![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 hours ago
Closed 5 hours ago
#20362 closed defect (duplicate)
Crash on Mac waking from sleep in OpenGL swap_buffers on status line expose event
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | 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-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 0x00000001f1947080 (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.surface._surface, PIL._imaging, chimerax.pdb_lib._load_libs, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 55)
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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 /Users/osperand/Downloads/Q9E005_1_2153_8qgu.1.B.cif
> /Users/osperand/Downloads/AF-0000000365765852-model_v1.cif
Summary of feedback from opening
/Users/osperand/Downloads/AF-0000000365765852-model_v1.cif
---
warning | Atom H is not in the residue template for ILE /A:1
Q9E005_1_2153_8qgu.1.B.cif title:
Model for UniProtKB entries Q9E005 [more info...]
Chain information for Q9E005_1_2153_8qgu.1.B.cif #1
---
Chain | Description
A B | .
Color Q9E005_1_2153_8qgu.1.B.cif by residue attribute QMEANDisCo_score
Alignment identifier is 1
Associated Q9E005_1_2153_8qgu.1.B.cif chain A to target with 0 mismatches
Associated Q9E005_1_2153_8qgu.1.B.cif chain B to target with 0 mismatches
Associated AF-0000000365765852-model_v1.cif chain A to target with 0
mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Alignment identifier is 2
Associated Q9E005_1_2153_8qgu.1.B.cif chain A to target with 0 mismatches
Associated Q9E005_1_2153_8qgu.1.B.cif chain B to target with 0 mismatches
Associated AF-0000000365765852-model_v1.cif chain A to target with 0
mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Chain information for AF-0000000365765852-model_v1.cif #2
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase L | L_ANDV
Color AF-0000000365765852-model_v1.cif by residue attribute pLDDT_score
Associated Q9E005_1_2153_8qgu.1.B.cif chain A to target with 0 mismatches
Associated Q9E005_1_2153_8qgu.1.B.cif chain B to target with 0 mismatches
Associated AF-0000000365765852-model_v1.cif chain A to target with 0
mismatches
Associated Q9E005_1_2153_8qgu.1.B.cif chain A to target with 0 mismatches
Associated Q9E005_1_2153_8qgu.1.B.cif chain B to target with 0 mismatches
Associated AF-0000000365765852-model_v1.cif chain A to target with 0
mismatches
Computing secondary structure
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF-0000000365765852-model_v1.cif, chain A (#2) with
Q9E005_1_2153_8qgu.1.B.cif, chain B (#1), sequence alignment score = 3493.1
RMSD between 335 pruned atom pairs is 1.216 angstroms; (across all 724 pairs:
4.159)
> lighting soft
> help indeep
> indeep predict #1 device cpu clusterPockets true pocketMap ligandability
> pocketThreshold 0.95 openPocketMaps true
> save /Users/osperand/.local/share/ChimeraX/indeep-
> runtime/runs/Q9E005_1_2153_8qgu.1.B.cif/Q9E005_1_2153_8qgu.1.B.cif.pdb
> format pdb models #1 selectedOnly true
Running InDeep externally:
/Users/osperand/.local/share/ChimeraX/indeep-runtime/bin/indeep-python
/Users/osperand/.local/share/ChimeraX/indeep-
runtime/InDeep/scripts/predict_maps.py --exp
/Users/osperand/.local/share/ChimeraX/indeep-
runtime/InDeep/results/experiments/HPO.exp --pdb
/Users/osperand/.local/share/ChimeraX/indeep-
runtime/runs/Q9E005_1_2153_8qgu.1.B.cif/Q9E005_1_2153_8qgu.1.B.cif.pdb --out-
prefix /Users/osperand/.local/share/ChimeraX/indeep-
runtime/runs/Q9E005_1_2153_8qgu.1.B.cif/Q9E005_1_2153_8qgu.1.B.cif --device
cpu --cluster-pockets --pocket-map ligandability --pocket-threshold 0.95
--pocket-min-voxels 20 --pocket-contact-radius 4.0
Missing Python environment at /Users/osperand/.local/share/ChimeraX/indeep-
runtime/.venv/bin/python
Run /Users/osperand/.local/share/ChimeraX/indeep-
runtime/setup_linux_chimerax_env.sh first.
