![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 days ago
Closed 8 days ago
#20266 closed defect (can't reproduce)
Crash in swap_buffers, Qt dispatched status line expose event during SideView makeCurrent()
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 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 0x0000000208d4b100 (most recent call first):
File "/Applications/ChimeraX-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 122 in make_current
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 555 in make_current
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 584 in use_shared_context
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 146 in render
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 115 in _redraw
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 100 in draw_new_frame
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 169 in update_graphics_now
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 153 in resizeEvent
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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, PIL._imaging, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, 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, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 58)
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mapped file 300000000-30b3dc000 [179.9M] r--\/rwx SM=COW Object_id=854c3add
GAP OF 0x106c24000 BYTES
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CoreGraphics 32K 2
CoreServices 624K 2
CoreUI image data 5856K 52
Foundation 48K 2
Kernel Alloc Once 208K 3
MALLOC 422.9M 181
MALLOC guard page 3744K 4
Mach message 64K 3
OpenGL GLSL 256K 3
PROTECTED_MEMORY 16K 1
STACK GUARD 720K 45
Stack 196.5M 46
Stack Guard 56.0M 1
VM_ALLOCATE 224.7M 227
VM_ALLOCATE (reserved) 256.0M 1 reserved VM address space (unallocated)
__AUTH 5968K 656
__AUTH_CONST 90.5M 1042
__CTF 824 1
__DATA 42.9M 1138
__DATA_CONST 59.7M 1185
__DATA_DIRTY 8499K 899
__FONT_DATA 2352 1
__GLSLBUILTINS 5176K 1
__INFO_FILTER 8 1
__LINKEDIT 619.8M 139
__OBJC_RO 78.4M 1
__OBJC_RW 2571K 1
__TEXT 1.5G 1172
__TEXT (graphics) 5360K 35
__TPRO_CONST 128K 2
dyld private memory 1584K 15
mapped file 636.8M 100
page table in kernel 1362K 1
shared memory 3680K 27
=========== ======= =======
TOTAL 4.2G 7187
TOTAL, minus reserved VM space 3.9G 7187
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===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open pdb:1e3i
Summary of feedback from opening 1e3i fetched from pdb
---
notes | Fetching compressed mmCIF 1e3i from http://files.rcsb.org/download/1e3i.cif
Fetching CCD CXF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/CXF/CXF.cif
Fetching CCD NAI from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/NAI/NAI.cif
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
1e3i title:
Mouse class II alcohol dehydrogenase complex with NADH and inhibitor [more
info...]
Chain information for 1e3i #1
---
Chain | Description | UniProt
A B | ALCOHOL DEHYDROGENASE, CLASS II | Q9QYY9 1-376
Non-standard residues in 1e3i #1
---
CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
> open 1e3i fromDatabase pdb format mmcif
1e3i title:
Mouse class II alcohol dehydrogenase complex with NADH and inhibitor [more
info...]
Chain information for 1e3i #2
---
Chain | Description | UniProt
A B | ALCOHOL DEHYDROGENASE, CLASS II | Q9QYY9 1-376
Non-standard residues in 1e3i #2
---
CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
> log metadata #2
Metadata for 1e3i #2
---
Title | Mouse class II alcohol dehydrogenase complex with NADH and inhibitor
Citations | Svensson, S., Hoeoeg, J.O., Schneider, G., Sandalova, T. (2000). Crystal Structure of Mouse Class II Alcohol Dehydrogenase Reveal Determinants of Substrate Specificity and Catalytic Efficiency. J.Mol.Biol., 302, 441. PMID: 10970744. DOI: 10.1006/JMBI.2000.4039
Svensson, S., Stroemberg, P., Hoeoeg, J.O. (1999). A Novel Subtype of Class II
Alcohol Dehydrogenase in Rodents. J.Biol.Chem., 274, 29712. PMID: 10514444.
