The following bug report has been submitted:
Platform: macOS-13.6.9-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x0000700012b97000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff8607dd7c0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 556 in swap_buffers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 202 in draw
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 59)
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{
"uptime" : 18000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookAir8,2",
"coalitionID" : 2062,
"osVersion" : {
"train" : "macOS 13.6.9",
"build" : "22G830",
"releaseType" : "User"
},
"captureTime" : "2024-08-29 19:22:15.4349 -0400",
"incident" : "00411C15-0D5F-4495-8677-4050E51040C8",
"pid" : 9832,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-29 15:29:45.4990 -0400",
"procStartAbsTime" : 7047107459735,
"procExitAbsTime" : 18496312634629,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"4D0B365C-204D-542C-A07E-5763B16546E4","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "CBE14579-138B-FDEF-F381-AC0025C3215A",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 805,
"bridgeVersion" : {"build":"21P6074","train":"8.6"},
"sleepWakeUUID" : "BB460FAA-4A3C-44AD-8821-78DA6E19B357",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":9832},
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000011\n"],
"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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"base" : 5328228352,
"size" : 442368,
"uuid" : "9141612b-bf67-390f-8b66-18a585729cab",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
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},
{
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"arch" : "x86_64",
"base" : 4791713792,
"size" : 180224,
"uuid" : "6d0a4aa1-f80b-3e16-baed-3f694111a75d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
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"base" : 5340798976,
"size" : 4210688,
"uuid" : "08a0cdf4-85d3-328a-98ac-8a7ec48356eb",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
"name" : "etree.cpython-311-darwin.so"
},
{
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"arch" : "x86_64",
"base" : 4588822528,
"size" : 147456,
"uuid" : "a66bb1e2-ecf4-3220-9c8e-a465d9305940",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
"name" : "_elementpath.cpython-311-darwin.so"
},
{
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"arch" : "x86_64",
"base" : 5472722944,
"size" : 49152,
"uuid" : "e85fa1ce-f4e4-3454-9368-bd7d363c7e9e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/iconengines\/libqsvgicon.dylib",
"name" : "libqsvgicon.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5212319744,
"size" : 32768,
"uuid" : "4cafbf15-47c9-3e93-abf0-7f8f01ea6b1d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
"name" : "_imagingmath.cpython-311-darwin.so"
},
{
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"arch" : "x86_64",
"base" : 4942692352,
"size" : 16384,
"uuid" : "946403b9-d874-3c5d-bc5b-104d68f45c19",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_multiprocessing.cpython-311-darwin.so",
"name" : "_multiprocessing.cpython-311-darwin.so"
},
{
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"arch" : "x86_64",
"base" : 140703615946752,
"size" : 237568,
"uuid" : "e8790d29-4132-3edf-ab37-16fbd7cf0d66",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
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"base" : 140703616184320,
"size" : 49152,
"uuid" : "60b15e1f-39ea-33a1-8616-3af57dc1094a",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
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"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
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"uuid" : "982c4eec-b380-3c37-ab95-14150e14dd61",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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"source" : "A",
"base" : 0,
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"uuid" : "b6362039-d4ec-3ef1-9802-ab9a092ef835",
"path" : "\/System\/Library\/PrivateFrameworks\/GPUSupport.framework\/Versions\/A\/Libraries\/libGPUSupportMercury.dylib",
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"path" : "\/System\/Library\/Extensions\/AppleIntelKBLGraphicsGLDriver.bundle\/Contents\/MacOS\/AppleIntelKBLGraphicsGLDriver",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/katiecasazza/Desktop/Chimera Msh2-Msh3 crosslinking
> analysis.cxs" format session
opened ChimeraX session
> ui mousemode right select
> select /A:626
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select /A:626
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /B:549
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:307
12 atoms, 12 bonds, 1 residue, 1 model selected
Drag select of 55 residues
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right distance
> distance /A:626@NZ /B:549@NZ
Distance between /A LYS 626 NZ and /B LYS 549 NZ: 35.097Å
> ui mousemode right translate
> ui mousemode right select
> select /A:1011
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select /B:870
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select /B:890
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> select /A:980
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select /B:549
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select /A:626
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select /a :893
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> select /b :980
Nothing selected
> ui mousemode right select
> select /A:893
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> ~distance /B:890@NZ /A:980@NZ
> distance /A:980@NZ /A:893@OG
Distance between /A LYS 980 NZ and SER 893 OG: 33.505Å
> select /a :549
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel navy
> select /b :549
