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Opened 2 hours ago
#19382 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.0.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x00000001f1a28800 (most recent call first):
File "/Applications/ChimeraX-1.10.1.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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, chimerax.pdb_lib._load_libs, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, 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.atom_search.ast, chimerax.chem_group._chem_group, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.coulombic._esp (total: 51)
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{
"uptime" : 650000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,1",
"coalitionID" : 43816,
"osVersion" : {
"train" : "macOS 26.0.1",
"build" : "25A362",
"releaseType" : "User"
},
"captureTime" : "2025-11-18 01:49:51.6857 -0500",
"codeSigningMonitor" : 2,
"incident" : "84BC1A35-6F94-4804-A237-CBFD37C0B9E4",
"pid" : 73959,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-11-17 12:29:55.1032 -0500",
"procStartAbsTime" : 15029463069757,
"procExitAbsTime" : 15776846562605,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"9E7D0C7D-5CF3-5B28-A222-F2591D95FB64","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "6A2C8B20-C464-C0A0-3C57-9A0AC8739D0E",
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "5A8C95F8-0F92-4329-8555-F32441AFBF30",
"wakeTime" : 4,
"sleepWakeUUID" : "4ABF1138-C14E-4CC9-B8C7-109E928B9E7B",
"sip" : "enabled",
"vmRegionInfo" : "0xa000016c0 is in 0x756000000-0xa4ec00000; bytes after start: 11442067136 bytes before end: 1321199935\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_LARGE 66f000000-66f4a0000 [ 4736K] rw-\/rwx SM=PRV \n GAP OF 0xe6b60000 BYTES\n---> commpage (reserved) 756000000-a4ec00000 [ 11.9G] ---\/--- SM=NUL reserved VM address space (unallocated)\n MALLOC_SMALL a4ec00000-a4f000000 [ 4096K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000002, 0x0000000a000016c0","rawCodes":[2,42949678784],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000a000016c0"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":73959},
"vmregioninfo" : "0xa000016c0 is in 0x756000000-0xa4ec00000; bytes after start: 11442067136 bytes before end: 1321199935\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_LARGE 66f000000-66f4a0000 [ 4736K] rw-\/rwx SM=PRV \n GAP OF 0xe6b60000 BYTES\n---> commpage (reserved) 756000000-a4ec00000 [ 11.9G] ---\/--- SM=NUL reserved VM address space (unallocated)\n MALLOC_SMALL a4ec00000-a4f000000 [ 4096K] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 1opj format mmcif fromDatabase pdb
1opj title:
Structural basis for the auto-inhibition of c-Abl tyrosine kinase [more
info...]
Chain information for 1opj #1
---
Chain | Description | UniProt
A B | Proto-oncogene tyrosine-protein kinase ABL1 | ABL1_MOUSE 248-534
Non-standard residues in 1opj #1
---
CL — chloride ion
MYR — myristic acid
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571; imatinib)
1opj mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> select : 248-256
162 atoms, 168 bonds, 18 residues, 1 model selected
> hbonds sel reveal true
29 hydrogen bonds found
> ~hbonds
> hbonds sel reveal true
29 hydrogen bonds found
> ~hbonds
> select all
5001 atoms, 4892 bonds, 812 residues, 1 model selected
> hbonds sel reveal true
1190 hydrogen bonds found
> ~hbonds
> hbonds sel reveal true
1190 hydrogen bonds found
> select : 248-256
162 atoms, 168 bonds, 7 pseudobonds, 18 residues, 2 models selected
> select all
5001 atoms, 4892 bonds, 1190 pseudobonds, 812 residues, 2 models selected
> ~hbonds
> select : 248-256
162 atoms, 168 bonds, 18 residues, 1 model selected
> style sel stick
Changed 162 atom styles
> style sel stick
Changed 162 atom styles
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> show sel atoms
> copy #1 model 1
Unknown command: copy #1 model 1
> copy help
Unknown command: copy help
> help copy
No help found for 'copy'
