Opened 7 months ago

Closed 7 months ago

#17132 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: halle.andrews-clark@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-13.0.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00000002046982c0 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 54)


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  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro17,1",
  "coalitionID" : 677,
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    "build" : "22A400",
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  "captureTime" : "2025-03-19 11:45:23.6267 +0100",
  "incident" : "A7076B4B-09E0-4115-B283-844A6DCE977F",
  "pid" : 44008,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-03-17 15:56:57.0871 +0100",
  "procStartAbsTime" : 542520001611,
  "procExitAbsTime" : 1115667688126,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "02E04C25-79CA-2EF6-F248-C1774882463F",
  "wakeTime" : 24,
  "sleepWakeUUID" : "FA97727D-8F4C-48C1-B379-ED6EF2F5C015",
  "sip" : "disabled",
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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/haandrew/Downloads/fold_2025_03_11_10_31/fold_2025_03_11_10_31_model_0.cif

Chain information for fold_2025_03_11_10_31_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> open /Users/haandrew/Downloads/fold_25s_snd/fold_25s_snd_model_0.cif

Chain information for fold_25s_snd_model_0.cif #2  
---  
Chain | Description  
A | .  
B | .  
  

> hide #1 models

> select #2/B:1-3396

72617 atoms, 81273 bonds, 3396 residues, 1 model selected  

> select #2/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> ~hide

Unknown command: ~hide  

> hide ~select

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide ~sel

> select #2/B:1-3396

72617 atoms, 81273 bonds, 3396 residues, 1 model selected  

> select #2/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select ~sel

79532 atoms, 88302 bonds, 4274 residues, 2 models selected  

> hide (#2 & sel) target a

> cartoon hide (#2 & sel)

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /PDB 8BQX.cif"

PDB 8BQX.cif title:  
Yeast 80S ribosome in complex with Map1 (conformation 2) [more info...]  
  
