![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 days ago
Last modified 8 days ago
#20265 assigned defect
Crash in swap_buffers exposing SideView during Mac wakeup, Qt 6.10
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | 1.12 |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | chimerax-programmers | |
| 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: 1.12.dev202605010205 (2026-05-01 02:05:23 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 0x00000001f4f23100 (most recent call first):
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 564 in swap_buffers
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 310 in render
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 119 in exposeEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 424 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 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, 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.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imaging, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 55)
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"codeSigningFlags" : 570491649,
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"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
unused __TEXT 2e36a4000-2e36a8000 [ 16K] r--\/r-- SM=COW unused unknown system shared lib __TEXT
GAP OF 0x1a8958000 BYTES
---> commpage (reserved) 48c000000-787000000 [ 11.9G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL 787000000-787400000 [ 4096K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000002, 0x0000000700000900","rawCodes":[2,30064773376],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000700000900"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":15376},
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
unused __TEXT 2e36a4000-2e36a8000 [ 16K] r--\/r-- SM=COW unused unknown system shared lib __TEXT
GAP OF 0x1a8958000 BYTES
---> commpage (reserved) 48c000000-787000000 [ 11.9G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL 787000000-787400000 [ 4096K] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
UCSF ChimeraX version: 1.12.dev202605010205 (2026-05-01)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/chiaramcallister/Downloads/1E3I.pdb
1E3I.pdb title:
Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more
info...]
Chain information for 1E3I.pdb #1
---
Chain | Description | UniProt
A B | alcohol dehydrogenase, class II | Q9QYY9 1-376
Non-standard residues in 1E3I.pdb #1
---
CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
> select /A:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> view sel
> lighting simple
> lighting shadows true
> lighting simple
> ui tool show "Selection Inspector"
> set bgColor white
> set bgColor black
> lighting simple
> select add #1
6059 atoms, 5792 bonds, 17 pseudobonds, 1126 residues, 2 models selected
> select subtract #1
Nothing selected
> show cartoons
> color bynucleotide
> view
> select /A:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> view sel
> view
> cartoon
> color red strands false
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color cyan strands
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color red helices
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color yellow coils
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color red :/isHelix
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color cyan :/isStrand
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color yellow :/isCoil
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> hide atoms
> show cartoons
> color byss
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select helix
1919 atoms, 1923 bonds, 259 residues, 1 model selected
> color red sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel red
> hide atoms
> cartoon
> color all yellow
> select helix
1919 atoms, 1923 bonds, 259 residues, 1 model selected
> color sel red
> select strand
1416 atoms, 1395 bonds, 188 residues, 1 model selected
> color sel cyan
> select clear
> view
> view orient
Drag select of 41 residues
> style sel stick
Changed 324 atom styles
> style sel stick
Changed 324 atom styles
> color sel magenta
> show sel atoms
> style sel stick
Changed 324 atom styles
> label sel residues
> style sel stick
Changed 324 atom styles
> style sel stick
Changed 324 atom styles
> clear
Unknown command: clear
> hide atoms
> cartoon
> select clear
> hide atoms
> cartoon
> color bychain
> hide names\
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide names\
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> label delete
> select /A
3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected
> view sel
> rainbow sel
> color /A:1-120 blue
> color /A:121-249 orange
> color /A:250-376 blue
> hide /B cartoons
> N-terminus: blue → green → yellow → orange → red: C-terminus
Unknown command: N-terminus: blue → green → yellow → orange → red: C-terminus
> rainbow sel
> select :NAI
88 atoms, 96 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 88 atom styles
> sequence chain #1/A
Alignment identifier is 1/A
> select /A:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:1-128
964 atoms, 984 bonds, 128 residues, 1 model selected
> lighting simple
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> ui tool show "Selection Inspector"
> select /A:1-120
898 atoms, 918 bonds, 120 residues, 1 model selected
> color sel white
> select /A:250-376
955 atoms, 970 bonds, 127 residues, 1 model selected
> color sel white
> show /A cartoons
> color /A rainbow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select clear
> rainbow
