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Opened 4 months ago
Closed 4 months ago
#18070 closed defect (can't reproduce)
Crash using open/save dialog
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | UI | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.0-arm64-arm-64bit
ChimeraX Version: 1.10rc202505100155 (2025-05-10 01:55:54 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00000001eed0f240 (most recent call first):
File "/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py", line 312 in show_open_file_dialog
File "/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py", line 268 in
File "/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, 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, PIL._imaging, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lxml._elementpath, lxml.etree (total: 50)
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"incident" : "C1416E5A-1D20-4B59-A16D-7D317AB23236",
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"procLaunch" : "2025-06-24 13:43:22.0229 +0200",
"procStartAbsTime" : 513036630760,
"procExitAbsTime" : 1000424058899,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10-rc2025.05.12.app\/Contents\/MacOS\/ChimeraX",
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===== Log before crash start =====
UCSF ChimeraX version: 1.10rc202505100155 (2025-05-10)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-RNA_hybrid/maps &
> mask/cryosparc_P18_J56_006_volume_map.mrc"
Failed opening file /Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-
RNA_hybrid/maps & mask/cryosparc_P18_J56_006_volume_map.mrc:
MRC file is truncated. Failed reading 1 values, type int32
> open "/Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-RNA_hybrid/maps &
> mask/cryosparc_P18_J56_006_volume_map_sharp.mrc"
Failed opening file /Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-
RNA_hybrid/maps & mask/cryosparc_P18_J56_006_volume_map_sharp.mrc:
MRC file is truncated. Failed reading 1 values, type int32
> open "/Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-RNA_hybrid/maps &
> mask/cryosparc_P18_J56_006_volume_map.mrc"
Failed opening file /Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-
RNA_hybrid/maps & mask/cryosparc_P18_J56_006_volume_map.mrc:
MRC file is truncated. Failed reading 1 values, type int32
> open "/Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-RNA_hybrid/maps &
> mask/cryosparc_P18_J56_006_volume_map_sharp.mrc"
Failed opening file /Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-
RNA_hybrid/maps & mask/cryosparc_P18_J56_006_volume_map_sharp.mrc:
MRC file is truncated. Failed reading 1 values, type int32
> open "/Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-RNA_hybrid/maps &
> mask/cryosparc_P18_J56_006_volume_map.mrc"
Opened cryosparc_P18_J56_006_volume_map.mrc as #1, grid size 392,392,392,
pixel 0.652, shown at level 0.0221, step 2, values float32
> open "/Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-RNA_hybrid/maps &
> mask/cryosparc_P18_J56_006_volume_map_sharp.mrc"
Opened cryosparc_P18_J56_006_volume_map_sharp.mrc as #2, grid size
392,392,392, pixel 0.652, shown at level 0.0346, step 2, values float32
> volume #2 step 1
> volume #2 level 0.05385
> volume #2 color #b9b88f
> open /Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-
> RNA_hybrid/phenix/RealSpaceRefine_6/8br2_fitted_real_space_refined_006.pdb
Chain information for 8br2_fitted_real_space_refined_006.pdb #3
---
Chain | Description
A B C D E F | No description available
G | No description available
H | No description available
132 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> show cartoons
> show atoms
> hide atoms
> show cartoons
> transparency #2.1 50
> select nucleic
820 atoms, 918 bonds, 40 residues, 1 model selected
> view sel
> show sel atoms
> hide sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 820 atom styles
> color sel byhetero
> select clear
> select /H:11@C7
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> cofr sel
> ui tool show "Side View"
> show #!1 models
> hide #!2 models
> volume #1 step 1
> volume #1 level 0.02588
> transparency #1.1 50
> show #!2 models
> hide #!1 models
> volume #2 level 0.03551
> open /Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-
> RNA_hybrid/coot/8br2_fitted_real_space_refined_006-coot-2.pdb
Chain information for 8br2_fitted_real_space_refined_006-coot-2.pdb #4
---
Chain | Description
A B C D E F | No description available
G | No description available
H | No description available
132 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!3 models
> select add #3
15442 atoms, 15624 bonds, 6 pseudobonds, 2044 residues, 2 models selected
> select subtract #3
Nothing selected
> select add #4
15455 atoms, 15637 bonds, 6 pseudobonds, 2044 residues, 2 models selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 833 atom styles
> color sel byhetero
> select protein
28608 atoms, 29016 bonds, 12 pseudobonds, 3732 residues, 4 models selected
> show sel & #!4 cartoons
> hide sel & #!4 atoms
> select clear
> volume #2 level 0.04516
> select #4/G:10@N6
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
433 atoms, 492 bonds, 20 residues, 1 model selected
> select down
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