InDeep prediction failed. Check the ChimeraX log for stderr from the external
process.
> indeep predict #2 device cpu clusterPockets true pocketMap ligandability
> pocketThreshold 0.95 openPocketMaps true
> save /Users/osperand/.local/share/ChimeraX/indeep-
> runtime/runs/AF-0000000365765852-model_v1.cif/AF-0000000365765852-model_v1.cif.pdb
> format pdb models #2 selectedOnly true
Running InDeep externally:
/Users/osperand/.local/share/ChimeraX/indeep-runtime/bin/indeep-python
/Users/osperand/.local/share/ChimeraX/indeep-
runtime/InDeep/scripts/predict_maps.py --exp
/Users/osperand/.local/share/ChimeraX/indeep-
runtime/InDeep/results/experiments/HPO.exp --pdb
/Users/osperand/.local/share/ChimeraX/indeep-
runtime/runs/AF-0000000365765852-model_v1.cif/AF-0000000365765852-model_v1.cif.pdb
--out-prefix /Users/osperand/.local/share/ChimeraX/indeep-
runtime/runs/AF-0000000365765852-model_v1.cif/AF-0000000365765852-model_v1.cif
--device cpu --cluster-pockets --pocket-map ligandability --pocket-threshold
0.95 --pocket-min-voxels 20 --pocket-contact-radius 4.0
Missing Python environment at /Users/osperand/.local/share/ChimeraX/indeep-
runtime/.venv/bin/python
Run /Users/osperand/.local/share/ChimeraX/indeep-
runtime/setup_linux_chimerax_env.sh first.
InDeep prediction failed. Check the ChimeraX log for stderr from the external
process.
> open
> /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd43-517_model_0.cif
Summary of feedback from opening
/Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd43-517_model_0.cif
---
warning | No mmCIF models found.
> open
> /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd517-43_model_0.cif
Summary of feedback from opening
/Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd517-43_model_0.cif
---
warning | No mmCIF models found.
> open
> /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd43-517-s_model_0.cif
bd43-517-s_model_0.cif title:
. [more info...]
Chain information for bd43-517-s_model_0.cif #3
---
Chain | Description
B | .
Q | .
Color bd43-517-s_model_0.cif by residue attribute pLDDT_score
> open
> /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd43-517-s2_model_0.cif
bd43-517-s2_model_0.cif title:
. [more info...]
Chain information for bd43-517-s2_model_0.cif #4
---
Chain | Description
B | .
Q | .
Color bd43-517-s2_model_0.cif by residue attribute pLDDT_score
Computing secondary structure
> close #1-2
> open
> /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd517-43_model_0.cif
bd517-43_model_0.cif title:
. [more info...]
Chain information for bd517-43_model_0.cif #1
---
Chain | Description
B | .
Q | .
Color bd517-43_model_0.cif by residue attribute pLDDT_score
Computing secondary structure
> open
> /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd43-517_model_0.cif
bd43-517_model_0.cif title:
. [more info...]
Chain information for bd43-517_model_0.cif #2
---
Chain | Description
B | .
Q | .