DOI: 10.1074/JBC.274.42.29712
Non-standard residues | CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
Gene source | Mus musculus (house mouse)
Experimental method | X-ray diffraction
Resolution | 2.100Å
> hide cartoons
> show cartoons
> style stick
Changed 12118 atom styles
> style sphere
Changed 12118 atom styles
> style ball
Changed 12118 atom styles
> style stick
Changed 12118 atom styles
> show cartoons
> show atoms
> style sphere
Changed 12118 atom styles
> ui tool show "Side View"
> view all
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 11898 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> style stick
Changed 12118 atom styles
> select #1/A
3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected
> hide sel cartoons
> select #1/A
3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color (#!1 & sel) red
> select add #2
9100 atoms, 8698 bonds, 25 pseudobonds, 1692 residues, 4 models selected
> select subtract #2
3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected
> select add #1
6059 atoms, 5792 bonds, 17 pseudobonds, 1126 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #2
6059 atoms, 5792 bonds, 17 pseudobonds, 1126 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2
6059 atoms, 5792 bonds, 17 pseudobonds, 1126 residues, 2 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> select add #1
6059 atoms, 5792 bonds, 17 pseudobonds, 1126 residues, 2 models selected
> select subtract #1
Nothing selected
> select #1/A
3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected
> select #1/A
3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected
> show sel cartoons
> show sel atoms
> hide sel atoms
> close #2
> close #1
> open pdb:1e3i format mmcif fromDatabase pdb
1e3i title:
Mouse class II alcohol dehydrogenase complex with NADH and inhibitor [more
info...]
Chain information for 1e3i #1
---
Chain | Description | UniProt
A B | ALCOHOL DEHYDROGENASE, CLASS II | Q9QYY9 1-376
Non-standard residues in 1e3i #1
---
CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
> select #1/A
3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected
> hide sel cartoons
> show sel atoms
> color sel red
> color sel byelement
Drag select of 1155 atoms, 3 pseudobonds, 1124 bonds
> select clear
> select /B:304
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:316
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /A:324@CA
1 atom, 1 residue, 1 model selected
> select /B:317
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:316
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 2337 atoms, 8 pseudobonds, 2265 bonds
> select clear
> select #1/A
3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select down
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
44 atoms, 47 bonds, 5 residues, 1 model selected
> select up
2800 atoms, 2849 bonds, 376 residues, 1 model selected
> select up
3041 atoms, 2906 bonds, 566 residues, 1 model selected
> select down
2800 atoms, 2849 bonds, 376 residues, 1 model selected
> select down
44 atoms, 47 bonds, 5 residues, 1 model selected
> select down
4 atoms, 3 bonds, 1 residue, 1 model selected
> select down
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add /A:181@C
5 atoms, 3 bonds, 2 residues, 1 model selected
> select clear
> select /B:308
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select /A:318@C
1 atom, 1 residue, 1 model selected
> label sel atoms attribute name
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> close
> open pdb:1e3i format mmcif fromDatabase pdb
1e3i title:
Mouse class II alcohol dehydrogenase complex with NADH and inhibitor [more
info...]
Chain information for 1e3i #1
---
Chain | Description | UniProt
A B | ALCOHOL DEHYDROGENASE, CLASS II | Q9QYY9 1-376
Non-standard residues in 1e3i #1
---
CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
> select #1/A
3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected
> save "/Users/ivana.kapustova/OneDrive - Karolinska
> Institutet/Teaching/Chemical
> biology/2026_ChimeraX/savefiles/CanvasExercises.cxs"
> save /Users/ivana.kapustova/Desktop/image1.png supersample 3
> hide sel cartoons
> hide sel atoms
> show sel atoms
> color (#!1 & sel) red
> undo
Undo failed, probably because structures have been modified.