> help swapaa
> swapaa lysine #1:255
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lysine 255
Missing or invalid "residues" argument: invalid residues specifier
> lighting simple
> lighting soft
> lighting full
> lighting soft
> set bgColor white
> set bgColor black
> lighting soft
> lighting full
> swapaa ARG #0:231.T
Missing or invalid "residues" argument: invalid residues specifier
> select all
5001 atoms, 4892 bonds, 812 residues, 1 model selected
> color sel bychain
> select : 248-256
162 atoms, 168 bonds, 18 residues, 1 model selected
> rainbow sel
> hbonds sel reveal true
29 hydrogen bonds found
> hbonds sel reveal true
29 hydrogen bonds found
> color sel byhetero
> style sel sphere
Changed 162 atom styles
> style sel ball
Changed 162 atom styles
> color sel byhetero
> rainbow sel
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 162 atom styles
> style sel ball
Changed 162 atom styles
> show sel cartoons
> show sel atoms
> color bfactor sel
162 atoms, 18 residues, atom bfactor range 21.9 to 61.9
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1opj_A SES surface #1.2: minimum, -23.82, mean -3.59,
maximum 14.30
Coulombic values for 1opj_B SES surface #1.3: minimum, -18.96, mean -3.38,
maximum 9.01
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> color sel bypolymer
> rainbow sel
> color sel bynucleotide
> style sel ball
Changed 162 atom styles
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> lighting simple
> lighting soft
> lighting full
> select ~sel & ##selected
4839 atoms, 4724 bonds, 22 pseudobonds, 794 residues, 2 models selected
> select ~sel & ##selected
162 atoms, 168 bonds, 7 pseudobonds, 18 residues, 2 models selected
> select ~sel & ##selected
4839 atoms, 4724 bonds, 22 pseudobonds, 794 residues, 2 models selected
> select ~sel & ##selected
162 atoms, 168 bonds, 7 pseudobonds, 18 residues, 2 models selected
> select ~sel & ##selected
4839 atoms, 4724 bonds, 22 pseudobonds, 794 residues, 2 models selected
> select ~sel & ##selected
162 atoms, 168 bonds, 7 pseudobonds, 18 residues, 2 models selected
> select ~sel & ##selected
4839 atoms, 4724 bonds, 22 pseudobonds, 794 residues, 2 models selected
> select ~sel & ##selected
162 atoms, 168 bonds, 7 pseudobonds, 18 residues, 2 models selected
> select ~sel & ##selected
4839 atoms, 4724 bonds, 22 pseudobonds, 794 residues, 2 models selected
> select ~sel & ##selected
162 atoms, 168 bonds, 7 pseudobonds, 18 residues, 2 models selected
> select ~sel & ##selected
4839 atoms, 4724 bonds, 22 pseudobonds, 794 residues, 2 models selected
> select ~sel & ##selected
162 atoms, 168 bonds, 7 pseudobonds, 18 residues, 2 models selected
> select ~sel & ##selected
4839 atoms, 4724 bonds, 22 pseudobonds, 794 residues, 2 models selected
> select ~sel & ##selected
162 atoms, 168 bonds, 7 pseudobonds, 18 residues, 2 models selected
> select ~sel & ##selected
4839 atoms, 4724 bonds, 22 pseudobonds, 794 residues, 2 models selected
> select ~sel & ##selected
162 atoms, 168 bonds, 7 pseudobonds, 18 residues, 2 models selected
> select ~sel & ##selected
4839 atoms, 4724 bonds, 22 pseudobonds, 794 residues, 2 models selected
> select ~sel & ##selected
162 atoms, 168 bonds, 7 pseudobonds, 18 residues, 2 models selected
> select ~sel & ##selected
4839 atoms, 4724 bonds, 22 pseudobonds, 794 residues, 2 models selected
> select ~sel & ##selected
162 atoms, 168 bonds, 7 pseudobonds, 18 residues, 2 models selected
> help swapaa
> swapaa lys :248.a
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys :248
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys :248.b
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys :248.0
Missing or invalid "residues" argument: invalid residues specifier
> info residues : 255
residue id /A:255 name GLU index 13
residue id /B:255 name GLU index 13
> Select #1:255.A
Unknown command: Select #1:255.A
> Select 255
Unknown command: Select 255
> Select : 255
Unknown command: Select : 255
> Select 248
Unknown command: Select 248
> help select
> select : 248-256