Color bd43-517_model_0.cif by residue attribute pLDDT_score
Computing secondary structure
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bd43-517_model_0.cif, chain Q (#2) with bd517-43_model_0.cif, chain
Q (#1), sequence alignment score = 1443.1
RMSD between 191 pruned atom pairs is 0.331 angstroms; (across all 276 pairs:
8.213)
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bd517-43_model_0.cif, chain Q (#1) with bd43-517_model_0.cif, chain
Q (#2), sequence alignment score = 1443.1
RMSD between 191 pruned atom pairs is 0.331 angstroms; (across all 276 pairs:
8.213)
> matchmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bd517-43_model_0.cif, chain Q (#1) with bd43-517-s_model_0.cif,
chain Q (#3), sequence alignment score = 1432.3
RMSD between 205 pruned atom pairs is 0.713 angstroms; (across all 276 pairs:
6.793)
> matchmaker #4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bd517-43_model_0.cif, chain Q (#1) with bd43-517-s2_model_0.cif,
chain Q (#4), sequence alignment score = 1417.9
RMSD between 206 pruned atom pairs is 0.624 angstroms; (across all 276 pairs:
5.255)
> show atoms
> hide #2 models
> hide #1 models
> hide #3 models
> show #2 models
> select #2/B:6@CA
1 atom, 1 residue, 1 model selected
> view sel
> ui tool show "Side View"
> select clear
> hide #4 models
> show #1 models
> show #3 models
> hide #2 models
> show #2 models
> show #4 models
> hide #3 models
> hide #1 models
> show #3 models
> hide #4 models
> hide #2-3 cartoons
> show #2-3 cartoons
> hide #2-3 cartoons
> show #2-3 cartoons
> hide #2-3 cartoons
> hide #2 models
> color #3 bychain
> color #3 byhetero
> show #3 cartoons
> style #3 ball
Changed 2346 atom styles
> show #2 models
> show #2-3 cartoons
> hide #3 models
> show #1 models
> show #3 models
> show #4 models
> hide cartoons
> style ball
Changed 9434 atom styles
> hide #3 models
> hide #4 models
> style #1-2 stick
Changed 4742 atom styles
> show #3 models
> hide #3 models
> hide #2 models
> show #3 models
> style #1,3 stick
Changed 4716 atom styles
> hide #3 models
> show #4 models
> style #1,4 stick
Changed 4716 atom styles
> show #3 models
> hide #4 models
> show #4 models
> hide #3 models
> show #2 models
> hide #1 models
> show #3 models
> hide #3 models
> hide #4 models
> show #3 models
> show #4 models
> show #1 models
> hide #1 models
> hide #4 models
> show #4 models
> hide #3 models
> hide #4 models
> show #3 models
> show #1 models
> hide #2 models
> hide #1 models
> show #4 models
> show #2 models
> hide #2 models
> hide #4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/Q #4/Q #1/Q #2/Q
Alignment identifier is 1
> select #3/Q:146 #4/Q:146 #1/Q:146 #2/Q:146
24 atoms, 20 bonds, 4 residues, 4 models selected
> select #3/Q:146-158 #4/Q:146-158 #1/Q:146-158 #2/Q:146-158
400 atoms, 408 bonds, 52 residues, 4 models selected
. [ID: 1] region 4 chains [146-158] RMSD: 0.554
> select #3/Q:196-197 #4/Q:196-197 #1/Q:196-197 #2/Q:196-197
88 atoms, 84 bonds, 8 residues, 4 models selected
> select #3/Q:149-196 #4/Q:149-196 #1/Q:149-196 #2/Q:149-196
1500 atoms, 1520 bonds, 192 residues, 4 models selected
. [ID: 1] region 4 chains [149-196] RMSD: 0.442
> select #3/Q:115 #4/Q:115 #1/Q:115 #2/Q:115
56 atoms, 60 bonds, 4 residues, 4 models selected
> select #3/Q:115-129 #4/Q:115-129 #1/Q:115-129 #2/Q:115-129
524 atoms, 544 bonds, 60 residues, 4 models selected
. [ID: 1] region 4 chains [115-129] RMSD: 0.766
> select #3/B:6@CA
1 atom, 1 residue, 1 model selected
> select #3/B:4@CB
1 atom, 1 residue, 1 model selected
> select clear
> select #3/Q:115-129 #4/Q:115-129 #1/Q:115-129 #2/Q:115-129
524 atoms, 544 bonds, 60 residues, 4 models selected
> select
> #3/Q:59-63,106-114,118-125,128-132,136-139,144-146,159-161,188-193,199-203,208-212,239-245,251-258
> #4/Q:59-63,106-114,118-125,128-132,136-139,144-146,159-161,188-193,199-203,208-212,239-245,251-258
> #1/Q:59-63,106-114,118-125,128-132,136-139,144-146,159-161,188-193,199-203,208-212,239-245,251-258
> #2/Q:59-63,106-114,118-125,128-132,136-139,144-146,159-161,188-193,199-203,208-212,239-245,251-258
2204 atoms, 2208 bonds, 272 residues, 4 models selected
> select clear
> show #4 models
> hide #4 models
> show #1 models
> hide #3 models
> show #4 models
> hide #1 models
> hide #4 models
> show #3 models
> show #4 models
> hide #4 models
> rock
> select #3/B:7@O
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
83 atoms, 84 bonds, 10 residues, 1 model selected
> select up
136 atoms, 139 bonds, 16 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select clear
> stop
> open
> /Users/osperand/Downloads/fold_2025_12_02_11_29/fold_2025_12_02_11_29_model_0.cif
Chain information for fold_2025_12_02_11_29_model_0.cif #5
---
Chain | Description
A | .