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 1
> select /A-B:95-96
32 atoms, 32 bonds, 4 residues, 1 model selected
> select /A-B:95
14 atoms, 14 bonds, 2 residues, 1 model selected
> sequence chain #1/A
Alignment identifier is 1/A
> select
> /A:7-13,22-28,35-44,68-76,88-91,134-136,139-141,153-157,161-163,198-202,222-226,243-245,268-271,292-295,302-306,315-318,348-353,371-375
695 atoms, 685 bonds, 92 residues, 1 model selected
> select /A:75
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:75
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:75
6 atoms, 5 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /A:235
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:235-238
28 atoms, 27 bonds, 4 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> undo
> select /A:235-238
28 atoms, 27 bonds, 4 residues, 1 model selected
> ~label sel residues
> sequence chain #1/B
Alignment identifier is 1/B
> select
> /B:46-52,100-105,119-123,172-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366
947 atoms, 949 bonds, 128 residues, 1 model selected
> select /B:235-236
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /B:235-238
28 atoms, 27 bonds, 4 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> label sel attribute label_one_letter_code
> select clear
> select
> /B:46-52,100-105,119-123,172-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366
947 atoms, 949 bonds, 128 residues, 1 model selected
> select /B:206-207
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /B:206-217
79 atoms, 78 bonds, 12 residues, 1 model selected
> color sel cyan
> select clear
> select
> /A:7-13,22-28,35-44,68-76,88-91,134-136,139-141,153-157,161-163,198-202,222-226,243-245,268-271,292-295,302-306,315-318,348-353,371-375
695 atoms, 685 bonds, 92 residues, 1 model selected
> select /A:316
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:316
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:316,351
13 atoms, 11 bonds, 2 residues, 1 model selected
> color sel magenta
> select
> /A:46-52,100-105,119-123,169-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366
972 atoms, 974 bonds, 131 residues, 1 model selected
> select
> /A:7-13,22-28,35-44,68-76,88-91,134-136,139-141,153-157,161-163,198-202,222-226,243-245,268-271,292-295,302-306,315-318,348-353,371-375
695 atoms, 685 bonds, 92 residues, 1 model selected
> select /A:246
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:246
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:351
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add /A:316
13 atoms, 11 bonds, 2 residues, 1 model selected
> label sel attribute label_specifier
> select clear
> select /A:246
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:246
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:246,281
13 atoms, 11 bonds, 2 residues, 1 model selected
> color sel purple
> color sel forest green
> label sel attribute label_specifier
> select /A:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:4,39
13 atoms, 11 bonds, 2 residues, 1 model selected
> color sel white
> color sel blue
> label sel attribute label_specifier
> select /A:176
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:176
8 atoms, 7 bonds, 1 residue, 1 model selected
> select
> /A:46-52,100-105,119-123,169-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366
972 atoms, 974 bonds, 131 residues, 1 model selected
> select /A:176
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:176
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:176,211
13 atoms, 11 bonds, 2 residues, 1 model selected
> color sel lime
> color sel red
> color sel orange
> label sel attribute label_specifier
> select clear
> select /A:5,176,211
22 atoms, 19 bonds, 3 residues, 1 model selected
> select clear
> select /A:5
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:5
9 atoms, 8 bonds, 1 residue, 1 model selected
> sequence chain #1/B
Alignment identifier is 1/B
> select /B:5
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:5
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select /B:5@NZ
1 atom, 1 residue, 1 model selected
> label sel atoms attribute name
> label sel attribute label_one_letter_code
> select clear
> save "/Users/ivana.kapustova/OneDrive - Karolinska
> Institutet/Teaching/Chemical
> biology/2026_ChimeraX/savefiles/CanvasExercises.cxs"
> select
> /B:46-52,100-105,119-123,172-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366