> color /A rainbow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select /A:1-180 color sel white
Expected a keyword
> select /A:1-180
1371 atoms, 1398 bonds, 180 residues, 1 model selected
> color sel white
> select /A:320-376
458 atoms, 468 bonds, 57 residues, 1 model selected
> color sel white
> rainbow sel
> select clear
> rainbow
> /A:181-319
Unknown command: /A:181-319
> color sel white
> select /A:181-319
971 atoms, 981 bonds, 139 residues, 1 model selected
> color sel white
> color /A rainbow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select /A:1-180,320-376
1829 atoms, 1866 bonds, 237 residues, 1 model selected
> color sel white
> rainbow sel
> select clear
> rainbow
> color /A rainbow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select /A:1-180,320-376
1829 atoms, 1866 bonds, 237 residues, 1 model selected
> color sel white
> color /A rainbow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select /A:1-120,250-376
1853 atoms, 1888 bonds, 247 residues, 1 model selected
> color sel white
> rainbow sel
> select clear
> rainbow
> select /A:1-180,320-376
1829 atoms, 1866 bonds, 237 residues, 1 model selected
> cartoon
> color bychain
> hbonds /A restrict /B reveal true
50 hydrogen bonds found
> select clear
> show atoms
> hide atoms
> color all gray
> select helix
1919 atoms, 1923 bonds, 259 residues, 1 model selected
> color sel red
> select strand
1416 atoms, 1395 bonds, 6 pseudobonds, 188 residues, 2 models selected
> color sel cyan
> select clear
> hide atoms
> cartoon
> color bychain
> hide atoms
> cartoon
> color bychain
> select /A & /B around 4
Expected a keyword
> select add /B & /A around 4
Expected a keyword
> hbonds /A & /B around 4 reveal true
Expected a keyword
> hbonds reveal true
1627 hydrogen bonds found
> hbonds hide true
Expected a keyword
> hbonds hide
Expected a keyword
> hbonds hide
Expected a keyword
> hidehbonds
Unknown command: hidehbonds
> hide hbonds
> select /A & : select /A & : select /A & : hbonds /A restrict /B reveal true
50 hydrogen bonds found
> select :ZN
4 atoms, 4 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 4 atom styles
> label sel residues
> color sel residues
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel residues white
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel rwhite
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel white
> select sel zr label sel residues
> show sel atoms
> style sel stick
Changed 4 atom styles
> select zone sel 3
Selected 18 atoms, 1 surfaces
> show sel atoms
> style sel stick
Changed 18 atom styles
> label sel residues
> distance sel
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 18 atoms and 0
measurable objects
> select zn
Expected an objects specifier or a keyword
> select zn381
Expected an objects specifier or a keyword
> select /A:ZN
2 atoms, 2 residues, 1 model selected
> select zone sel 2.6
Selected 8 atoms, 1 surfaces
> distance sel & :ZN sel & ~:ZN
Expected a keyword
> distance :ZN & sel, ~:ZN & sel
Expected a keyword
> select /A:ZN
2 atoms, 2 residues, 1 model selected
> name zn
"zn" is not defined
> select zone zn 2.6
Missing or invalid "near" argument: invalid objects specifier
> select sel & ~zn
Expected a keyword
> name near
"near" is not defined
> distance zn, near
Missing or invalid "objects" argument: invalid objects specifier
> distance /A:ZN /A:46@SG
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 3 atoms and 0
measurable objects
> distance /A:ZN /A:67@NE2
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 3 atoms and 0
measurable objects
> distance /A:ZN /A:178@SG
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 3 atoms and 0
measurable objects
> select /A:ZN
2 atoms, 2 residues, 1 model selected
> label sel atoms
> distance /A:380@ZN /A:46@SG
Distance between /A ZN 380 ZN and CYS 46 SG: 2.305Å
> distance /A:380@ZN /A:67@NE2
Distance between /A ZN 380 ZN and HIS 67 NE2: 2.196Å
> distance /A:380@ZN /A:174@SG
Distance between /A ZN 380 ZN and CYS 174 SG: 12.244Å
> show target m
> distance /A:380@ZN /A:178@SG
Distance between /A ZN 380 ZN and CYS 178 SG: 2.287Å
> distance /A:381@ZN /A:97@SG distance /A:381@ZN /A:100@SG distance /A:381@ZN
> /A:103@SG distance /A:381@ZN /A:111@SG
Expected a keyword
> distance /A:381@ZN /A:97@SGS
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 1 atoms and 0
measurable objects
> distance /A:381@ZN /A:97@SG
Distance between /A ZN 381 ZN and CYS 97 SG: 2.312Å
> distance /A:381@ZN /A:100@SG
Distance between /A ZN 381 ZN and CYS 100 SG: 2.306Å
> distance /A:381@ZN /A:103@SG
Distance between /A ZN 381 ZN and CYS 103 SG: 2.287Å
> distance /A:381@ZN /A:111@SG
Distance between /A ZN 381 ZN and CYS 111 SG: 2.299Å
> delete /B
> clear sel
Unknown command: clear sel
> select clear
> select :NAI
44 atoms, 48 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 44 atom styles
> color sel byelement
> view sel
> select zone sel 4 protein residues true
Selected 188 atoms
> show sel atoms
> style sel stick
Changed 188 atom styles
> color sel byelement
> hbonds sel reveal true
73 hydrogen bonds found
> select :NAI@C4N
1 atom, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 1 atom style
> color sel magenta
> style sel ball
Changed 1 atom style
> select zone sel 3 protein residues true
Selected 6 atoms
> ~hbonds
> ~distances
Unknown command: ~distances
> ~distance
> ~zn
Unknown command: ~zn
> hide atoms
> hide cartoons
> show :NAI atoms
> show :CXF atoms
> style :NAI stick
Changed 44 atom styles
> style :CXF stick
Changed 9 atom styles
> color :NAI byelement
> color :CXF byelement
> close session
> open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb
1E3I.pdb title:
Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more
info...]