433 atoms, 492 bonds, 20 residues, 1 model selected
> select clear
> select #4/H:11@O2'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/G:10@N6
21 atoms, 21 bonds, 2 residues, 1 model selected
> select up
41 atoms, 44 bonds, 2 residues, 1 model selected
> view sel
> select clear
> volume #2 level 0.05192
> select #4/H:11@O4
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> select clear
> volume #2 level 0.053
> volume #2 level 0.05
> volume #2 level 0.045
> open 3la5
Summary of feedback from opening 3la5 fetched from pdb
---
notes | Fetching compressed mmCIF 3la5 from http://files.rcsb.org/download/3la5.cif
Fetching CCD 5AZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/5AZ/5AZ.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
3la5 title:
X-ray crystal structure of mc6 RNA Riboswitch bound to azacytosine [more
info...]
Chain information for 3la5 #5
---
Chain | Description
A | Adenosine RIboswitch
Non-standard residues in 3la5 #5
---
5AZ — 6-amino-1,3,5-triazin-2(1H)-one (5-Azacytosine)
MG — magnesium ion
Computing secondary structure
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10-rc2025.05.12.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-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/nucleotides/_data.py", line 559, in rebuild
_rebuild_molecule('internal', mol)
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/nucleotides/_data.py", line 713, in _rebuild_molecule
nd.add_shapes(all_shapes)
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/shapedrawing.py", line 297, in add_shapes
if atoms is not None and all(atoms.selected):
^^^^^^^^^^^^^^
AttributeError: 'list' object has no attribute 'selected'
Error processing trigger "new frame":
AttributeError: 'list' object has no attribute 'selected'
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/shapedrawing.py", line 297, in add_shapes
if atoms is not None and all(atoms.selected):
^^^^^^^^^^^^^^
See log for complete Python traceback.
Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/bug_reporter/tool.py", line 253, in submit
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields, timeout=10)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/post_form.py", line 43, in
post_multipart_formdata
h.request('POST', url, body=body, headers=headers)
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1286, in request
self._send_request(method, url, body, headers, encode_chunked)
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1332, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1281, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1041, in _send_output
self.send(msg)
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 979, in send
self.connect()
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 945, in connect
self.sock = self._create_connection(
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py",
line 851, in create_connection
raise exceptions[0]
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py",
line 836, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 61] Connection refused
Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/bug_reporter/tool.py", line 253, in submit
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields, timeout=10)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/post_form.py", line 43, in
post_multipart_formdata
h.request('POST', url, body=body, headers=headers)
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1286, in request
self._send_request(method, url, body, headers, encode_chunked)
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1332, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1281, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1041, in _send_output
self.send(msg)
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 979, in send
self.connect()
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 945, in connect
self.sock = self._create_connection(
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py",
line 851, in create_connection
raise exceptions[0]
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py",
line 836, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 61] Connection refused
> view #5 clip false
> hide #!4 models
> hide #!2 models
> select #5/A:17@N3
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> select add #5/A:79@N1
21 atoms, 21 bonds, 2 residues, 1 model selected
> select up
43 atoms, 46 bonds, 2 residues, 1 model selected
> view sel
> ui tool show "Color Actions"
> color sel cornflower blue
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10-rc2025.05.12.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-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/nucleotides/_data.py", line 713, in _rebuild_molecule
nd.add_shapes(all_shapes)
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/shapedrawing.py", line 297, in add_shapes
if atoms is not None and all(atoms.selected):
^^^^^^^^^^^^^^
AttributeError: 'list' object has no attribute 'selected'
Error processing trigger "changes":
AttributeError: 'list' object has no attribute 'selected'
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/shapedrawing.py", line 297, in add_shapes
if atoms is not None and all(atoms.selected):
^^^^^^^^^^^^^^
See log for complete Python traceback.