Chain information for PDB 8BQX.cif #3  
---  
Chain | Description | UniProt  
2 | 18S rRNA |   
A | 40S ribosomal protein S3 | RS3_YEAST 4-225  
AA | 60S ribosomal protein L8-A | RL8A_YEAST 24-256  
AB | 60S ribosomal protein L23-A | RL23A_YEAST 2-137  
AC | 60S ribosomal protein L36-A | RL36A_YEAST 2-100  
AD | 60S ribosomal protein L9-A | RL9A_YEAST 1-191  
AE | 60S ribosomal protein L24-A | RL24A_YEAST 1-126  
AF | 60S ribosomal protein L37-A | RL37A_YEAST 2-82  
AG | RPL11B isoform 1 | A0A6A5PYM2_YEASX 6-174  
AH | 60S ribosomal protein L25 | RL25_YEAST 22-142  
AI | RPL38 isoform 1 | A0A6A5PUL8_YEASX 2-78  
AJ | 60S ribosomal protein L13-A | RL13A_YEAST 2-194  
AK | 60S ribosomal protein L26-A | RL26A_YEAST 2-126  
AL | 60S ribosomal protein L39 | RL39_YEAST 2-51  
AM | 60S ribosomal protein L14-A | RL14A_YEAST 3-138  
AN | 60S ribosomal protein L27-A | RL27A_YEAST 2-136  
AO | 60S ribosomal protein L40-A | RL40A_YEAST 77-128  
AP | 60S ribosomal protein L42-A | RL44A_YEAST 2-104  
AQ | 60S ribosomal protein L15-A | RL15A_YEAST 2-204  
AR | 60S ribosomal protein L28 | RL28_YEAST 2-149  
AS | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
AT | 60S ribosomal protein L43-A | RL43A_YEAST 2-92  
AU | 60S ribosomal protein L16-A | RL16A_YEAST 3-199  
AV | 60S ribosomal protein L29 | A0A6A5PWR1_YEASX 2-59  
AW | 60S ribosomal protein L2-A | RL2A_YEAST 2-252  
AX | 60S ribosomal protein L17-A | RL17A_YEAST 2-184  
AY | 60S ribosomal protein L30 | RL30_YEAST 9-104  
B | 40S ribosomal protein S5 | RS5_YEAST 20-225  
BA | 60S ribosomal protein L3 | RL3_YEAST 2-387  
BB | 60S ribosomal protein L18-A | RL18A_YEAST 2-186  
BC | 60S ribosomal protein L31-A | RL31A_YEAST 4-112  
BD | RPL10 isoform 1 | A0A6A5PUZ5_YEASX 2-219  
BE | 60S ribosomal protein L4-A | RL4A_YEAST 2-362  
BF | 60S ribosomal protein L19-A | RL19A_YEAST 2-189  
BG | RPL32 isoform 1 | A0A6A5Q1M9_YEASX 2-128  
BH | 60S ribosomal protein L20-A | RL20A_YEAST 2-172  
BI | 60S ribosomal protein L5 | RL5_YEAST 4-297  
BJ | 60S ribosomal protein L21-A | RL21A_YEAST 2-160  
BK | 60S ribosomal protein L33-A | RL33A_YEAST 2-107  
BL | 60S ribosomal protein L22-A | RL22A_YEAST 9-108  
BM | 60S ribosomal protein L6-B | RL6B_YEAST 2-176  
BN | 60S ribosomal protein L34-A | RL34A_YEAST 2-113  
BO | 60S ribosomal protein L7-A | RL7A_YEAST 23-244  
BP | 60S ribosomal protein L35-A | RL35A_YEAST 2-120  
BQ | 25S rRNA |   
BR | 5S rRNA |   
BS | 5.8S rRNA |   
BT | 60S ribosomal protein L1-A | RL1A_YEAST 1-217  
C | 40S ribosomal protein S10-A | RS10A_YEAST 1-92  
D | 40S ribosomal protein S12 | RS12_YEAST 23-143  
E | 40S ribosomal protein S15 | RS15_YEAST 1-142  
F | 40S ribosomal protein S16-A | RS16A_YEAST 3-143  
G | 40S ribosomal protein S17-A | RS17A_YEAST 2-126  
H | 40S ribosomal protein S18-A | RS18A_YEAST 2-146  
I | 40S ribosomal protein S19-A | RS19A_YEAST 2-144  
J | 40S ribosomal protein S20 | RS20_YEAST 20-119  
K | 40S ribosomal protein S25-A | RS25A_YEAST 24-105  
L | 40S ribosomal protein S28-A | RS28A_YEAST 5-67  
M | 40S ribosomal protein S29-A | RS29A_YEAST 4-56  
N | 40S ribosomal protein S31 | RS31_YEAST 80-152  
O | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 5-316  
P | 40S ribosomal protein S0-A | RSSA1_YEAS1 2-207  
Q | 40S ribosomal protein S1-A | RS3A1_YEAS1 2-233  
R | 40S ribosomal protein S2 | RS2_YEAST 34-249  
S | 40S ribosomal protein S4-A | RS4A_YEAST 2-259  
T | 40S ribosomal protein S6-A | RS6A_YEAST 1-228  
U | 40S ribosomal protein S7-A | RS7A_YEAST 4-187  
V | 40S ribosomal protein S8-A | RS8A_YEAST 2-199  
W | 40S ribosomal protein S9-A | RS9A_YEAST 2-185  
X | 40S ribosomal protein S11-A | RS11A_YEAST 4-145  
Y | 40S ribosomal protein S13 | RS13_YEAST 2-151  
Z | 40S ribosomal protein S14-B | RS14B_YEAST 11-137  
a | 40S ribosomal protein S21-A | RS21A_YEAST 1-87  
b | 40S ribosomal protein S22-A | RS22A_YEAST 2-130  
c | 40S ribosomal protein S23-A | RS23A_YEAST 2-145  
d | 40S ribosomal protein S24-A | RS24A_YEAST 2-135  
e | 40S ribosomal protein S26-B | RS26B_YEAST 2-98  
f | 40S ribosomal protein S27-A | RS27A_YEAST 2-82  
g | 40S ribosomal protein S30-A | RS30A_YEAST 2-61  
x | Methionine aminopeptidase 1 | MAP1_YEAST 1-387  
  
Non-standard residues in PDB 8BQX.cif #3  
---  
ZN — zinc ion  
  
1555 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!3 models

> show #!3 models

> select add #3

285340 atoms, 309283 bonds, 5155 pseudobonds, 21343 residues, 6 models
selected  

> select subtract #3

79532 atoms, 88302 bonds, 4274 residues, 2 models selected  

> sequence chain #3/BQ

Alignment identifier is 3/BQ  

> select add #3

285340 atoms, 309283 bonds, 5155 pseudobonds, 21343 residues, 6 models
selected  

> cartoon (#2#!3 & sel)

> hide (#2#!3 & sel) target a

> select add #2

292254 atoms, 316312 bonds, 5155 pseudobonds, 22220 residues, 6 models
selected  

> select subtract #2

212723 atoms, 228010 bonds, 5155 pseudobonds, 17947 residues, 5 models
selected  

> select subtract #3

6915 atoms, 7029 bonds, 878 residues, 1 model selected  

> select subtract #1

Nothing selected  

> sequence chain #3/BQ

Destroying pre-existing alignment with identifier 3/BQ  
Alignment identifier is 3/BQ  