162 atoms, 168 bonds, 7 pseudobonds, 18 residues, 2 models selected
> select #1:255.A
Expected an objects specifier or a keyword
> models
Unknown command: models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> hide #1.2 models
> show #1.2 models
> hide #!1 models
> show #!1 models
> info models
model id #1 type AtomicStructure name 1opj
model id #1.1 type PseudobondGroup name "hydrogen bonds"
model id #1.2 type MolecularSurface name "1opj_A SES surface"
model id #1.3 type MolecularSurface name "1opj_B SES surface"
> info selection
atom id /A:248@N idatm_type Npl
atom id /A:248@CA idatm_type C3
atom id /A:248@C idatm_type C2
atom id /A:248@O idatm_type O2
atom id /A:248@CB idatm_type C3
atom id /A:248@OG idatm_type O3
atom id /A:249@N idatm_type Npl
atom id /A:249@CA idatm_type C3
atom id /A:249@C idatm_type C2
atom id /A:249@O idatm_type O2
atom id /A:249@CB idatm_type C3
atom id /A:249@CG idatm_type C3
atom id /A:249@CD idatm_type C3
atom id /A:250@N idatm_type Npl
atom id /A:250@CA idatm_type C3
atom id /A:250@C idatm_type C2
atom id /A:250@O idatm_type O2
atom id /A:250@CB idatm_type C3
atom id /A:250@CG idatm_type C2
atom id /A:250@OD1 idatm_type O2
atom id /A:250@ND2 idatm_type Npl
atom id /A:251@N idatm_type Npl
atom id /A:251@CA idatm_type C3
atom id /A:251@C idatm_type C2
atom id /A:251@O idatm_type O2
atom id /A:251@CB idatm_type C3
atom id /A:251@CG idatm_type Car
atom id /A:251@CD1 idatm_type Car
atom id /A:251@CD2 idatm_type Car
atom id /A:251@CE1 idatm_type Car
atom id /A:251@CE2 idatm_type Car
atom id /A:251@CZ idatm_type Car
atom id /A:251@OH idatm_type O3
atom id /A:252@N idatm_type Npl
atom id /A:252@CA idatm_type C3
atom id /A:252@C idatm_type C2
atom id /A:252@O idatm_type O2
atom id /A:252@CB idatm_type C3
atom id /A:252@CG idatm_type Cac
atom id /A:252@OD1 idatm_type O2-
atom id /A:252@OD2 idatm_type O2-
atom id /A:253@N idatm_type Npl
atom id /A:253@CA idatm_type C3
atom id /A:253@C idatm_type C2
atom id /A:253@O idatm_type O2
atom id /A:253@CB idatm_type C3
atom id /A:253@CG idatm_type C3
atom id /A:253@CD idatm_type C3
atom id /A:253@CE idatm_type C3
atom id /A:253@NZ idatm_type N3+
atom id /A:254@N idatm_type Npl
atom id /A:254@CA idatm_type C3
atom id /A:254@C idatm_type C2
atom id /A:254@O idatm_type O2
atom id /A:254@CB idatm_type C3
atom id /A:254@CG idatm_type Car
atom id /A:254@CD1 idatm_type Car
atom id /A:254@CD2 idatm_type Car
atom id /A:254@NE1 idatm_type Npl
atom id /A:254@CE2 idatm_type Car
atom id /A:254@CE3 idatm_type Car
atom id /A:254@CZ2 idatm_type Car
atom id /A:254@CZ3 idatm_type Car
atom id /A:254@CH2 idatm_type Car
atom id /A:255@N idatm_type Npl
atom id /A:255@CA idatm_type C3
atom id /A:255@C idatm_type C2
atom id /A:255@O idatm_type O2
atom id /A:255@CB idatm_type C3
atom id /A:255@CG idatm_type C3
atom id /A:255@CD idatm_type Cac
atom id /A:255@OE1 idatm_type O2-
atom id /A:255@OE2 idatm_type O2-
atom id /A:256@N idatm_type Npl
atom id /A:256@CA idatm_type C3
atom id /A:256@C idatm_type C2
atom id /A:256@O idatm_type O2
atom id /A:256@CB idatm_type C3
atom id /A:256@CG idatm_type C3
atom id /A:256@SD idatm_type S3
atom id /A:256@CE idatm_type C3
atom id /B:248@N idatm_type Npl
atom id /B:248@CA idatm_type C3
atom id /B:248@C idatm_type C2
atom id /B:248@O idatm_type O2
atom id /B:248@CB idatm_type C3
atom id /B:248@OG idatm_type O3
atom id /B:249@N idatm_type Npl
atom id /B:249@CA idatm_type C3
atom id /B:249@C idatm_type C2
atom id /B:249@O idatm_type O2
atom id /B:249@CB idatm_type C3
atom id /B:249@CG idatm_type C3
atom id /B:249@CD idatm_type C3
atom id /B:250@N idatm_type Npl
atom id /B:250@CA idatm_type C3
atom id /B:250@C idatm_type C2
atom id /B:250@O idatm_type O2
atom id /B:250@CB idatm_type C3
atom id /B:250@CG idatm_type C2
atom id /B:250@OD1 idatm_type O2
atom id /B:250@ND2 idatm_type Npl
atom id /B:251@N idatm_type Npl
atom id /B:251@CA idatm_type C3
atom id /B:251@C idatm_type C2
atom id /B:251@O idatm_type O2
atom id /B:251@CB idatm_type C3
atom id /B:251@CG idatm_type Car
atom id /B:251@CD1 idatm_type Car
