunit 1 | KU70_YEAST 28-602
B D F | ATP-dependent DNA helicase II subunit 2 | KU80_YEAST 2-629
X Y Z | TLC1 |
5Y58.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> select add #2
9472 atoms, 9500 bonds, 55 pseudobonds, 1327 residues, 3 models selected
> select subtract #2
Nothing selected
> save /Users/jbaral/5y58.pdb models #3
> hide #!2 models
> hide #!3 atoms
> show #!3 cartoons
> sym #3 assembly 1
Made 1 copies for 5Y58.cif assembly 1
> view
> sym #3 assembly 2
Made 1 copies for 5Y58.cif assembly 2
> view
> sym #3 assembly 3
Made 1 copies for 5Y58.cif assembly 3
> view
> sym #3 assembly 1
Made 1 copies for 5Y58.cif assembly 1
> view
> sym #3 assembly 1
Made 1 copies for 5Y58.cif assembly 1
> view
> sym #3 assembly 1
Made 1 copies for 5Y58.cif assembly 1
> view
> sym #3 assembly 2
Made 1 copies for 5Y58.cif assembly 2
> view
> close #4
> close #5
> close #6
> close #7
> close #8
> close #9
> close #10
> show #!3 models
> select #3/a,b,x,y,z
11141 atoms, 11381 bonds, 83 pseudobonds, 1366 residues, 3 models selected
> select ~sel & ##selected
18179 atoms, 18375 bonds, 11 pseudobonds, 2367 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #3/a,b,x
9839 atoms, 9947 bonds, 31 pseudobonds, 1286 residues, 3 models selected
> select ~sel & ##selected
19481 atoms, 19809 bonds, 63 pseudobonds, 2447 residues, 3 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #3/a,b,x,y,z
9839 atoms, 9947 bonds, 31 pseudobonds, 1286 residues, 3 models selected
> select #3/a,b,x
9839 atoms, 9947 bonds, 31 pseudobonds, 1286 residues, 3 models selected
> select ~sel & ##selected
Nothing selected
> select #3/a,b,x
9839 atoms, 9947 bonds, 31 pseudobonds, 1286 residues, 3 models selected
> save /Users/jbaral/5y58.pdb models #3 selectedOnly true
> show #!2 models
> open "/Users/jbaral/Desktop/PDB/mKu dimer structure.pdb"
Chain information for mKu dimer structure.pdb #4
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
> matchmaker #!2-3 to #4
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 mKu dimer structure.pdb, chain B (#4) with 1jey, chain B (#2),
sequence alignment score = 180.2
RMSD between 88 pruned atom pairs is 1.267 angstroms; (across all 224 pairs:
7.490)
Matchmaker mKu dimer structure.pdb, chain B (#4) with 5Y58.cif, chain A (#3),
sequence alignment score = 211.2
RMSD between 72 pruned atom pairs is 1.239 angstroms; (across all 222 pairs:
5.627)
> hide #!2 models
> hide #4 models
> show #4 models
> hide #!3 models
> select subtract #3
Nothing selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #4 models
> show #!2 cartoons
> show #!3 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> ui tool show Matchmaker
> matchmaker #!1-2 to #4
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 mKu dimer structure.pdb, chain B (#4) with 5Y58.cif, chain A (#1),
sequence alignment score = 210
RMSD between 72 pruned atom pairs is 1.239 angstroms; (across all 221 pairs:
5.634)
Matchmaker mKu dimer structure.pdb, chain B (#4) with 1jey, chain B (#2),
sequence alignment score = 180.2
RMSD between 88 pruned atom pairs is 1.267 angstroms; (across all 224 pairs:
7.490)
> show #!2 models
> hide #!2 models
> show #4 models
> set bgColor white
> show #!2 models
> hide #!1 models
> hide #4 models
> select #2/B:243-545
2450 atoms, 2504 bonds, 303 residues, 1 model selected
> select #2/B:243-244
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/B:243-244
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/B:245
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:245
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:6-241
1781 atoms, 1813 bonds, 1 pseudobond, 226 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> sequence chain #2/b
Alignment identifier is 2/B
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:252-253
20 atoms, 19 bonds, 2 residues, 1 model selected
> select #2/A:252-534
2297 atoms, 2346 bonds, 283 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> undo
Undo failed, probably because structures have been modified.