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> select /b :549
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /a :549
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> select /a :672
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel navy
> show sel atoms
> ui mousemode right distance
> ui mousemode right translate
> ui mousemode right distance
> distance /B:549@NZ /A:672@NZ
Distance between /B LYS 549 NZ and /A LYS 672 NZ: 18.097Å
> set bgColor black
> set bgColor white
> select /b :575
9 atoms, 8 bonds, 1 residue, 1 model selected
> select color navy
Expected an objects specifier or a keyword
> color sel navy
> show sel atoms
> distance /A:672@NZ /B:575@NZ
Distance between /A LYS 672 NZ and /B LYS 575 NZ: 13.171Å
> select /b :950
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel navy
> select /a :999
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel navy
> show sel atoms
> select /b :950
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> distance /A:999@NZ /B:950@NZ
Distance between /A LYS 999 NZ and /B LYS 950 NZ: 27.942Å
> select /b :549
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /a :667
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel purple
> show sel atoms
> distance /A:667@NZ /B:549@NZ
Distance between /A LYS 667 NZ and /B LYS 549 NZ: 7.714Å
> select /b :890
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /a :995
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel orange
> show sel atoms
> ui mousemode right translate
> ui mousemode right distance
> distance /A:995@NZ /B:890@NZ
Distance between /A LYS 995 NZ and /B LYS 890 NZ: 16.151Å
> color #1.1 #ff2600ff models
> select add #1.1
9 atoms, 8 bonds, 1 residue, 3 models selected
> color #1 #ff2600ff models
> rename #1 "distances- lines"
> rename #1.1 "labels- numbers"
> select /b
7655 atoms, 7787 bonds, 964 residues, 1 model selected
> save "/Users/katiecasazza/Desktop/Msh2-Msh3 XL- updated 8-29-2024.cxs"
> ui mousemode right translate
> select /b
7655 atoms, 7787 bonds, 964 residues, 1 model selected
> color sel light blue
> color sel green
> color sea green
> select /b
7655 atoms, 7787 bonds, 964 residues, 1 model selected
> color sea green
> select /a
8196 atoms, 8344 bonds, 1 pseudobond, 1018 residues, 2 models selected
> color sel dodger blue
> color sel steel blue
> select /b :549,870,890,893
36 atoms, 32 bonds, 4 residues, 1 model selected
> ui mousemode right label
> label #4/A:1010
> label #4/A:1012
> label #4/A:1009
> select add #1
36 atoms, 32 bonds, 8 pseudobonds, 4 residues, 4 models selected
> delete sel
> ui mousemode right translate
> delete sel
> ui mousemode right select
> select /B:546
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> delete sel
> select add #4.3
5 pseudobonds, 2 models selected
> show #4.3 target m
> close #4.3
> select add #1
3 pseudobonds, 2 models selected
> open
> /Users/katiecasazza/Downloads/output_msh2msh6_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
output_msh2msh6_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#2
---
Chain | Description
A | No description available
B | No description available
> undo
> close session
> open
> /Users/katiecasazza/Downloads/output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #1
---
Chain | Description
A | No description available
B | No description available
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select /A
8196 atoms, 8344 bonds, 1018 residues, 1 model selected
> select /a :672
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /a
8196 atoms, 8344 bonds, 1018 residues, 1 model selected
> color sel teal
> color sel steel blue
> select /b
7655 atoms, 7787 bonds, 964 residues, 1 model selected
> color sel medium sea green
> show sel atoms
> hide sel atoms
> select /b :498,502
18 atoms, 16 bonds, 2 residues, 1 model selected
> color sel red
> show sel atoms
> label sel
> distance /b:498@NZ /b:502@NZ
Distance between /B LYS 498 NZ and LYS 502 NZ: 8.080Å
> select /b :890,893
18 atoms, 16 bonds, 2 residues, 1 model selected
> color sel red
> label sel
> show sel atoms
> distance /b:890@NZ /b:893@NZ
Distance between /B LYS 890 NZ and LYS 893 NZ: 14.201Å
> select /b:950
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> label sel
> show sel atoms
> distance /b:950@NZ /b:893@NZ
Distance between /B LYS 950 NZ and LYS 893 NZ: 30.413Å
> select /957
Nothing selected
> select /b:957
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> show sel atoms
> label sel
> distance /b:957@NZ /b:893@NZ
Distance between /B LYS 957 NZ and LYS 893 NZ: 15.865Å
> select /a:77,70
18 atoms, 16 bonds, 2 residues, 1 model selected
> color sel red
> label sel
> show sel atoms
> distance /a:77@NZ /a:70@NZ
Distance between /A LYS 77 NZ and LYS 70 NZ: 30.219Å
> select /a:92
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /a:92,140,126,160,626,634,959,965,999,995
90 atoms, 80 bonds, 10 residues, 1 model selected
> color sel red
> show sel atoms
> label sel
> distance /a:92@NZ /a:70@NZ
Distance between /A LYS 92 NZ and LYS 70 NZ: 36.097Å
> distance /a:140@NZ /a:126@NZ
Distance between /A LYS 140 NZ and LYS 126 NZ: 23.560Å
> distance /a:160@NZ /a:126@NZ
Distance between /A LYS 160 NZ and LYS 126 NZ: 32.057Å
> distance /a:626@NZ /a:634@NZ
Distance between /A LYS 626 NZ and LYS 634 NZ: 18.029Å
> distance /a:959@NZ /a:965@NZ
Distance between /A LYS 959 NZ and LYS 965 NZ: 6.074Å
> distance /a:999@NZ /a:995@NZ
Distance between /A LYS 999 NZ and LYS 995 NZ: 4.190Å
> select /b :549,870 /a:1011,980
36 atoms, 32 bonds, 4 residues, 1 model selected
> color sel red
> show sel atoms
> label sel
> ui mousemode right "color key"
> key delete
> ui mousemode right select
> save "/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs"
> ui tool show Distances
> distance style color #005493
> distance style color #ff2600
Exactly two atoms must be selected!