947 atoms, 949 bonds, 128 residues, 1 model selected
> select
> /B:7-14,22-28,35-44,63-64,68-76,88-91,134-136,139-141,153-157,161-164,198-202,222-226,243-245,268-271,292-295,302-306,315-318,348-353,371-375
721 atoms, 710 bonds, 96 residues, 1 model selected
> select
> /B:46-52,100-105,119-123,172-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366
947 atoms, 949 bonds, 128 residues, 1 model selected
> select /B:47
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:47
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:47
7 atoms, 7 bonds, 1 residue, 1 model selected
> select
> /B:46-52,100-105,119-123,172-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366
947 atoms, 949 bonds, 128 residues, 1 model selected
> select clear
> select /B:349
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:349
7 atoms, 6 bonds, 1 residue, 1 model selected
> sequence chain #1/A
Alignment identifier is 1/A
> select
> /A:7-13,22-28,35-44,68-76,88-91,134-136,139-141,153-157,161-163,198-202,222-226,243-245,268-271,292-295,302-306,315-318,348-353,371-375
695 atoms, 685 bonds, 92 residues, 1 model selected
> select /B:349
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:349
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:349-350
17 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:349-350
17 atoms, 17 bonds, 2 residues, 1 model selected
> select
> /A:7-13,22-28,35-44,68-76,88-91,134-136,139-141,153-157,161-163,198-202,222-226,243-245,268-271,292-295,302-306,315-318,348-353,371-375
695 atoms, 685 bonds, 92 residues, 1 model selected
> select /A:349
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:349
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:349
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:349
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select
> /B:46-52,100-105,119-123,172-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366
947 atoms, 949 bonds, 128 residues, 1 model selected
> select clear
> select /B:349
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> ~label sel residues
> save "/Users/ivana.kapustova/OneDrive - Karolinska
> Institutet/Teaching/Chemical
> biology/2026_ChimeraX/savefiles/CanvasExercises-PrimaryStructure.cxs"
> close session
> open "/Users/ivana.kapustova/OneDrive - Karolinska
> Institutet/Teaching/Chemical
> biology/2026_ChimeraX/savefiles/CanvasExercises.cxs" format session
> view name session-start
opened ChimeraX session
Drag select of 357 atoms, 749 residues, 17 pseudobonds, 304 bonds
> close session
> open pdb:1e3i format mmcif fromDatabase pdb
1e3i title:
Mouse class II alcohol dehydrogenase complex with NADH and inhibitor [more
info...]
Chain information for 1e3i #1
---
Chain | Description | UniProt
A B | ALCOHOL DEHYDROGENASE, CLASS II | Q9QYY9 1-376
Non-standard residues in 1e3i #1
---
CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
> view
> view all
> select helix
1919 atoms, 1923 bonds, 259 residues, 1 model selected
> color sel red
> select clear
> select strand
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> color sel purple
> select up
5580 atoms, 5678 bonds, 749 residues, 1 model selected
> select up
6059 atoms, 5792 bonds, 1126 residues, 1 model selected
> select down
5580 atoms, 5678 bonds, 749 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select up
5580 atoms, 5678 bonds, 749 residues, 1 model selected
> select up
6059 atoms, 5792 bonds, 1126 residues, 1 model selected
> select up
6059 atoms, 5792 bonds, 1126 residues, 1 model selected
> select up
6059 atoms, 5792 bonds, 1126 residues, 1 model selected
> select down
5580 atoms, 5678 bonds, 749 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select down
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select strand
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> select coil
2245 atoms, 2238 bonds, 302 residues, 1 model selected
> color sel white
> select clear
> save "/Users/ivana.kapustova/OneDrive - Karolinska
> Institutet/Teaching/Chemical
> biology/2026_ChimeraX/savefiles/CanvasExercises-SecondaryStructure.cxs"
> color helix red
> color helix orange
> color helix red
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 1
> select /A-B:253
14 atoms, 14 bonds, 2 residues, 1 model selected
> select /A-B:253-262
154 atoms, 154 bonds, 20 residues, 1 model selected
> sequence chain #1/A
Alignment identifier is 1/A