atom id /B:251@CD2 idatm_type Car
atom id /B:251@CE1 idatm_type Car
atom id /B:251@CE2 idatm_type Car
atom id /B:251@CZ idatm_type Car
atom id /B:251@OH idatm_type O3
atom id /B:252@N idatm_type Npl
atom id /B:252@CA idatm_type C3
atom id /B:252@C idatm_type C2
atom id /B:252@O idatm_type O2
atom id /B:252@CB idatm_type C3
atom id /B:252@CG idatm_type Cac
atom id /B:252@OD1 idatm_type O2-
atom id /B:252@OD2 idatm_type O2-
atom id /B:253@N idatm_type Npl
atom id /B:253@CA idatm_type C3
atom id /B:253@C idatm_type C2
atom id /B:253@O idatm_type O2
atom id /B:253@CB idatm_type C3
atom id /B:253@CG idatm_type C3
atom id /B:253@CD idatm_type C3
atom id /B:253@CE idatm_type C3
atom id /B:253@NZ idatm_type N3+
atom id /B:254@N idatm_type Npl
atom id /B:254@CA idatm_type C3
atom id /B:254@C idatm_type C2
atom id /B:254@O idatm_type O2
atom id /B:254@CB idatm_type C3
atom id /B:254@CG idatm_type Car
atom id /B:254@CD1 idatm_type Car
atom id /B:254@CD2 idatm_type Car
atom id /B:254@NE1 idatm_type Npl
atom id /B:254@CE2 idatm_type Car
atom id /B:254@CE3 idatm_type Car
atom id /B:254@CZ2 idatm_type Car
atom id /B:254@CZ3 idatm_type Car
atom id /B:254@CH2 idatm_type Car
atom id /B:255@N idatm_type Npl
atom id /B:255@CA idatm_type C3
atom id /B:255@C idatm_type C2
atom id /B:255@O idatm_type O2
atom id /B:255@CB idatm_type C3
atom id /B:255@CG idatm_type C3
atom id /B:255@CD idatm_type Cac
atom id /B:255@OE1 idatm_type O2-
atom id /B:255@OE2 idatm_type O2-
atom id /B:256@N idatm_type Npl
atom id /B:256@CA idatm_type C3
atom id /B:256@C idatm_type C2
atom id /B:256@O idatm_type O2
atom id /B:256@CB idatm_type C3
atom id /B:256@CG idatm_type C3
atom id /B:256@SD idatm_type S3
atom id /B:256@CE idatm_type C3
> select : 255
18 atoms, 16 bonds, 2 residues, 1 model selected
> swapaa lys : 255
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys :255
Missing or invalid "residues" argument: invalid residues specifier
> lighting simple
> lighting soft
> lighting full
> swapaa lys :255
Missing or invalid "residues" argument: invalid residues specifier
> info residues :255
residue id /A:255 name GLU index 13
residue id /B:255 name GLU index 13
> hide sel atoms
> show sel atoms
> lighting full
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting full
> color sel bynucleotide
> swapaa lys :255.a
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys :255.b
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys :255.a
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys : 255.a
Missing or invalid "residues" argument: invalid residues specifier
> help swap
> set bgColor white
> set bgColor black
> set bgColor white
> set bgColor black
> swapaa lys #1
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys :255
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys :255.a
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys : 255
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys :
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys :255
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys #1:255
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys #1:255
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys #1:255
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lysine :255
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys :255
Missing or invalid "residues" argument: invalid residues specifier
> info residues :255
residue id /A:255 name GLU index 13
residue id /B:255 name GLU index 13
> swapaa lys /A:255
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys /A:255
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys /A:255
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys /A:255
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys /A:255
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lys /A:255
Missing or invalid "residues" argument: invalid residues specifier
> select /A
2508 atoms, 2442 bonds, 20 pseudobonds, 417 residues, 2 models selected
> 255
Unknown command: 255
> select /A:255
9 atoms, 8 bonds, 1 residue, 1 model selected