B | .
Computing secondary structure
> matchmaker #5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bd517-43_model_0.cif, chain Q (#1) with
fold_2025_12_02_11_29_model_0.cif, chain A (#5), sequence alignment score =
1422.7
RMSD between 186 pruned atom pairs is 0.478 angstroms; (across all 276 pairs:
9.241)
> hide #5 models
> show #5 models
> select add #5
2342 atoms, 2387 bonds, 292 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select clear
> hide #!3 models
> show #!3 models
> hide #!3 models
> select add #5
2342 atoms, 2387 bonds, 292 residues, 1 model selected
> color sel bychain
> color sel byhetero
> select clear
> show #!3 models
> hide #5 models
> show #5 models
> hide #5 models
> open
> /Users/osperand/Downloads/bd43-517-s-s2/fold_2025_12_02_11_29_model_0.cif
Chain information for fold_2025_12_02_11_29_model_0.cif #6
---
Chain | Description
A | .
B | .
Computing secondary structure
> matchmaker #6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bd517-43_model_0.cif, chain Q (#1) with
fold_2025_12_02_11_29_model_0.cif, chain A (#6), sequence alignment score =
1401.1
RMSD between 195 pruned atom pairs is 0.656 angstroms; (across all 276 pairs:
10.056)
> show #6#!3 atoms
> hide #6#!3 cartoons
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> open
> /Users/osperand/Downloads/bd43-517-s-s2/fold_2025_12_02_11_29_model_1.cif
Chain information for fold_2025_12_02_11_29_model_1.cif #7
---
Chain | Description
A | .
B | .
Computing secondary structure
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bd517-43_model_0.cif, chain Q (#1) with
fold_2025_12_02_11_29_model_1.cif, chain A (#7), sequence alignment score =
1411.9
RMSD between 192 pruned atom pairs is 0.675 angstroms; (across all 276 pairs:
10.634)
> show #6-7#!3 atoms
> hide #6-7#!3 cartoons
> close #7
> hide #!3 models
> open
> /Users/osperand/Downloads/bd43-517-s-s3/fold_2025_12_02_11_29_model_0.cif
Chain information for fold_2025_12_02_11_29_model_0.cif #7
---
Chain | Description
A | .
B | .
Computing secondary structure
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bd517-43_model_0.cif, chain Q (#1) with
fold_2025_12_02_11_29_model_0.cif, chain A (#7), sequence alignment score =
1420.9
RMSD between 182 pruned atom pairs is 0.643 angstroms; (across all 276 pairs:
13.990)
> color #6-7 bychain
> hide #6-7 cartoons
> hide #6 models
> hide #7 models
> show #7 models
> open
> /Users/osperand/Downloads/bd43-517-s-s3/fold_2025_12_02_11_29_model_1.cif
Chain information for fold_2025_12_02_11_29_model_1.cif #8
---
Chain | Description
A | .
B | .
Computing secondary structure
> open
> /Users/osperand/Downloads/bd43-517-s-s3/fold_2025_12_02_11_29_model_0.cif
Chain information for fold_2025_12_02_11_29_model_0.cif #9
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #9 models
> hide #8 models
> close #8-9
> show #7 target m
> view #7 clip false
No displayed objects specified.