> select clear
> select /A:253-254
14 atoms, 14 bonds, 2 residues, 1 model selected
> select /A:253-262
77 atoms, 77 bonds, 10 residues, 1 model selected
> label sel attribute label_one_letter_code
> show sel atoms
> view sel
> view
> ui tool show "Side View"
> view sel
> ui tool show H-Bonds
> cartoon suppressBackboneDisplay false
> ui tool show H-Bonds
> hbonds sel reveal true
29 hydrogen bonds found
> view
> select clear
> select /A:371
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:371-375
41 atoms, 40 bonds, 5 residues, 1 model selected
> color sel byelement
> cartoon suppressBackboneDisplay false
> view
> view sel
> cartoon suppressBackboneDisplay false
> show sel atoms
> ui tool show "Side View"
> view
> select /A:253
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:253-262
77 atoms, 77 bonds, 11 pseudobonds, 10 residues, 2 models selected
> color (#!1 & sel) byelement
> select /A:371
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:371-375
41 atoms, 40 bonds, 5 residues, 1 model selected
> select sel @ show sel atoms
> cartoon suppressBackboneDisplay false
> show sel atoms
> cartoon suppressBackboneDisplay false
> color sel byelement
> select clear
> select /A:371
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:371-375
41 atoms, 40 bonds, 5 residues, 1 model selected
> select sel: show sel atoms
> color sel byelement
> save "/Users/ivana.kapustova/OneDrive - Karolinska
> Institutet/Teaching/Chemical
> biology/2026_ChimeraX/savefiles/CanvasExercises-SecondaryStructure.cxs"
> hide sel cartoons
> hbonds sel reveal true
69 hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel restrict both reveal true
32 hydrogen bonds found
> hbonds sel reveal true
69 hydrogen bonds found
> select clear
> select /A:371
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:371-375
41 atoms, 40 bonds, 5 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> select /A:371
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:371-375
41 atoms, 40 bonds, 5 residues, 1 model selected
> label sel attribute label_specifier
> select clear
> view
> select /A:369
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:369
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:371
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:371-375
41 atoms, 40 bonds, 5 residues, 1 model selected
> select strand
1416 atoms, 1395 bonds, 16 pseudobonds, 188 residues, 2 models selected
> show sel cartoons
> select clear
> view
Drag select of 817 atoms, 743 residues, 86 pseudobonds, 751 bonds
> select clear
> select /A:371
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:371-375
41 atoms, 40 bonds, 5 residues, 1 model selected
> select sel: transparency 50,r #0
Missing or invalid "percent" argument: Expected a number
> select transparency 50,r #0
Expected an objects specifier or a keyword
> transparency sel 50 target c
> select ~sel & ##selected
5856 atoms, 5594 bonds, 54 pseudobonds, 1100 residues, 3 models selected
> transparency sel 50 target c
> select clear
> select
> /A:46-52,100-105,119-123,169-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366
972 atoms, 974 bonds, 3 pseudobonds, 131 residues, 2 models selected
> select /A:253-254
14 atoms, 14 bonds, 2 residues, 1 model selected
> select /A:253-262
77 atoms, 77 bonds, 10 residues, 1 model selected
> select up
2800 atoms, 2849 bonds, 376 residues, 1 model selected
> select down
77 atoms, 77 bonds, 10 residues, 1 model selected
> hbonds sel reveal true
29 hydrogen bonds found
> select /A:371
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:371-375
41 atoms, 40 bonds, 5 residues, 1 model selected
> select sel: hbonds sel reveal true
69 hydrogen bonds found
> select clear
> select /A:349
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:349
7 atoms, 6 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select sel: hbonds sel reveal true
14 hydrogen bonds found
> select clear
> select /A:349
7 atoms, 6 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
3 hydrogen bonds found
> select /A:371@O
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select down
1 atom, 1 residue, 1 model selected
> view sel
> label sel atoms attribute name
> select /A:349@OG1
1 atom, 1 residue, 1 model selected
> select clear
> select /A:349@N
1 atom, 1 residue, 1 model selected
> label sel atoms attribute name
> select /A:349
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select /A:349@O