Chain information for 1E3I.pdb #1
---
Chain | Description | UniProt
A B | alcohol dehydrogenase, class II | Q9QYY9 1-376
Non-standard residues in 1E3I.pdb #1
---
CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
> delete /B
> color byelement
> show :NAI atoms
> show :CXF atoms
> style :NAI stick
Changed 44 atom styles
> style :CXF stick
Changed 9 atom styles
> color :NAI byelement
> color :CXF byelement
> select :NAI
44 atoms, 48 bonds, 1 residue, 1 model selected
> select zone sel 3.5 protein residues true
Selected 128 atoms
> show sel atoms
> style sel stick
Changed 128 atom styles
> color sel byelement
> label sel residues
> view sel
> hbonds sel restrict cross reveal true
59 hydrogen bonds found
> ui mousemode right zoom
> ~select atoms
> select subtract atoms
Expected an objects specifier or a keyword
> ~struts sel atoms
> struts delete sel atoms
Missing "atoms" keyword's argument
> hide sel atoms
> ui mousemode right select
> select /A:377@C2N
1 atom, 1 residue, 1 model selected
> select /A:377@C4N
1 atom, 1 residue, 1 model selected
> style sel ball
Changed 1 atom style
> hide residues
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide atoms
> show atoms\
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show atoms
> ~atoms
Unknown command: ~atoms
> ~struts atoms
> struts delete atoms
Missing "atoms" keyword's argument
> ~struts atoms
> struts delete atoms
Missing "atoms" keyword's argument
> hide atoms
> hide residdues
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide residues
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide bonds
> hide hbonds
> select /A:377@C4N
1 atom, 1 residue, 1 model selected
> select :NAI
44 atoms, 48 bonds, 1 residue, 1 model selected
> select zone sel 3.5 protein residues true
Selected 128 atoms
> show :NAI atoms
> style :NAI stick
Changed 44 atom styles
> color :NAI byelement
> show :NAI atoms
> style :NAI stick
Changed 44 atom styles
> color :NAI byelement
> style :NAI ball stick
Expected a keyword
> style :NAI ball-and-stick
Expected a keyword
> stylw :NAI ball-and-stick
Unknown command: stylw :NAI ball-and-stick
> style:NAI ball-and-stick
Unknown command: style:NAI ball-and-stick
> style :NAI ball-and-stick
Expected a keyword
> style :NAI ball
Changed 44 atom styles
> show :NAI atoms
> style :NAI ball-and-stick
Expected a keyword
> color :NAI byelement
> close session
> open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb
1E3I.pdb title:
Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more
info...]
Chain information for 1E3I.pdb #1
---
Chain | Description | UniProt
A B | alcohol dehydrogenase, class II | Q9QYY9 1-376
Non-standard residues in 1E3I.pdb #1
---
CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
> hide /B
> delete /B
> hide atoms
> hide cartoons
> show :NAI atoms
> style :NAI ball-and-stick
Expected a keyword
> color :NAI byelement
> view :NAI
> select :NAI@C4N
1 atom, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 1 atom style
> color sel magenta
> label sel atoms
> view sel
> style sel ball
Changed 1 atom style
> select :NAI@C4N
1 atom, 1 residue, 1 model selected
> select zone sel 4 protein residues true
Selected 6 atoms
> show sel atoms
> style sel stick
Changed 6 atom styles
> color sel byelement
> label sel residues
> view sel
> select :NAD
Nothing selected
> show sel
> style sel stick
Changed 0 atom styles
> hide protein
> select protein & within 4 of :NAD
Expected a keyword
> show sel
> select protein & within 4 of sel
Expected a keyword
> select protein & within 4 of sel
Expected a keyword
> select protein & (within 4 of :NAD)
Expected a keyword
> hide
> show :NAD
> style :NAD stick
Changed 0 atom styles
> zone :NAD 4
Expected a keyword
> zone :NAD show ligand
> style ligand stick
Changed 53 atom styles
> contacts ligand protein
Expected a keyword
> show atoms
> select sel @ select :NAD
Nothing selected
> select ligand
53 atoms, 57 bonds, 2 residues, 1 model selected
> select clear
> view
> select :NAD
Nothing selected
> show sel
> style sel stick
Changed 0 atom styles
> hide protein
> hide atoms]
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide atoms]
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> close session
> open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb
1E3I.pdb title:
Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more
info...]
Chain information for 1E3I.pdb #1
---
Chain | Description | UniProt
A B | alcohol dehydrogenase, class II | Q9QYY9 1-376
Non-standard residues in 1E3I.pdb #1
---
CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
> delete /B
> hide protein
> select main
2800 atoms, 2849 bonds, 376 residues, 1 model selected
> hide sel
> view sel
> view
> delete sel
> select ligand
53 atoms, 57 bonds, 2 residues, 1 model selected
> select sel @ show sel
> hbonds sel reveal true
11 hydrogen bonds found
> view sel
> show protein
> close session
> open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb
1E3I.pdb title:
Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more
info...]