> ui mousemode right select
> color sel blye
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel blue
> undo
> hide #2.1 models
> distance /b:549@NZ /a:626@NZ
Distance between /B LYS 549 NZ and /A LYS 626 NZ: 35.097Å
> ui mousemode right select
> color sel navy
> color sel magenta
> color sel gold
> color sel bue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel blue
> color sel dark magenta
> color sel dark blue
> color sel darkred purple
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel purple
> color sel lime
> color sel midnight blue
> color sel midnightblue golden rod
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel goldenrod
> distance style color #ff2f92
> distance style color #0433ff
> distance style color #531b93
> distance style color #945200
> distance style color #ff2600
> distance style color #ff2f92
> distance style color #ff2600
> color sel black
> select clear
> color sel coral
> select clear
> color sel saddle brown
> set bgColor black
> set bgColor white
> select /b
7655 atoms, 7787 bonds, 4 pseudobonds, 964 residues, 2 models selected
> color sel pale green
> select /a
8196 atoms, 8344 bonds, 7 pseudobonds, 1018 residues, 2 models selected
> set bgColor black
> color sel light pink
> set bgColor black
> set bgColor white
> select clear
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> set bgColor black
> color sel midnight blue
> select /a
8196 atoms, 8344 bonds, 7 pseudobonds, 1018 residues, 2 models selected
> color sel midnight blue
> select /b
7655 atoms, 7787 bonds, 4 pseudobonds, 964 residues, 2 models selected
> color sel teal
> set bgColor white
> select /A:325
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> hide #2.1 models
> color sel red
> select /b :498,502,890,893,950,957,549,870,890
72 atoms, 64 bonds, 4 pseudobonds, 8 residues, 2 models selected
> color sel red
> show sel atoms
> label sel
> select /a :77,70,92,140,126,160,626,634,959,965,999,995
108 atoms, 96 bonds, 7 pseudobonds, 12 residues, 2 models selected
> select /a :77,70,92,140,126,160,626,634,959,965,999,995,626,1011,980
126 atoms, 112 bonds, 7 pseudobonds, 14 residues, 2 models selected
> color sel red
> show sel atoms
> label sel
> color sel lime
> color sel cyan
> color sel blue
> color sel dodger blue
> select clear
> color sel magneta
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel magenta
> color sel gold
> select clear
> ui mousemode right translate
> color sel lime
> ui mousemode right select
> color sel lime
> distance /b:870@NZ /a:1011@NZ
Distance between /B LYS 870 NZ and /A LYS 1011 NZ: 13.674Å
> color sel lime
> distance style dashes 6
> distance style dashes 7
> distance style dashes 8
> distance style dashes 9
> distance style dashes 8
> distance style dashes 7
> distance style dashes 6
> distance style dashes 5
> distance style dashes 4
> distance style dashes 5
> distance style dashes 6
> distance style dashes 7
> distance style dashes 8
> distance style dashes 9
> distance style dashes 10
> distance style dashes 11
> distance style dashes 12
> distance style dashes 13
> distance style dashes 14
> distance style dashes 15
> distance style dashes 16
> distance style dashes 25
> distance /b:890@NZ /a:980@NZ
Distance between /B LYS 890 NZ and /A LYS 980 NZ: 10.736Å
> color sel lime
> distance /b:893@NZ /a:980@NZ
Distance between /B LYS 893 NZ and /A LYS 980 NZ: 18.731Å
> color sel lime
> label height 8
> label height 4
> label height 3
> label color white
> set bgColor black
> ui mousemode right "move label"
> move label
Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms
> save "/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs"
> view #2.1 clip false
No displayed objects specified.