> select #3/BQ:3-3396

70586 atoms, 79003 bonds, 3108 pseudobonds, 3301 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #2 to #3

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 PDB 8BQX.cif, chain BQ (#3) with fold_25s_snd_model_0.cif, chain B
(#2), sequence alignment score = 19589.3  
RMSD between 2666 pruned atom pairs is 0.915 angstroms; (across all 3301
pairs: 5.800)  
  

> ~struts sel

> select clear

> select #2/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select #2/B:1-3396

72617 atoms, 81273 bonds, 3396 residues, 1 model selected  

> select #2/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select #2/B:1-3396

72617 atoms, 81273 bonds, 3396 residues, 1 model selected  

> select #2/B:1-3396

72617 atoms, 81273 bonds, 3396 residues, 1 model selected  

> select #2/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> color sel red

> select clear

> log metadata #3

Metadata for PDB 8BQX.cif #3  
---  
Title | Yeast 80S ribosome in complex with Map1 (conformation 2)  
Citation | Knorr, A.G., Mackens-Kiani, T., Musial, J., Berninghausen, O., Becker, T., Beatrix, B., Beckmann, R. (2023). The dynamic architecture of Map1- and NatB-ribosome complexes coordinates the sequential modifications of nascent polypeptide chains. Plos Biol., 21, e3001995-e3001995. PMID: 37079644. DOI: 10.1371/journal.pbio.3001995  
Non-standard residue | ZN — zinc ion  
Sources (natural) | Saccharomyces cerevisiae  
Saccharomyces cerevisiae (baker's yeast)  
CryoEM Map | EMDB 16191 — open map  
Experimental method | Electron microscopy  
Resolution | 3.8Å  
  
> select add #3

205808 atoms, 220981 bonds, 5155 pseudobonds, 17069 residues, 4 models
selected  

> color (#!3 & sel) gray

> select subtract #3

Nothing selected  

> select #2/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select #2/B:1-3396

72617 atoms, 81273 bonds, 3396 residues, 1 model selected  

> select #2/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select ~ sel

285340 atoms, 309283 bonds, 5155 pseudobonds, 21343 residues, 6 models
selected  

> hide (#2#!3 & sel) target a

> cartoon hide (#2#!3 & sel)

> cartoon (#2#!3 & sel)

> ~struts sel

> select clear

> hide #!3 models

> select #2/B:1-3396

72617 atoms, 81273 bonds, 3396 residues, 1 model selected  

> select #2/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select ~ sel

285340 atoms, 309283 bonds, 5155 pseudobonds, 21343 residues, 6 models
selected  

> cartoon hide (#2 & sel)

> show #!3 models

> select ~ sel

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> ~struts sel

> select clear

> save /Users/haandrew/Desktop/image24.png supersample 3

> movie record

> turn y 2 180

> wait 180

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 176, in capture_image  
i.save(save_path, self.img_fmt)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 2459, in save  
save_handler(self, fp, filename)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/PpmImagePlugin.py", line 356, in _save  
ImageFile._save(im, fp, [("raw", (0, 0) + im.size, 0, (rawmode, 0,
row_order))])  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/ImageFile.py", line 538, in _save  
_encode_tile(im, fp, tile, bufsize, fh)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/ImageFile.py", line 565, in _encode_tile  
errcode = encoder.encode_to_file(fh, bufsize)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
OSError: [Errno 28] No space left on device  
  
Out of disk space  

> movie encode /Users/haandrew/Desktop/movie2.mp4

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 182, in enqueue  
self.save()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 212, in save  
self._history.save(self._queue)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 120, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Out of disk space  
An error occurred during encoding. See Reply Log for details.  

> save /Users/haandrew/Desktop/image25.png supersample 3

> save /Users/haandrew/Desktop/image26.png supersample 3

> ui tool show "Side View"

> save /Users/haandrew/Desktop/image27.png supersample 3

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /fold_25s_snd/fold_25s_snd_model_1.cif"

Chain information for fold_25s_snd_model_1.cif #4  
---  
Chain | Description  
A | .  
B | .  
  

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /fold_25s_snd/fold_25s_snd_model_2.cif"

Chain information for fold_25s_snd_model_2.cif #5  
---  
Chain | Description  
A | .  
B | .  
  

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /fold_25s_snd/fold_25s_snd_model_3.cif"

Chain information for fold_25s_snd_model_3.cif #6  
---  
Chain | Description  
A | .  
B | .  
  

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /fold_25s_snd/fold_25s_snd_model_4.cif"

Chain information for fold_25s_snd_model_4.cif #7  
---  
Chain | Description  
A | .  
B | .  
  