Chain information for 1E3I.pdb #1
---
Chain | Description | UniProt
A B | alcohol dehydrogenase, class II | Q9QYY9 1-376
Non-standard residues in 1E3I.pdb #1
---
CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
> select :NAD
Nothing selected
> show sel
> style sel stick
Changed 0 atom styles
> view
> hide /B
> select :NAD show sel
Expected a keyword
> close session
> open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb
1E3I.pdb title:
Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more
info...]
Chain information for 1E3I.pdb #1
---
Chain | Description | UniProt
A B | alcohol dehydrogenase, class II | Q9QYY9 1-376
Non-standard residues in 1E3I.pdb #1
---
CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
> select ((/A & ::polymer_type>0 ) & ((/B & ::polymer_type>0 ) :0 ) & ((/A & ::polymer_type>0 ) : select clear
> select ligand
106 atoms, 114 bonds, 4 residues, 1 model selected
> select sel : show sel
> hide ~ sel
> view sel
> hide /B
> delete /B
> view sel
Drag select of 5 atoms, 14 residues, 4 bonds
> select ligand
53 atoms, 57 bonds, 2 residues, 1 model selected
> hbonds sel reveal true
23 hydrogen bonds found
> select sel : hide ~sel
> hide
> undo
> hide
> show sel
> hide
> hide protein
> select /A
3041 atoms, 2906 bonds, 31 pseudobonds, 566 residues, 3 models selected
> hide
> delete
Missing or invalid "atoms" argument: empty atom specifier
> delete /A
> open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb
1E3I.pdb title:
Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more
info...]
Chain information for 1E3I.pdb #1
---
Chain | Description | UniProt
A B | alcohol dehydrogenase, class II | Q9QYY9 1-376
Non-standard residues in 1E3I.pdb #1
---
CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
> hide /A
> hide /A ?B
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide /B
> select /A
3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected
> hide /B
> hide #!1 models
> show #!1 models
> hide /B
> hide #!1 target m
> show #!1 models
> select add #1
6059 atoms, 5792 bonds, 17 pseudobonds, 1126 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #1.1 models
> show #1.1 target m
> hide #1.1 models
> select /B
3018 atoms, 2886 bonds, 9 pseudobonds, 560 residues, 2 models selected
> hide /sel
> select ::name="NAI"
88 atoms, 96 bonds, 2 residues, 1 model selected
> show sel atoms
> select sel : show sel atoms
> style sel ball
Changed 372 atom styles
> style sel stick
Changed 372 atom styles
> color sel byelement
> select ::name="NAI"
88 atoms, 96 bonds, 2 residues, 1 model selected
> style sel ball
Changed 88 atom styles
> hide /sel
> hide /B
> hide /chainB
> select /B
3018 atoms, 2886 bonds, 9 pseudobonds, 560 residues, 2 models selected
> hide sel cartoons
> select ::name="NAI"
88 atoms, 96 bonds, 2 residues, 1 model selected
> select sel : select sel : 3.5 & ~sel
Nothing selected
> hide cartoons
> hbonds reveal true
1627 hydrogen bonds found
> ~hbonds
> select ligand
106 atoms, 114 bonds, 4 residues, 1 model selected
> select /B
3018 atoms, 2886 bonds, 11 pseudobonds, 560 residues, 3 models selected
> hide sel atoms
> select /ligand
Nothing selected
> select ::name="NAI"
88 atoms, 96 bonds, 2 residues, 1 model selected
> select sel :> 3.5 & ~sel
5687 atoms, 5399 bonds, 14 pseudobonds, 1071 residues, 3 models selected
> hide sel atoms
> hide #* target a
> show (#!1 & sel) target ab
> undo
> select ::name="NAI"
88 atoms, 96 bonds, 2 residues, 1 model selected
> show sel atoms
> delete /B
> select sel : style sel stick
Changed 143 atom styles
> show sel atoms
> hbonds sel reveal true
78 hydrogen bonds found
> undo
> view sel
No displayed objects specified.
> select ::name="NAI"
44 atoms, 48 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
21 hydrogen bonds found
> close session
> open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb
1E3I.pdb title:
Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more
info...]
Chain information for 1E3I.pdb #1
---
Chain | Description | UniProt
A B | alcohol dehydrogenase, class II | Q9QYY9 1-376
Non-standard residues in 1E3I.pdb #1
---
CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
> fetch3cos
Unknown command: fetch3cos
> fetch 3cos
Unknown command: fetch 3cos
Select a database from the database table
> open 3cos fromDatabase pdbe_bio format mmcif
Summary of feedback from opening 3cos fetched from pdbe_bio
---
warnings | Missing or incorrect sequence information. Inferred polymer connectivity.
Missing or incorrect sequence information. Inferred polymer connectivity.
notes | Fetching compressed 3cos bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/3cos-assembly-1.cif.gz
Fetching CCD ACY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/ACY/ACY.cif
Fetching CCD EDO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif
Fetching CCD NAD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/NAD/NAD.cif
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
Fetching compressed 3cos bioassembly 2 from
https://www.ebi.ac.uk/pdbe/static/entry/download/3cos-assembly-2.cif.gz
3cos bioassembly 1 title:
Crystal structure of human class II alcohol dehydrogenase (ADH4) in complex
with NAD and Zn [more info...]