> ui mousemode right select
> select /A:1011
9 atoms, 8 bonds, 1 residue, 1 model selected
> label sel
> label number
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label sel number
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label number
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label residues number
Expected a keyword
> save "/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs"
> open
> /Users/katiecasazza/Downloads/output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
> format pdb
Chain information for
output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #4
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/katiecasazza/Downloads/output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
> format pdb
Chain information for
output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #5
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/katiecasazza/Downloads/output_msh2msh6_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
> format pdb
Chain information for
output_msh2msh6_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#6
---
Chain | Description
A | No description available
B | No description available
> undo
> close session
> open "/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs" format session
opened ChimeraX session
> close session
> open "/Users/katiecasazza/Desktop/Msh2-Msh3 XL- updated 8-29-2024.cxs"
> format session
opened ChimeraX session
> select /A:371
9 atoms, 8 bonds, 1 residue, 1 model selected
> label (#!4 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label (#!4 & sel) residues attribute number
> select /A:166
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B:469
9 atoms, 8 bonds, 1 residue, 1 model selected
> label (#!4 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label (#!4 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label (#!4 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label (#!4 & sel) residues attribute number
> close session
> open "/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs" format session
opened ChimeraX session
> select /b:498,502,890,893,950,957,549,870,890,893
> /a:77,70,92,140,126,160,626,634,959,965,999,995,626,1011,980,980
198 atoms, 176 bonds, 15 pseudobonds, 22 residues, 2 models selected
> label (#!1 & sel) residues attribute number
> select clear
Drag select of 22 residues
> ui mousemode right translate
> ui mousemode right select
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/katiecasazza/Desktop/movie1.mp4
Movie saved to /Users/katiecasazza/Desktop/movie1.mp4
> close session
> open
> /Users/katiecasazza/Downloads/output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #1
---
Chain | Description
A | No description available
B | No description available
> sel/b
Unknown command: sel/b
> select /b
7655 atoms, 7787 bonds, 964 residues, 1 model selected
> color sel teal
> select /a
8196 atoms, 8344 bonds, 1018 residues, 1 model selected
> color sel midnight blue
> select clear
> save "/Users/katiecasazza/Desktop/Msh2-Msh3 HOMODUPLEX XLs.cxs"
> open "/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs" format session
opened ChimeraX session
> select /a :176,158
18 atoms, 16 bonds, 2 residues, 1 model selected
> color sel red
> show sel atoms
> label sel
> label height 4
> label sel residues attribute number
> select add #2.1
18 atoms, 16 bonds, 2 residues, 2 models selected
> label height 4
> label (#!1 & sel) residues attribute number
> select clear
> select add #2.1
1 model selected
No visible residues selected
> select subtract #2.1
Nothing selected
> select add #1.1
1 model selected
No visible residues selected
> select subtract #1.1
Nothing selected
> select /b:498,502,890,893,950,893,957,549,870,890,893
> /a:176,158,77,70,92,140,126,160,626,634,959,965,999,995,626,1011,980
216 atoms, 192 bonds, 15 pseudobonds, 24 residues, 2 models selected
> label (#!1 & sel) residues attribute number
> label height 6
> label height 4
> label height 4.5
> ui mousemode right translate
> ui mousemode right distance
> distance /A:176@NZ /A:158@NZ
Distance between /A LYS 176 NZ and LYS 158 NZ: 11.661Å
> save "/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs"
> ui mousemode right select
> select clear
> show #!2 target m
> ui tool show Distances
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/katiecasazza/Desktop/movie1.mp4
Movie saved to /Users/katiecasazza/Desktop/movie1.mp4
> save "/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs"
> open "/Users/katiecasazza/Desktop/Msh2-Msh3 HOMODUPLEX XLs.cxs" format
> session
opened ChimeraX session
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select /b:549,890,575,870,498,502,893,890,957,893
> /a:672,980,995,672,1011,999,995,131,140,241,248,626,634,959,965,705,248
198 atoms, 176 bonds, 22 residues, 1 model selected
> select /b:549,890,575,870,498,502,893,890,957,893
> /a:672,980,995,672,1011,999,995,131,140,241,248,626,634,959,965,705,248
198 atoms, 176 bonds, 22 residues, 1 model selected
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.7.2
OpenGL renderer: Intel(R) UHD Graphics 617
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir8,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 1.6 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: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
OS Loader Version: 577.140.2~22
Software:
System Software Overview:
System Version: macOS 13.6.9 (22G830)
Kernel Version: Darwin 22.6.0
Time since boot: 9 hours, 42 minutes
Graphics/Displays:
Intel UHD Graphics 617:
Chipset Model: Intel UHD Graphics 617
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x87c0
Revision ID: 0x0002
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
DELL S2721NX:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 9BGB9H3
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Apple Intel graphics driver crash.