> hide #7 models
> show #7 models
> close #7
> show #4 models
> hide #4 models
> show #!3 models
> show #5 models
> hide #5 models
> show #6 models
> select add #6
2343 atoms, 2387 bonds, 292 residues, 1 model selected
> color sel byhetero
> select clear
> hide #6 models
> open
> /Users/osperand/Downloads/bd43-517-s-s3/fold_2025_12_02_11_29_model_0.cif
Chain information for fold_2025_12_02_11_29_model_0.cif #7
---
Chain | Description
A | .
B | .
Computing secondary structure
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bd517-43_model_0.cif, chain Q (#1) with
fold_2025_12_02_11_29_model_0.cif, chain A (#7), sequence alignment score =
1420.9
RMSD between 182 pruned atom pairs is 0.643 angstroms; (across all 276 pairs:
13.990)
> show #7#!3 atoms
> color #7#!3 bychain
> color #7#!3 byhetero
> hide #7#!3 cartoons
> hide #!3 models
> show #!3 models
> hide #7 models
> show #7 models
> hide #!3 models
> show #4 models
> show #!3 models
> hide #7 models
> hide #4 models
> show #7 models
> hide #!3 models
> ui tool show H-Bonds
> hbonds reveal true
9600 hydrogen bonds found
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #7/B:9@CA
10 atoms, 8 bonds, 2 residues, 1 model selected
> select add #7/B:10@N
11 atoms, 8 bonds, 3 residues, 1 model selected
> select add #7/B:10@C
12 atoms, 8 bonds, 3 residues, 1 model selected
> select up
21 atoms, 20 bonds, 3 residues, 1 model selected
> show #4 models
> hide #8 models
> hide #7 models
> ui tool show H-Bonds
> hbonds reveal true
9600 hydrogen bonds found
> show #8 models
> show #5 models
> hide #4 models
> show #4 models
> hide #5 models
> open
> /Users/osperand/Downloads/bd43-517-s-s4/fold_2025_12_02_11_29_model_0.cif
Chain information for fold_2025_12_02_11_29_model_0.cif #9
---
Chain | Description
A | .
B | .
Computing secondary structure
> matchmaker #9 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bd517-43_model_0.cif, chain Q (#1) with
fold_2025_12_02_11_29_model_0.cif, chain A (#9), sequence alignment score =
1399.3
RMSD between 175 pruned atom pairs is 0.605 angstroms; (across all 276 pairs:
9.666)
> show #4,9 atoms
> color #4,9 bychain
> color #4,9 byhetero
> hide #4,9 cartoons
> hide #8 models
> hide #4 models
> show #!3 models
> hide #!3 models
> hide #9 models
> show #!3 models
> show #9 models
> hide #!3 models
> open "/Users/osperand/Downloads/fold_2025_12_02_11_29
> (4)/fold_2025_12_02_11_29_model_0.cif"
Chain information for fold_2025_12_02_11_29_model_0.cif #10
---
Chain | Description
A | .
B | .
Computing secondary structure
> matchmaker #10 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bd517-43_model_0.cif, chain Q (#1) with
fold_2025_12_02_11_29_model_0.cif, chain A (#10), sequence alignment score =
1422.7
RMSD between 179 pruned atom pairs is 0.632 angstroms; (across all 276 pairs:
10.382)
> show #9-10 atoms
> hide #9 models
> hide #10 cartoons
===== 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
> open
> /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/bd43-517-s-s7/bd43-517-s-s7_model_0.cif
Chain information for bd43-517-s-s7_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3 Ultra
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: Mac Studio
Model Identifier: Mac15,14
Model Number: Z1CE000FKFN/A
Chip: Apple M3 Ultra
Total Number of Cores: 28 (20 Performance and 8 Efficiency)
Memory: 96 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3 (25D125)
Kernel Version: Darwin 25.3.0
Time since boot: 35 jours, 1 heure et 53 minutes
Graphics/Displays:
Apple M3 Ultra:
Chipset Model: Apple M3 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 60
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Studio Display XDR:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 120.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Studio Display XDR:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 120.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
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-InDeep: 0.1.1
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-SDFFrames: 0.1.1
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 , 5 hours ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep in OpenGL swap_buffers on status line expose event |
comment:2 by , 5 hours ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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