3cos bioassembly 1 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Chain information for 3cos bioassembly 1 #2.1
---
Chain | Description
A B | Alcohol dehydrogenase 4
Non-standard residues in 3cos bioassembly 1 #2.1
---
ACY — (ACY)
EDO — (EDO)
NAD — (NAD)
ZN — (ZN)
3cos bioassembly 2 title:
Crystal structure of human class II alcohol dehydrogenase (ADH4) in complex
with NAD and Zn [more info...]
3cos bioassembly 2 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for 3cos bioassembly 2 #2.2
---
Chain | Description
C | Alcohol dehydrogenase 4
D | Alcohol dehydrogenase 4
Non-standard residues in 3cos bioassembly 2 #2.2
---
ACY — (ACY)
EDO — (EDO)
NAD — (NAD)
ZN — (ZN)
Opened 2 biological assemblies for 3cos
Computing secondary structure
> hide #!1 models
> hide #!2 models
> show #!2 models
> view
> hide #2.2 models
> show #2.2 models
> show #!1 models
> select #2.2/C
2789 atoms, 2840 bonds, 379 residues, 1 model selected
> hide sel
> hide /sel
> hide sel cartoons
> select #2.2/D
2802 atoms, 2853 bonds, 381 residues, 1 model selected
> hide sel cartoons
> ui tool show Matchmaker
> matchmaker #2.1/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1E3I.pdb, chain A (#1) with 3cos bioassembly 1, chain A (#2.1),
sequence alignment score = 1563.8
RMSD between 363 pruned atom pairs is 0.675 angstroms; (across all 376 pairs:
1.032)
> matchmaker #2.1/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1E3I.pdb, chain A (#1) with 3cos bioassembly 1, chain A (#2.1),
sequence alignment score = 1563.8
RMSD between 363 pruned atom pairs is 0.675 angstroms; (across all 376 pairs:
1.032)
> select ::name="THR"
1127 atoms, 970 bonds, 161 residues, 3 models selected
> select :48
54 atoms, 52 bonds, 6 residues, 3 models selected
Drag select of 75 residues, 6 atoms, 4 bonds
> undo
> view sel
Drag select of 344 atoms, 322 bonds
Drag select of 123 atoms, 116 bonds
Drag select of 390 atoms, 362 bonds
> delete sel
> view
> select :48.A
Expected an objects specifier or a keyword
> select :48
44 atoms, 42 bonds, 5 residues, 3 models selected
> view sel
> ui tool show "Side View"
> view orient
Drag select of 6 atoms, 16 residues, 4 bonds
> undo
Drag select of 23 residues, 3 atoms, 3 bonds
> ui mousemode right rotate
> ui mousemode right translate
> undo
> select sel :> 3.5
17318 atoms, 16486 bonds, 33 pseudobonds, 3284 residues, 5 models selected
> delete sel
> select :48
44 atoms, 42 bonds, 5 residues, 3 models selected
> ui mousemode right select
Drag select of 146 atoms, 15 residues, 145 bonds, 3 pseudobonds
> hbonds sel reveal true
57 hydrogen bonds found
> select clear
> ~hbonds
> open /Users/chiaramcallister/Downloads/3COS.pdb
3COS.pdb title:
Crystal structure of human class II alcohol dehydrogenase (ADH4) In complex
with nad and Zn [more info...]
Chain information for 3COS.pdb #3
---
Chain | Description | UniProt
A B C D | alcohol dehydrogenase class II π chain | ADH4_HUMAN 1-380
Non-standard residues in 3COS.pdb #3
---
ACY — acetic acid
EDO — 1,2-ethanediol (ethylene glycol)
NAD — nicotinamide-adenine-dinucleotide
ZN — zinc ion
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close session
> open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb
1E3I.pdb title:
Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more
info...]
Chain information for 1E3I.pdb #1
---
Chain | Description | UniProt
A B | alcohol dehydrogenase, class II | Q9QYY9 1-376
Non-standard residues in 1E3I.pdb #1
---
CXF — cyclohexylformamide
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
ZN — zinc ion
> open /Users/chiaramcallister/Downloads/3COS.pdb
3COS.pdb title:
Crystal structure of human class II alcohol dehydrogenase (ADH4) In complex
with nad and Zn [more info...]