> hide #4 models

> hide #5 models

> hide #6 models

> hide #7 models

> show #4 models

> select #4/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select #4/B:1-3396

72617 atoms, 81273 bonds, 3396 residues, 1 model selected  

> hide #!3 models

> hide #2 models

> select #4/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select ~ sel

603464 atoms, 662491 bonds, 5155 pseudobonds, 38435 residues, 10 models
selected  

> select clear

> select #4/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select #4/B:1-3396

72617 atoms, 81273 bonds, 3396 residues, 1 model selected  

> select clear

> ui tool show Matchmaker

> matchmaker #4-7 to #3

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 PDB 8BQX.cif, chain BQ (#3) with fold_25s_snd_model_1.cif, chain B
(#4), sequence alignment score = 19589.3  
RMSD between 2667 pruned atom pairs is 0.941 angstroms; (across all 3301
pairs: 6.096)  
  
Matchmaker PDB 8BQX.cif, chain BQ (#3) with fold_25s_snd_model_2.cif, chain B
(#5), sequence alignment score = 19589.3  
RMSD between 2688 pruned atom pairs is 0.943 angstroms; (across all 3301
pairs: 10.416)  
  
Matchmaker PDB 8BQX.cif, chain BQ (#3) with fold_25s_snd_model_3.cif, chain B
(#6), sequence alignment score = 19589.3  
RMSD between 2726 pruned atom pairs is 0.987 angstroms; (across all 3301
pairs: 7.361)  
  
Matchmaker PDB 8BQX.cif, chain BQ (#3) with fold_25s_snd_model_4.cif, chain B
(#7), sequence alignment score = 19589.3  
RMSD between 2634 pruned atom pairs is 0.964 angstroms; (across all 3301
pairs: 7.614)  
  

> select #4/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select #4/B:1-3396

72617 atoms, 81273 bonds, 3396 residues, 1 model selected  

> cartoon hide sel

> hide sel target a

> hide #4 models

> show #5 models

> select #5/B:1-3396

72617 atoms, 81273 bonds, 3396 residues, 1 model selected  

> select #5/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select ~ sel

603464 atoms, 662491 bonds, 5155 pseudobonds, 38435 residues, 10 models
selected  

> cartoon hide (#5 & sel)

> hide (#5 & sel) target a

> hide #5 models

> show #6 models

> select #6/B:1-3396

72617 atoms, 81273 bonds, 3396 residues, 1 model selected  

> select #6/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select ~ sel

603464 atoms, 662491 bonds, 5155 pseudobonds, 38435 residues, 10 models
selected  

> hide (#6 & sel) target a

> cartoon hide (#6 & sel)

> hide #6 models

> show #7 models

> select #7/B:1-3396

72617 atoms, 81273 bonds, 3396 residues, 1 model selected  

> select #7/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select ~ sel

603464 atoms, 662491 bonds, 5155 pseudobonds, 38435 residues, 10 models
selected  

> hide (#7 & sel) target a

> cartoon hide (#7 & sel)

> show #6 models

> show #5 models

> show #4 models

> show #!3 models

> show #2 models

> select clear

> ui tool show Matchmaker

> matchmaker #!3 to #4

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 fold_25s_snd_model_1.cif, chain B (#4) with PDB 8BQX.cif, chain BQ
(#3), sequence alignment score = 19589.3  
RMSD between 2667 pruned atom pairs is 0.941 angstroms; (across all 3301
pairs: 6.096)  
  

> sequence chain #3/BQ

Alignment identifier is 3/BQ  

> select #3/BQ:3-3396

70586 atoms, 79003 bonds, 3108 pseudobonds, 3301 residues, 2 models selected  

> color (#!3 & sel) cyan

> select clear

> save "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /80s ribosome + 25S SND1 model ALL.jpg" width 706 height 608
> supersample 3

> select #3/x:21-387

2899 atoms, 2970 bonds, 367 residues, 1 model selected  

> hide sel target a

> cartoon hide sel

> select clear


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Model Number: Z11D000L9D/A
      Chip: Unknown
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0.1 (22A400)
      Kernel Version: Darwin 22.1.0
      Time since boot: 4 days, 2 hours, 39 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      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
        DELL P2722H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by pett, 7 months ago

Component: Unassigned → Window Toolkit
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

comment:2 by pett, 7 months ago

Resolution: → duplicate
Status: assigned → closed

ChimeraX 1.9 may encounter this crash less often. It is a bug in the Qt 6.7 window toolkit and ChimeraX 1.9 gives this message in its Report a Bug panel which explains what we know.

"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here ​​​https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX."

We have updated to Qt version 6.8 in the daily builds which may fix this problem, so you might consider trying the daily build.

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