> close #2
> open 1jey
1jey title:
Crystal Structure of the Ku heterodimer bound to DNA [more info...]
Chain information for 1jey #2
---
Chain | Description | UniProt
A | Ku70 | KU70_HUMAN 1-609
B | Ku80 | KU86_HUMAN 1-565
C | DNA
(5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3') |
D | DNA (34-MER) |
> hide #!2 models
> close #3
> ui tool show Matchmaker
> matchmaker #!1-2 to #4
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 mKu dimer structure.pdb, chain B (#4) with 5Y58.cif, chain A (#1),
sequence alignment score = 210
RMSD between 72 pruned atom pairs is 1.239 angstroms; (across all 221 pairs:
5.634)
Matchmaker mKu dimer structure.pdb, chain B (#4) with 1jey, chain B (#2),
sequence alignment score = 180.2
RMSD between 88 pruned atom pairs is 1.267 angstroms; (across all 224 pairs:
7.490)
> show #!1 models
> show #!2 models
> hide #!1 models
> sequence chain #2/b
Alignment identifier is 2/B
> select #2/B:242
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:242-545
2461 atoms, 2515 bonds, 304 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> close #2
> open 1jey
1jey title:
Crystal Structure of the Ku heterodimer bound to DNA [more info...]
Chain information for 1jey #2
---
Chain | Description | UniProt
A | Ku70 | KU70_HUMAN 1-609
B | Ku80 | KU86_HUMAN 1-565
C | DNA
(5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3') |
D | DNA (34-MER) |
> ui tool show Matchmaker
> matchmaker #!1-2 to #4
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 mKu dimer structure.pdb, chain B (#4) with 5Y58.cif, chain A (#1),
sequence alignment score = 210
RMSD between 72 pruned atom pairs is 1.239 angstroms; (across all 221 pairs:
5.634)
Matchmaker mKu dimer structure.pdb, chain B (#4) with 1jey, chain B (#2),
sequence alignment score = 180.2
RMSD between 88 pruned atom pairs is 1.267 angstroms; (across all 224 pairs:
7.490)
> sequence chain #2/b
Alignment identifier is 2/B
> select #2/B:6-241
1781 atoms, 1813 bonds, 1 pseudobond, 226 residues, 2 models selected
> select #2/B:243
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:6-243
1802 atoms, 1835 bonds, 1 pseudobond, 228 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> sequence chain #2/a
Alignment identifier is 2/A
> select #2/A:34-257
1735 atoms, 1763 bonds, 1 pseudobond, 216 residues, 2 models selected
> select #2/A:259
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:259
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:256
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:34-256
1729 atoms, 1757 bonds, 1 pseudobond, 215 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> show #!1 models
> show #4 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> cartoon style #1,4 modeHelix tube sides 20
> show #!2 models
> cartoon style xsection oval modeHelix default
> hide cartoons
> hide (protein|nucleic) target a
> cartoon hide
> show backbone target ab
> style stick
Changed 18995 atom styles
> hide atoms
> show cartoons
> hide #!2 models
> hide #4 models
> select #1/B:614
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/B:621
20 atoms, 18 bonds, 2 residues, 1 model selected
> select add #1/B:315
29 atoms, 26 bonds, 3 residues, 1 model selected
> select subtract #1/B:315
20 atoms, 18 bonds, 2 residues, 1 model selected
> select subtract #1/B:614
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #1/B:614
20 atoms, 18 bonds, 2 residues, 1 model selected
> select clear
> select #1/B:621
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/b:614-621
8 atoms, 8 residues, 1 model selected
> select #1/b:614-621
69 atoms, 69 bonds, 8 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> open 5y85
Summary of feedback from opening 5y85 fetched from pdb
---
note | Fetching compressed mmCIF 5y85 from
http://files.rcsb.org/download/5y85.cif
5y85 title:
Structure-based Insights into Self-Cleavage by a Four-way Junctional Twister-
Sister Ribozyme [more info...]
Chain information for 5y85 #3
---
Chain | Description
A C | RNA (5'-R(P*AP*CP*CP*CP*GP*CP*AP*AP*GP*GP*CP*CP*GP*AP*CP*GP*GP*C)-3')
B D | DNA/RNA (50-MER)
Non-standard residues in 5y85 #3
---
MG — magnesium ion
5y85 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> close #3
> open 5y58
5y58 title:
Crystal structure of Ku70/80 and TLC1 [more info...]