Chain information for 3COS.pdb #2
---
Chain | Description | UniProt
A B C D | alcohol dehydrogenase class II π chain | ADH4_HUMAN 1-380
Non-standard residues in 3COS.pdb #2
---
ACY — acetic acid
EDO — 1,2-ethanediol (ethylene glycol)
NAD — nicotinamide-adenine-dinucleotide
ZN — zinc ion
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select :48
54 atoms, 52 bonds, 6 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #2/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1E3I.pdb, chain A (#1) with 3COS.pdb, chain A (#2), sequence
alignment score = 1563.8
RMSD between 363 pruned atom pairs is 0.675 angstroms; (across all 376 pairs:
1.032)
> matchmaker #2/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1E3I.pdb, chain A (#1) with 3COS.pdb, chain A (#2), sequence
alignment score = 1563.8
RMSD between 363 pruned atom pairs is 0.675 angstroms; (across all 376 pairs:
1.032)
> matchmaker #2/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1E3I.pdb, chain A (#1) with 3COS.pdb, chain A (#2), sequence
alignment score = 1563.8
RMSD between 363 pruned atom pairs is 0.675 angstroms; (across all 376 pairs:
1.032)
> select #2/C
3040 atoms, 2894 bonds, 8 pseudobonds, 581 residues, 2 models selected
> hide sel
> hide sel cartoons
> select #2/D
3047 atoms, 2910 bonds, 8 pseudobonds, 574 residues, 2 models selected
> hide sel cartoons
> select clear
> select :48
54 atoms, 52 bonds, 6 residues, 2 models selected
> select sel :> 3.5
17575 atoms, 16749 bonds, 36 pseudobonds, 3334 residues, 4 models selected
> hide sel cartoons
> hide sel atoms
> select #1/B
3018 atoms, 2886 bonds, 9 pseudobonds, 560 residues, 2 models selected
> hide sel
> hide sel cartoons
> select #2/B
2995 atoms, 2893 bonds, 8 pseudobonds, 537 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
Drag select of 52 atoms, 56 bonds
> select clear
> select :48
54 atoms, 52 bonds, 6 residues, 2 models selected
> select clear
> select :48
54 atoms, 52 bonds, 6 residues, 2 models selected
> select sel : show sel
> select sel : show sel
> select :48
54 atoms, 52 bonds, 6 residues, 2 models selected
> view sel
Drag select of 40 atoms, 4 residues, 38 bonds
> select :48
54 atoms, 52 bonds, 6 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,1,0,0,-0.57062,0,1,0,1.0709,0,0,1,-0.184,#2,-0.97764,0.13032,0.16502,60.643,-0.19865,-0.8297,-0.52167,126.97,0.068938,-0.54279,0.83703,13.217
> view matrix models
> #1,1,0,0,1.0187,0,1,0,0.37111,0,0,1,2.3508,#2,-0.97764,0.13032,0.16502,62.232,-0.19865,-0.8297,-0.52167,126.27,0.068938,-0.54279,0.83703,15.752
> view matrix models
> #1,1,0,0,4.4031,0,1,0,-2.8243,0,0,1,7.6286,#2,-0.97764,0.13032,0.16502,65.616,-0.19865,-0.8297,-0.52167,123.08,0.068938,-0.54279,0.83703,21.03
> view matrix models
> #1,1,0,0,6.3148,0,1,0,-3.9021,0,0,1,11.132,#2,-0.97764,0.13032,0.16502,67.528,-0.19865,-0.8297,-0.52167,122,0.068938,-0.54279,0.83703,24.534
> view matrix models
> #1,1,0,0,5.7578,0,1,0,-2.9656,0,0,1,13.067,#2,-0.97764,0.13032,0.16502,66.971,-0.19865,-0.8297,-0.52167,122.94,0.068938,-0.54279,0.83703,26.468
> view matrix models
> #1,1,0,0,5.1394,0,1,0,-1.8949,0,0,1,15.557,#2,-0.97764,0.13032,0.16502,66.353,-0.19865,-0.8297,-0.52167,124.01,0.068938,-0.54279,0.83703,28.958
> view matrix models
> #1,1,0,0,3.5394,0,1,0,0.5167,0,0,1,18.05,#2,-0.97764,0.13032,0.16502,64.753,-0.19865,-0.8297,-0.52167,126.42,0.068938,-0.54279,0.83703,31.452
> view matrix models
> #1,1,0,0,-2.6756,0,1,0,2.5741,0,0,1,15.921,#2,-0.97764,0.13032,0.16502,58.538,-0.19865,-0.8297,-0.52167,128.48,0.068938,-0.54279,0.83703,29.322
> view matrix models
> #1,1,0,0,-6.0326,0,1,0,2.0178,0,0,1,13.12,#2,-0.97764,0.13032,0.16502,55.181,-0.19865,-0.8297,-0.52167,127.92,0.068938,-0.54279,0.83703,26.521
> view matrix models
> #1,1,0,0,-7.0317,0,1,0,1.1619,0,0,1,11.603,#2,-0.97764,0.13032,0.16502,54.182,-0.19865,-0.8297,-0.52167,127.07,0.068938,-0.54279,0.83703,25.005
> view matrix models
> #1,1,0,0,-7.8944,0,1,0,0.60728,0,0,1,13.615,#2,-0.97764,0.13032,0.16502,53.319,-0.19865,-0.8297,-0.52167,126.51,0.068938,-0.54279,0.83703,27.016
> view matrix models
> #1,1,0,0,-9.5228,0,1,0,-0.60241,0,0,1,17.751,#2,-0.97764,0.13032,0.16502,51.69,-0.19865,-0.8297,-0.52167,125.3,0.068938,-0.54279,0.83703,31.153
> view matrix models
> #1,1,0,0,-9.879,0,1,0,-2.2451,0,0,1,21.527,#2,-0.97764,0.13032,0.16502,51.334,-0.19865,-0.8297,-0.52167,123.66,0.068938,-0.54279,0.83703,34.928
> view matrix models
> #1,1,0,0,-8.7981,0,1,0,-2.8785,0,0,1,21.773,#2,-0.97764,0.13032,0.16502,52.415,-0.19865,-0.8297,-0.52167,123.02,0.068938,-0.54279,0.83703,35.174
> view matrix models
> #1,1,0,0,-11.782,0,1,0,-8.2767,0,0,1,19.794,#2,-0.97764,0.13032,0.16502,49.431,-0.19865,-0.8297,-0.52167,117.63,0.068938,-0.54279,0.83703,33.195
> view matrix models
> #1,1,0,0,-10.617,0,1,0,-8.6174,0,0,1,19.963,#2,-0.97764,0.13032,0.16502,50.596,-0.19865,-0.8297,-0.52167,117.29,0.068938,-0.54279,0.83703,33.365
> view matrix models