1 atom, 1 residue, 1 model selected
> label sel atoms attribute name
> select clear
> select /A:349@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> view
> save "/Users/ivana.kapustova/OneDrive - Karolinska
> Institutet/Teaching/Chemical
> biology/2026_ChimeraX/savefiles/CanvasExercises-SecondaryStructure.cxs"
> select /A:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select sel: show sel atoms
> color sel byelement
> select /A:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select /A:27@O
1 atom, 1 residue, 1 model selected
> select sel: select /A:23
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:23-32
79 atoms, 80 bonds, 10 residues, 1 model selected
> select /A:24
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:24-31
62 atoms, 63 bonds, 8 residues, 1 model selected
> show sel atoms
> color sel byelement
> select /A:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> save "/Users/ivana.kapustova/OneDrive - Karolinska
> Institutet/Teaching/Chemical
> biology/2026_ChimeraX/savefiles/CanvasExercises-SecondaryStructure.cxs"
> undo
> redo
> undo
> select sel: hide sel atoms
> ~label sel residues
> select clear
> select /A:262@N
1 atom, 1 residue, 1 model selected
> select /A:262@N
1 atom, 1 residue, 1 model selected
> select /A:262
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:262
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:261
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:260
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:259
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:258
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> view
> save "/Users/ivana.kapustova/OneDrive - Karolinska
> Institutet/Teaching/Chemical
> biology/2026_ChimeraX/savefiles/CanvasExercises-SecondaryStructure.cxs"
> select /A:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:1-376
2800 atoms, 2849 bonds, 3 pseudobonds, 376 residues, 2 models selected
> select ~sel & ##selected
3259 atoms, 2943 bonds, 17 pseudobonds, 750 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> undo
> select clear
> save "/Users/ivana.kapustova/OneDrive - Karolinska
> Institutet/Teaching/Chemical
> biology/2026_ChimeraX/savefiles/CanvasExercises-SecondaryStructure.cxs"
> open "/Users/ivana.kapustova/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Teaching/Chemical
> biology/2026_ChimeraX/savefiles/CanvasExercises.cxs"
> view name session-start
opened ChimeraX session
> close session
> open pdb:1e3i format mmcif fromDatabase pdb
1e3i title:
Mouse class II alcohol dehydrogenase complex with NADH and inhibitor [more
info...]
Chain information for 1e3i #1
---
Chain | Description | UniProt
A B | ALCOHOL DEHYDROGENASE, CLASS II | Q9QYY9 1-376
Non-standard residues in 1e3i #1
---
CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
> save "/Users/ivana.kapustova/OneDrive - Karolinska
> Institutet/Teaching/Chemical
> biology/2026_ChimeraX/savefiles/CanvasExercises-TertiaryStructure.cxs"
> select chain 1/A
Expected an objects specifier or a keyword
> select chain1/A
Expected an objects specifier or a keyword
> select chainA
Expected an objects specifier or a keyword
> select chain A
Expected an objects specifier or a keyword
> select #1/A
3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected
> select #1/A
3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected
> select ~sel & ##selected
3018 atoms, 2886 bonds, 9 pseudobonds, 560 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select /A
3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected
> hide sel atoms
> select coil
2245 atoms, 2238 bonds, 302 residues, 1 model selected
> select clear
Drag select of 376 residues
> ui tool show "Color Actions"
> color sel bychain
> color sel bypolymer
> color sel bynucleotide
> color sel byelement
> color sel byhetero
> color sel byhetero target c
> color sel bychain target c
> close session
> open "/Users/ivana.kapustova/OneDrive - Karolinska
> Institutet/Teaching/Chemical
> biology/2026_ChimeraX/savefiles/CanvasExercises-TertiaryStructure.cxs"
> format session
> view name session-start
opened ChimeraX session
> select /B
3018 atoms, 2886 bonds, 9 pseudobonds, 560 residues, 2 models selected
> hide sel atoms
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> view
> rainbow
> select
3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected
> hide sel atoms
> select clear