Chain information for 5y58 #3
---
Chain | Description | UniProt
A C E | ATP-dependent DNA helicase II subunit 1 | KU70_YEAST 28-602
B D F | ATP-dependent DNA helicase II subunit 2 | KU80_YEAST 2-629
X Y Z | TLC1 |
5y58 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> hide #!1,3 atoms
> show #!1,3 cartoons
> hide #!1 models
> select #3/a,b,x
9839 atoms, 9947 bonds, 31 pseudobonds, 1286 residues, 3 models selected
> select ~sel & ##selected
19481 atoms, 19809 bonds, 63 pseudobonds, 2447 residues, 3 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> save "/Users/jbaral/Desktop/PDB/5y58 single.pdb" models #3
> show #4 models
> hide #4 models
> hide #!3 models
> show #4 models
> open /Users/jbaral/Desktop/PDB/40bp-super.pdb
Chain information for 40bp-super.pdb #5
---
Chain | Description
A C E | No description available
B D F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
> hide #4-5 atoms
> show #4-5 cartoons
> select ~sel & ##selected
Nothing selected
> select #5/A,B,G,H
9592 atoms, 9847 bonds, 527 residues, 1 model selected
> select ~sel & ##selected
15862 atoms, 16114 bonds, 950 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #5/G:1-37
1168 atoms, 1255 bonds, 37 residues, 1 model selected
Drag select of 27 residues
> select clear
> save "/Users/jbaral/Desktop/PDB/mKu-DNA structure.pdb"
> show #!2 models
> hide #4 models
> hide #5 models
> save "/Users/jbaral/Desktop/PDB/Human core Ku dimer.pdb"
> select add #2
5941 atoms, 5906 bonds, 53 pseudobonds, 884 residues, 2 models selected
> show sel cartoons
> save "/Users/jbaral/Desktop/PDB/Human core Ku dimer.pdb" models #2
> selectedOnly true
> hide #!2 models
> select subtract #2
Nothing selected
> show #!1 models
> select #5/X
Nothing selected
> show #!3 models
> hide #!1 models
> view #3
> show #!1 models
> ui tool show Matchmaker
> matchmaker #4#!1-3 to #5
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 40bp-super.pdb, chain B (#5) with mKu dimer structure.pdb, chain B
(#4), sequence alignment score = 1159.6
RMSD between 227 pruned atom pairs is 0.000 angstroms; (across all 227 pairs:
0.000)
Matchmaker 40bp-super.pdb, chain B (#5) with 5Y58.cif, chain A (#1), sequence
alignment score = 210
RMSD between 72 pruned atom pairs is 1.239 angstroms; (across all 221 pairs:
5.634)
Matchmaker 40bp-super.pdb, chain B (#5) with 1jey, chain B (#2), sequence
alignment score = 178.3
RMSD between 88 pruned atom pairs is 1.267 angstroms; (across all 223 pairs:
7.472)
Matchmaker 40bp-super.pdb, chain B (#5) with 5y58, chain A (#3), sequence
alignment score = 211.2
RMSD between 72 pruned atom pairs is 1.239 angstroms; (across all 222 pairs:
5.627)
> view all
> show sequence #1
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #3/A
Alignment identifier is 1
> sequence chain #1/B #3/B
Alignment identifier is 2
> select #/A:28-264
Expected an objects specifier or a keyword
> select #3/A:28-264
1878 atoms, 1914 bonds, 1 pseudobond, 228 residues, 2 models selected
> delete atoms
> open /Users/jbaral/5y58.pdb format pdb
No such file/path: /Users/jbaral/5y58.pdb
> open 5y58 format mmcif fromDatabase pdb
5y58 title:
Crystal structure of Ku70/80 and TLC1 [more info...]
Chain information for 5y58 #1
---
Chain | Description | UniProt
A C E | ATP-dependent DNA helicase II subunit 1 | KU70_YEAST 28-602
B D F | ATP-dependent DNA helicase II subunit 2 | KU80_YEAST 2-629
X Y Z | TLC1 |
5y58 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> open 5y58 format mmcif fromDatabase pdb
5y58 title:
Crystal structure of Ku70/80 and TLC1 [more info...]