> #1,1,0,0,-11.145,0,1,0,-8.436,0,0,1,20.081,#2,-0.97764,0.13032,0.16502,50.068,-0.19865,-0.8297,-0.52167,117.47,0.068938,-0.54279,0.83703,33.482
> view matrix models
> #1,1,0,0,-13.623,0,1,0,-4.677,0,0,1,19.748,#2,-0.97764,0.13032,0.16502,47.59,-0.19865,-0.8297,-0.52167,121.23,0.068938,-0.54279,0.83703,33.149
> view matrix models
> #1,1,0,0,-10.698,0,1,0,-3.5663,0,0,1,22.647,#2,-0.97764,0.13032,0.16502,50.516,-0.19865,-0.8297,-0.52167,122.34,0.068938,-0.54279,0.83703,36.048
> view matrix models
> #1,1,0,0,-9.455,0,1,0,-5.0995,0,0,1,18.67,#2,-0.97764,0.13032,0.16502,51.758,-0.19865,-0.8297,-0.52167,120.8,0.068938,-0.54279,0.83703,32.072
> view matrix models
> #1,1,0,0,-6.7459,0,1,0,-9.7289,0,0,1,16.934,#2,-0.97764,0.13032,0.16502,54.467,-0.19865,-0.8297,-0.52167,116.17,0.068938,-0.54279,0.83703,30.336
> close session
> open /Users/chiaramcallister/Downloads/1EEO.pdb
1EEO.pdb title:
Crystal structure of protein tyrosine phosphatase 1B complexed with acetyl-E-
L-E-F-ptyr-M-D-Y-E-NH2 [more info...]
Chain information for 1EEO.pdb #1
---
Chain | Description | UniProt
A | PTP1B | PTN1_HUMAN 1-321
B | acetyl-E-L-E-F-ptyr-M-D-Y-E-NH2 peptide |
Non-standard residues in 1EEO.pdb #1
---
MG — magnesium ion
NH2 — amino group
> select /A
2648 atoms, 2481 bonds, 1 pseudobond, 519 residues, 2 models selected
> select /B
87 atoms, 84 bonds, 14 residues, 1 model selected
> hide atoms
> show cartoons
> color /A lightgray
> show /B atoms
> style /B stick
Changed 87 atom styles
> color /B & C orange
> view matrix models #1,1,0,0,12.09,0,1,0,-6.8875,0,0,1,13.873
> select /B:PTR
16 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ballstick
Expected a keyword
> color sel byelement
> view sel
> style sel ball
Changed 16 atom styles
> select zone /B:PTR 5 protein residues true
Selected 142 atoms
> show sel atoms
> style sel stick
Changed 142 atom styles
> color sel byelement
> select /B:PTR
16 atoms, 16 bonds, 1 residue, 1 model selected
> hbonds sel restrict both reveal true
0 hydrogen bonds found
> hbonds sel reveal true
14 hydrogen bonds found
> view matrix models #1,1,0,0,11.6,0,1,0,-5.9816,0,0,1,14.389
> ~hbonds
> hbonds /B:PTR restrict both reveal true
0 hydrogen bonds found
> hbonds /B:PTR restrict both interModel false reveal true
0 hydrogen bonds found
> hbonds sel reveal true
14 hydrogen bonds found
> select solvent
226 atoms, 226 residues, 1 model selected
> hide sel
> cartoon suppressBackboneDisplay false
> transparency #1 50
> cartoons
Unknown command: cartoons
> undo
> redo
> transparency #1 50cartoons
Missing or invalid "percent" argument: Expected a number
> transparency 50 cartoons
> label /A:215,221 residues
> view matrix models #1,1,0,0,9.2217,0,1,0,-4.7929,0,0,1,11.963
> clip slab true
Expected a keyword
> hide solvent
> hide ligands
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select /B
87 atoms, 84 bonds, 5 pseudobonds, 14 residues, 2 models selected
> hide sel
> hide sel cartoons
> show :PTR
> select /A
2648 atoms, 2481 bonds, 1 pseudobond, 519 residues, 2 models selected
> hide sel
> hide sel cartoons
> show :PTR zone 5 extend true
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select zone /B:PTR 5 protein residues true
Selected 142 atoms
> show sel atoms
> hide sel atoms
> show sel cartoons
> transparency 50 cartoons
> transparency 70 cartoons
> transparency 90 cartoons
> transparency 50 cartoons
> label /B:PTR 4
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label /B:PTR4
> hide all
> show :PTR
> show :PTR zone 4.5 extend true
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> cartoon suppressBackboneDisplay false
> select PTR4
Expected an objects specifier or a keyword
> select PTR 4
Expected an objects specifier or a keyword
> show :PTR
> select :PTR
16 atoms, 16 bonds, 1 residue, 1 model selected
> select sel : show sel atoms
> hide solvent
> hide ~sel
> select :PTR
16 atoms, 16 bonds, 1 residue, 1 model selected
> select sel :> 3.5 & ~sel
2623 atoms, 2446 bonds, 1 pseudobond, 518 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> view matrix models #1,1,0,0,14.4,0,1,0,-3.8904,0,0,1,15.436
> ui mousemode right select
Drag select of 27 atoms, 4 residues, 26 bonds, 1 pseudobonds
> select clear
Drag select of 11 atoms, 3 residues, 11 bonds
> select clear
Drag select of 4 atoms, 1 residues, 4 bonds
> hide sel
> hide sel cartoons
Drag select of 7 atoms, 1 residues, 6 bonds
> hide sel atoms
> hide sel cartoons
> select clear
Drag select of 4 atoms, 1 residues, 5 bonds
> hide sel atoms
Drag select of 1 atoms, 2 residues, 1 bonds
Drag select of 2 residues, 1 bonds
> select clear
Drag select of 3 atoms, 4 bonds
> hide sel atoms
Drag select of 2 atoms, 2 residues, 3 bonds
> select clear
Drag select of 1 residues
> hide sel atoms
> select clear
> view
> label :PTR
> show :48
> hide :48
> show :46
> color :PTR green
> color :215,221,216 blue
> undo
> color :215,221,216 byhetero
> color :215,221,216 & element C cornflower blue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color :PTR byhetero