> save "/Users/ivana.kapustova/OneDrive - Karolinska
> Institutet/Teaching/Chemical
> biology/2026_ChimeraX/savefiles/CanvasExercises-TertiaryStructure.cxs"
> select /A:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> label sel atoms attribute name
> label sel attribute label_specifier
> select clear
> select /A:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:3-4
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> cartoon suppressBackboneDisplay false
> ~label sel atoms
> select /A:1@N
1 atom, 1 residue, 1 model selected
> label sel atoms attribute name
> select clear
> select /A:376
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:376
12 atoms, 12 bonds, 1 residue, 1 model selected
> cartoon suppressBackboneDisplay false
> show sel atoms
> select /A:376@N
1 atom, 1 residue, 1 model selected
> select /A:376@N
1 atom, 1 residue, 1 model selected
> label sel atoms attribute name
> label sel attribute label_specifier
> select clear
Drag select of 7 residues
> select /A:318
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add /A:317
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add /A:316
20 atoms, 17 bonds, 3 residues, 1 model selected
> select add /A:315
26 atoms, 22 bonds, 4 residues, 1 model selected
> select add /A:292
32 atoms, 27 bonds, 5 residues, 1 model selected
> select add /A:293
38 atoms, 32 bonds, 6 residues, 1 model selected
> select add /A:294
45 atoms, 38 bonds, 7 residues, 1 model selected
> select add /A:295
52 atoms, 44 bonds, 8 residues, 1 model selected
> select add /A:270
60 atoms, 51 bonds, 9 residues, 1 model selected
> select add /A:271
68 atoms, 58 bonds, 10 residues, 1 model selected
> select add /A:269
74 atoms, 63 bonds, 11 residues, 1 model selected
> select add /A:268
86 atoms, 75 bonds, 12 residues, 1 model selected
> select add /A:198
93 atoms, 81 bonds, 13 residues, 1 model selected
> select add /A:199
99 atoms, 86 bonds, 14 residues, 1 model selected
> select add /A:200
104 atoms, 90 bonds, 15 residues, 1 model selected
> select add /A:201
111 atoms, 96 bonds, 16 residues, 1 model selected
> select add /A:202
122 atoms, 107 bonds, 17 residues, 1 model selected
> select add /A:225
127 atoms, 111 bonds, 18 residues, 1 model selected
> select add /A:226
135 atoms, 118 bonds, 19 residues, 1 model selected
> select add /A:224
143 atoms, 125 bonds, 20 residues, 1 model selected
> select add /A:223
151 atoms, 132 bonds, 21 residues, 1 model selected
> select add /A:222
162 atoms, 142 bonds, 22 residues, 1 model selected
> select add /A:243
170 atoms, 149 bonds, 23 residues, 1 model selected
> select add /A:244
176 atoms, 154 bonds, 24 residues, 1 model selected
> select add /A:245
184 atoms, 161 bonds, 25 residues, 1 model selected
> label sel text " Parallel beta sheet"
> undo
> redo
> select /A:1@N
1 atom, 1 residue, 1 model selected
> label sel atoms text "N terminus"
> select /A:376@N
1 atom, 1 residue, 1 model selected
> ~label sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel byelement
> select /A:376@C
1 atom, 1 residue, 1 model selected
> label sel atoms text "C terminus"
> select clear
> select add /A:243
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /A:244
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add /A:245
22 atoms, 19 bonds, 3 residues, 1 model selected
> select add /A:222
33 atoms, 29 bonds, 4 residues, 1 model selected
> select add /A:223
41 atoms, 36 bonds, 5 residues, 1 model selected
> select add /A:224
49 atoms, 43 bonds, 6 residues, 1 model selected
> select add /A:225
54 atoms, 47 bonds, 7 residues, 1 model selected
> select add /A:226
62 atoms, 54 bonds, 8 residues, 1 model selected
> select add /A:198
69 atoms, 60 bonds, 9 residues, 1 model selected
> select add /A:199
75 atoms, 65 bonds, 10 residues, 1 model selected
> select add /A:200
80 atoms, 69 bonds, 11 residues, 1 model selected
> select add /A:201
87 atoms, 75 bonds, 12 residues, 1 model selected
> select add /A:202
98 atoms, 86 bonds, 13 residues, 1 model selected
> select add /A:268
110 atoms, 98 bonds, 14 residues, 1 model selected
> select add /A:269
116 atoms, 103 bonds, 15 residues, 1 model selected
> select add /A:270
124 atoms, 110 bonds, 16 residues, 1 model selected
> select add /A:271
132 atoms, 117 bonds, 17 residues, 1 model selected
> select add /A:292
138 atoms, 122 bonds, 18 residues, 1 model selected
> select add /A:293
144 atoms, 127 bonds, 19 residues, 1 model selected