Chain information for 5y58 #2
---
Chain | Description | UniProt
A C E | ATP-dependent DNA helicase II subunit 1 | KU70_YEAST 28-602
B D F | ATP-dependent DNA helicase II subunit 2 | KU80_YEAST 2-629
X Y Z | TLC1 |
5y58 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> hide atoms
> show cartoons
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> close #1
> select #1/a,b,x
Nothing selected
> select #1/A,B,X
Nothing selected
> select #2/A,B,X
9839 atoms, 9947 bonds, 31 pseudobonds, 1286 residues, 3 models selected
> select ~sel & ##selected
19481 atoms, 19809 bonds, 63 pseudobonds, 2447 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/A:28-264
1878 atoms, 1914 bonds, 1 pseudobond, 228 residues, 2 models selected
> hide sel cartoons
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/B:1-106
775 atoms, 789 bonds, 1 pseudobond, 98 residues, 2 models selected
> select #2/B:1-206
1499 atoms, 1519 bonds, 2 pseudobonds, 189 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> color byattribute chain
No known/registered numeric attribute chain
> color bychain
> save "/Users/jbaral/Desktop/PDB/Yeast Ku core.pdb" relModel #2
> open "/Users/jbaral/Desktop/PDB/Human core Ku dimer.pdb"
> "/Users/jbaral/Desktop/PDB/mKu-DNA structure.pdb"
Summary of feedback from opening /Users/jbaral/Desktop/PDB/mKu-DNA
structure.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU A 276
ASN A 279 1 4
Start residue of secondary structure not found: HELIX 2 2 SER A 345 ALA A 355
1 11
Start residue of secondary structure not found: HELIX 3 3 SER A 372 SER A 374
1 3
Start residue of secondary structure not found: HELIX 4 4 GLY A 396 LYS A 411
1 16
Start residue of secondary structure not found: HELIX 5 5 PHE A 451 ILE A 455
1 5
76 messages similar to the above omitted
End residue of secondary structure not found: SHEET 6 6 1 ASP A 341 ILE A 342
0
Start residue of secondary structure not found: SHEET 7 7 1 PHE A 362 SER A
370 0
Start residue of secondary structure not found: SHEET 8 8 1 SER A 385 PRO A
389 0
Start residue of secondary structure not found: SHEET 9 9 1 TYR A 394 GLU A
395 0
Start residue of secondary structure not found: SHEET 10 10 1 LYS A 413 LYS A
420 0
Start residue of secondary structure not found: SHEET 11 11 1 SER A 428 PRO A
434 0
66 messages similar to the above omitted
Chain information for Human core Ku dimer.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Chain information for mKu-DNA structure.pdb
---
Chain | Description
3.1/A | No description available
3.2/A 3.5/A | No description available
3.3/A | No description available
3.4/A | No description available
3.1/B | No description available
3.2/B 3.5/B | No description available
3.3/B | No description available
3.4/B | No description available
3.3/C | No description available
3.3/D | No description available
3.5/G | No description available
3.5/H | No description available
3.4/X | No description available
===== 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.dev202308300120 (2023-08-30)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.7.3
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
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: MacBookPro14,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 529.140.2.0.0
OS Loader Version: 577.140.2~30
SMC Version (system): 2.43f11
Software:
System Software Overview:
System Version: macOS 13.7.6 (22H625)
Kernel Version: Darwin 22.6.0
Time since boot: 32 days, 44 minutes
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
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: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.47.1
ChimeraX-AtomicLibrary: 10.0.8
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: 2.10.4
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202308300120
ChimeraX-CoreFormats: 1.1
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: 1.1.2
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
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9
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
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: 1.5.12
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: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.2
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: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.9
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.2
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-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: 1.31.4
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.4
contourpy: 1.1.0
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7.post1
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.42.1
funcparserlib: 1.0.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.7.10
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.0
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.8
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.7
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.5
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.10.0
prompt-toolkit: 3.0.39
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
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.0
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: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.2
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: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.7.1
tzdata: 2023.3
urllib3: 2.0.4
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.8
Change History (2)
comment:1 by , 5 weeks ago
| 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 , 5 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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