> color sel byhetero
> open 9I62
Summary of feedback from opening 9I62 fetched from pdb
---
notes | Fetching compressed mmCIF 9i62 from http://files.rcsb.org/download/9i62.cif
Fetching CCD ATP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif
9i62 title:
CryoEM structure of a RAD51 D-loop [more info...]
Chain information for 9i62 #6
---
Chain | Description | UniProt
A B C D E F G H I | DNA repair protein RAD51 homolog 1 | RAD51_HUMAN 1-339
J | DNA (26-MER) |
K | DNA (41-MER) |
L | DNA (41-MER) |
Non-standard residues in 9i62 #6
---
ATP — adenosine-5'-triphosphate
CA — calcium ion
44 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> view #6 clip false
> hide #!5 models
> select add #5
1903 atoms, 1686 bonds, 126 pseudobonds, 464 residues, 3 models selected
> show #!6 cartoons
> hide #!6 atoms
> select nucleic
5360 atoms, 5990 bonds, 177 pseudobonds, 259 residues, 6 models selected
> show sel & #!6 atoms
> color sel & #!6 byhetero
> nucleotides sel & #!6 atoms
> style nucleic & sel & #!6 stick
Changed 2204 atom styles
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
23 atoms, 24 bonds, 2 residues, 1 model selected
> view sel
> select #6/K:16@N3
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #6/J:18@N3
23 atoms, 24 bonds, 2 residues, 1 model selected
> select up
42 atoms, 45 bonds, 2 residues, 1 model selected
> view sel
> select clear
> select #6/J:18@O4
1 atom, 1 residue, 1 model selected
> select add #6/K:16@O6
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #6/J:18@O4 #6/K:16@O6
Distance between 9i62 #6/J DT 18 O4 and /K DG 16 O6: 3.408Å
> select #6/J:18@N3
1 atom, 1 residue, 1 model selected
> select add #6/K:16@N1
2 atoms, 2 residues, 1 model selected
> distance #6/J:18@N3 #6/K:16@N1
Distance between 9i62 #6/J DT 18 N3 and /K DG 16 N1: 3.096Å
> select #6/J:18@O2
1 atom, 1 residue, 1 model selected
> select add #6/K:16@N2
2 atoms, 2 residues, 1 model selected
> distance #6/J:18@O2 #6/K:16@N2
Distance between 9i62 #6/J DT 18 O2 and /K DG 16 N2: 2.570Å
> ui tool show "Side View"
> open emdb:52646
Summary of feedback from opening 52646 fetched from emdb
---
notes | Fetching compressed map 52646 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-52646/map/emd_52646.map.gz
Fetching map header 52646 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-52646/header/emd-52646.xml
Opened emdb 52646 as #8, grid size 416,416,416, pixel 0.652, shown at level
0.017, step 2, values float32, fit PDB 9i62
> volume #8 step 1
> volume #8 color #89aaac
> transparency #8.1 50
> volume #8 level 0.02499
> ui tool show "Side View"
> volume #2 level 0.045
> volume #8 level 0.02765
> open "/Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51 synapsis/PDB
> DEPOSITION/maps/cryosparc_P8_J803_006_volume_map_zflip_sharpenB=75.mrc"
MRC file is truncated. Failed reading 1 values, type int32
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10rc202505100155 (2025-05-10)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: Z1AV0010MB/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 GB
System Firmware Version: 11881.1.1
OS Loader Version: 11881.1.1
Software:
System Software Overview:
System Version: macOS 15.0 (24A335)
Kernel Version: Darwin 24.0.0
Time since boot: 2 days, 1 hour, 25 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.3.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.3.2
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.3
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.5
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.6
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10rc202505100155
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.1
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.8.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.5.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.5
pytest-cov: 6.1.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 26.4.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.13.2
tzdata: 2025.2
urllib3: 2.4.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 4 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → UI |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash using open/save dialog |
comment:2 by , 4 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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