> swapaa sel
Missing or invalid "resTypes" argument: Expected a text string
> swapaa lys sel
Missing or invalid "residues" argument: invalid residues specifier
> swapaa lysine /A:255
Missing or invalid "residues" argument: invalid residues specifier
> swapaa /A:255 lys
Using Dunbrack library
/A GLU 255: phi -63.2, psi 131.5 trans
Applying LYS rotamer (chi angles: -62.9 -72.4 100.3 78.3) to /A LYS 255
> swapaa /A:255 lys
Using Dunbrack library
/A LYS 255: phi -63.2, psi 131.5 trans
Applying LYS rotamer (chi angles: -62.9 -72.4 100.3 78.3) to /A LYS 255
> swapaa /A:255 GLU
Using Dunbrack library
/A LYS 255: phi -63.2, psi 131.5 trans
Applying GLU rotamer (chi angles: -67.6 -69.7 -22.9) to /A GLU 255
> swapaa /A:255 Lys
Using Dunbrack library
/A GLU 255: phi -63.2, psi 131.5 trans
Applying LYS rotamer (chi angles: -62.9 -72.4 100.3 78.3) to /A LYS 255
> hbonds sel reveal true
2 hydrogen bonds found
> select : 246-255
172 atoms, 180 bonds, 1 pseudobond, 20 residues, 2 models selected
> select : 240-260
295 atoms, 303 bonds, 1 pseudobond, 35 residues, 2 models selected
> hbonds sel reveal true
48 hydrogen bonds found
> hbonds sel reveal true
48 hydrogen bonds found
> hbonds sel reveal true
48 hydrogen bonds found
> ~hbonds
> hbonds sel reveal true
48 hydrogen bonds found
> swapaa /A:255 lys
Using Dunbrack library
/A LYS 255: phi -63.2, psi 131.5 trans
Applying LYS rotamer (chi angles: -62.9 -72.4 100.3 78.3) to /A LYS 255
> swapaa /A:255 glu
Using Dunbrack library
/A LYS 255: phi -63.2, psi 131.5 trans
Applying GLU rotamer (chi angles: -67.6 -69.7 -22.9) to /A GLU 255
> swapaa /A:255 lys
Using Dunbrack library
/A GLU 255: phi -63.2, psi 131.5 trans
Applying LYS rotamer (chi angles: -62.9 -72.4 100.3 78.3) to /A LYS 255
> swapaa /A:255 glu
Using Dunbrack library
/A LYS 255: phi -63.2, psi 131.5 trans
Applying GLU rotamer (chi angles: -67.6 -69.7 -22.9) to /A GLU 255
> swapaa /A:255 lys
Using Dunbrack library
/A GLU 255: phi -63.2, psi 131.5 trans
Applying LYS rotamer (chi angles: -62.9 -72.4 100.3 78.3) to /A LYS 255
> swapaa /A:255 glu
Using Dunbrack library
/A LYS 255: phi -63.2, psi 131.5 trans
Applying GLU rotamer (chi angles: -67.6 -69.7 -22.9) to /A GLU 255
> swapaa /A:255 lys
Using Dunbrack library
/A GLU 255: phi -63.2, psi 131.5 trans
Applying LYS rotamer (chi angles: -62.9 -72.4 100.3 78.3) to /A LYS 255
> swapaa /A:255 glu
Using Dunbrack library
/A LYS 255: phi -63.2, psi 131.5 trans
Applying GLU rotamer (chi angles: -67.6 -69.7 -22.9) to /A GLU 255
> swapaa /A:255 lys
Using Dunbrack library
/A GLU 255: phi -63.2, psi 131.5 trans
Applying LYS rotamer (chi angles: -62.9 -72.4 100.3 78.3) to /A LYS 255
> hide unselected
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide
> show
> hide
> select : 240-260
295 atoms, 303 bonds, 16 pseudobonds, 35 residues, 2 models selected
> show
> hide
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel ball
Changed 295 atom styles
> style sel ball
Changed 295 atom styles
> style sel ball
Changed 295 atom styles
> style sel stick
Changed 295 atom styles
> style sel sphere
Changed 295 atom styles
> style sel ball
Changed 295 atom styles
> show
> hide
> show : 240-260
> show hbonds
> help show
> show spec
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show pbonds
> hide pbonds
> show pbonds
> hide hbonds
> show hbonds
Unsupported scale factor (0.000000) detected on Display0
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,1
Model Number: MW2V3LL/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 16 GB
System Firmware Version: 13822.1.2
OS Loader Version: 13822.1.2
Software:
System Software Overview:
System Version: macOS 26.0.1 (25A362)
Kernel Version: Darwin 25.0.0
Time since boot: 15 days, 10 hours, 27 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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-MutationScores: 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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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