> select add /A:294
151 atoms, 133 bonds, 20 residues, 1 model selected
> select add /A:295
158 atoms, 139 bonds, 21 residues, 1 model selected
> select add /A:315
164 atoms, 144 bonds, 22 residues, 1 model selected
> select add /A:316
172 atoms, 151 bonds, 23 residues, 1 model selected
> select add /A:317
180 atoms, 158 bonds, 24 residues, 1 model selected
> select add /A:318
184 atoms, 161 bonds, 25 residues, 1 model selected
> ~label sel residues
> select clear
> select /A:244
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /A:224
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add /A:200
19 atoms, 16 bonds, 3 residues, 1 model selected
> select add /A:269
25 atoms, 21 bonds, 4 residues, 1 model selected
> select subtract /A:269
19 atoms, 16 bonds, 3 residues, 1 model selected
> select add /A:270
27 atoms, 23 bonds, 4 residues, 1 model selected
> select subtract /A:270
19 atoms, 16 bonds, 3 residues, 1 model selected
> select add /A:269
25 atoms, 21 bonds, 4 residues, 1 model selected
> select add /A:293
31 atoms, 26 bonds, 5 residues, 1 model selected
> select add /A:316
39 atoms, 33 bonds, 6 residues, 1 model selected
> label sel text "Parallel beta sheet"
> select /A:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel byelement
> select clear
> select /A:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> ~label sel residues
> select /A:376
12 atoms, 12 bonds, 1 residue, 1 model selected
> ~label sel residues
> select clear
> select add /A:339
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /A:338
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add /A:337
29 atoms, 27 bonds, 3 residues, 1 model selected
> select add /A:336
37 atoms, 34 bonds, 4 residues, 1 model selected
> select add /A:335
43 atoms, 39 bonds, 5 residues, 1 model selected
> select add /A:334
50 atoms, 45 bonds, 6 residues, 1 model selected
> select add /A:333
58 atoms, 52 bonds, 7 residues, 1 model selected
> select add /A:332
66 atoms, 59 bonds, 8 residues, 1 model selected
> select add /A:331
73 atoms, 66 bonds, 9 residues, 1 model selected
> select add /A:330
80 atoms, 72 bonds, 10 residues, 1 model selected
> select add /A:329
86 atoms, 77 bonds, 11 residues, 1 model selected
> select add /A:328
94 atoms, 84 bonds, 12 residues, 1 model selected
> select add /A:327
101 atoms, 90 bonds, 13 residues, 1 model selected
> select add /A:326
107 atoms, 95 bonds, 14 residues, 1 model selected
> select add /A:325
116 atoms, 103 bonds, 15 residues, 1 model selected
> save "/Users/ivana.kapustova/OneDrive - Karolinska
> Institutet/Teaching/Chemical
> biology/2026_ChimeraX/savefiles/CanvasExercises-TertiaryStructure.cxs"
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 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 M2 Max
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,5
Model Number: Z17K000SYKS/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 Performance and 4 Efficiency)
Memory: 64 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (a) (25D771280a)
Kernel Version: Darwin 25.3.0
Time since boot: 1 day, 6 hours, 11 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
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:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
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: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
Change History (2)
comment:1 by , 8 days ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in swap_buffers exposing status line during Mac wakeup |
comment:2 by , 8 days ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash in swap_buffers exposing status line during Mac wakeup → Crash in swap_buffers, Qt dispatched status line expose event during SideView makeCurrent() |
Note:
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ChimeraX was trying to draw the SideView and during the OpenGL makeCurrent() call Qt dispatched an expose event to the status line where swap_buffers() crashed, possibly because it was in a QOpenGLContext.makeCurrent() call. This bug appeared with macOS 26. A possible work-around is to ignore status line expose events since there are other Qt OpenGL errors associated with handling those expose events in macOS 26.
Ticket #20265 is a similar crash in Qt 6.10.
Ticket #20267 is the more common status line expose event OpenGL error without a crash, but probably disabling ChimeraX use.