> color :PTR & element C lime green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select /B:PTR
16 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ballstick
Expected a keyword
> color sel & C orange
> color sel byelement target a
> view sel
> select zone /B:PTR 4 protein residues true
Selected 110 atoms
> show sel atoms
> style sel stick
Changed 110 atom styles
> color sel & C tan
> color sel byelement target a
> select clear
> undo
> color :PTR & element C orange
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color :PTR & element C #FF8C00
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color :PTR orange
> color :PTR byelement
> color :PTR & C orange
> color :PTR & C lightorange
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color :PTR & C lyellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color :PTR & C yellow
> color :PTR & C gray
> select clear
Drag select of 1 atoms, 1 bonds
> select /A:262@OE1
1 atom, 1 residue, 1 model selected
Drag select of 1 atoms, 3 bonds
> show sel atoms
> hide sel atoms
> hide sel cartoons
> undo
Drag select of 7 atoms, 7 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.12.dev202605010205 (2026-05-01)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN93N/A
Chip: Apple M1
Total Number of Cores: 8 (4 Performance and 4 Efficiency)
Memory: 8 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: 3 dagen, 22 uur en 35 minuten
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.1.2
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
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: 1.67.1
ChimeraX-AtomicLibrary: 14.4
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: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12.dev202605010205
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: 1.2.1
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: 1.8.2
ChimeraX-Label: 1.4
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.1
ChimeraX-MatchMaker: 2.4
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.8
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.0.1
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: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
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: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
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: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.6
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
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: 8.3.3
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.5
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.20
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.62.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.13
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
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: 6.7.1
narwhals: 2.20.0
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: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.6
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: 4.9.6
plotly: 6.7.0
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: 2.13.3
pydantic-settings: 2.14.0
pydantic_core: 2.46.3
pydata-sphinx-theme: 0.17.1
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
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: 6.10.2
PyQt6-Qt6: 6.10.1
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.1
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.27
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 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: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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: 3.4.1
stack-data: 0.6.3
starlette: 1.0.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.5
tqdm: 4.67.3
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.6.3
uvicorn: 0.46.0
wcwidth: 0.6.0
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.23.0
Change History (4)
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
| Cc: | added |
|---|---|
| Milestone: | → 1.12 |
| Summary: | Crash in swap_buffers exposing status line during Mac wakeup → Crash in swap_buffers exposing SideView during Mac wakeup, Qt 6.10 |
comment:4 by , 8 days ago
I put in a more aggressive work-around in ChimeraX daily builds dated May 4, 2026 or newer that ignores status line expose events on Mac. I expect this will avoid this crash by preventing the expose event that is dispatched from within QOpenGLContext.makeCurrent() from doing damage by running other OpenGL code. I don't have a way to test this since I have never been able to reproduce this crash.
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Expose events on the status line and side view have led to OpenGL error and crashes like this one since macOS 26. We may want to use a more aggressive work-around of ignoring expose events, ie not redrawing the OpenGL for status line or side view. This probably would lead to few cases where the GUI does not redraw.