The following bug report has been submitted:
Platform: macOS-14.2-arm64-arm-64bit
ChimeraX Version: 1.7rc202311220128 (2023-11-22 01:28:33 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 0x00000001de351000 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 907 in atomspec_atoms
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 627 in _add_model_parts
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 476 in _check
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 490 in _check
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 470 in find_matches
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 612 in find_matches
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 455 in find_matches
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1004 in find_matches
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1001 in evaluate
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1091 in evaluate
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py", line 36 in parse
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py", line 71 in parse
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2499 in _parse_arg
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2640 in _process_positional_arguments
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2864 in run
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/tool.py", line 303 in run_matchmaker
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/tool.py", line 171 in
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7-rc2023.11.22.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw (total: 53)
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===== Log before crash start =====
UCSF ChimeraX version: 1.7rc202311220128 (2023-11-22)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/markfrank/Desktop/DARC_Project/ForAndy/Current_State/newChimeraXarchive/mafChapter3.html
Opened mafChapter3.html
> cd
> /Users/markfrank/Desktop/DARC_Project/ForAndy/Current_State/newChimeraXarchive
Current working directory is:
/Users/markfrank/Desktop/DARC_Project/ForAndy/Current_State/newChimeraXarchive
> close session
> open 4p00_H.pdb
Summary of feedback from opening 4p00_H.pdb
---
warnings | Ignored bad PDB record found on line 1193
SSBOND *** CYS B 163 CYS B 430 1555 1555 2.03
Ignored bad PDB record found on line 1223
SITE *** AC1 17 PRO A 147 SER A 148 TYR A 149 GLU A 151
Ignored bad PDB record found on line 1224
SITE *** AC1 17 ASP A 180 ALA A 225 LYS A 226 ASP A 246
Ignored bad PDB record found on line 1225
SITE *** AC1 17 ALA A 247 GLN A 379 ARG A 382 TRP A 383
Ignored bad PDB record found on line 1226
SITE *** AC1 17 PHE A 503 VAL A 505 THR A 506 LYS A 508
24 messages similar to the above omitted
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
10834 messages similar to the above omitted
4p00_H.pdb title:
Bacterial cellulose synthase In complex with cyclic-di-GMP and udp [more
info...]
Chain information for 4p00_H.pdb #1
---
Chain | Description | UniProt
A | cellulose synthase A subunit | Q3J125_RHOS4 2-788
B | cellulose synthase B subunit | Q3J126_RHOS4 1-724
D | unidentified peptide |
Non-standard residues in 4p00_H.pdb #1
---
3PE — 1,2-diacyl-Sn-glycero-3-phosphoethanolamine (3-Sn-
phosphatidylethanolamine)
BGC — β-D-glucose
C2E —
9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-D:3',2'-J][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
(C-di-GMP, cyclic diguanosine monophosphate)
MG — magnesium ion
PLC — diundecyl phosphatidyl choline
UDP — uridine-5'-diphosphate
> lighting full
> hide atoms
> hide ribbons
> show /a ribbons
> name frozen AY
> /a:142,151,159,168,169,179,180,216,219,226,227,246,248,272,273,278,320,325,342,343,355,359,370,379,382,383,503,506,508
> style AY stick
Changed 500 atom styles
> show AY
> color AY yellow
> name frozen AR
> /a:80,83,84,88,89,104,108,148,149,163,202,222,225,229,274,284,285,297,301,305,312,318,322,368,380,417,423,433,443,477,498,505
> style AR stick
Changed 556 atom styles
> show AR
> color AR red
> open 4p00_dcPairs.pb
Opened Pseudobonds 4p00_dcPairs.pb, 25 bonds
> color /a tan target r
> ~select
Nothing selected
> select AY
500 atoms, 488 bonds, 29 residues, 1 model selected
> save 4p00_AY.pdb format pdb selectedOnly true
> ~select
Nothing selected
> select AR
556 atoms, 539 bonds, 32 residues, 1 model selected
> save 4p00_AR.pdb format pdb selectedOnly true
> ~select
Nothing selected
> name frozen cellulose /a:bgc
> style cellulose sphere
Changed 187 atom styles
> show cellulose
> color cellulose powder blue
> preset pub
Multiple preset names match 'pub': publication 1 (silhouettes); publication 2
(depth-cued)
> select /a: e8e
Nothing selected
> select /a: 383
24 atoms, 25 bonds, 1 residue, 1 model selected
> view sel
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> close session
> pwd
Current working directory is: /Users/markfrank/Desktop
> cd DARC_Project
Current working directory is: /Users/markfrank/Desktop/DARC_Project
> cd /ForAndy/Current_State/newChimeraXarchive
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> cd /ForAndy/Current_State/
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> cd ForAndy/Current_State/
Current working directory is:
/Users/markfrank/Desktop/DARC_Project/ForAndy/Current_State
> cd newChimeraXarchive
Current working directory is:
/Users/markfrank/Desktop/DARC_Project/ForAndy/Current_State/newChimeraXarchive
> open 6wlb_H.pdb
Summary of feedback from opening 6wlb_H.pdb
---
warnings | Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
383 messages similar to the above omitted
Chain information for 6wlb_H.pdb #1
---
Chain | Description
A B C | No description available
> open 4p00_H.pdb
Summary of feedback from opening 4p00_H.pdb
---
warnings | Ignored bad PDB record found on line 1193
SSBOND *** CYS B 163 CYS B 430 1555 1555 2.03
Ignored bad PDB record found on line 1223
SITE *** AC1 17 PRO A 147 SER A 148 TYR A 149 GLU A 151
Ignored bad PDB record found on line 1224
SITE *** AC1 17 ASP A 180 ALA A 225 LYS A 226 ASP A 246
Ignored bad PDB record found on line 1225
SITE *** AC1 17 ALA A 247 GLN A 379 ARG A 382 TRP A 383
Ignored bad PDB record found on line 1226
SITE *** AC1 17 PHE A 503 VAL A 505 THR A 506 LYS A 508
24 messages similar to the above omitted
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
10834 messages similar to the above omitted
4p00_H.pdb title:
Bacterial cellulose synthase In complex with cyclic-di-GMP and udp [more
info...]
Chain information for 4p00_H.pdb #2
---
Chain | Description | UniProt
A | cellulose synthase A subunit | Q3J125_RHOS4 2-788
B | cellulose synthase B subunit | Q3J126_RHOS4 1-724
D | unidentified peptide |
Non-standard residues in 4p00_H.pdb #2
---
3PE — 1,2-diacyl-Sn-glycero-3-phosphoethanolamine (3-Sn-
phosphatidylethanolamine)
BGC — β-D-glucose
C2E —
9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-D:3',2'-J][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
(C-di-GMP, cyclic diguanosine monophosphate)
MG — magnesium ion
PLC — diundecyl phosphatidyl choline
UDP — uridine-5'-diphosphate
> ui tool show Matchmaker
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7rc202311220128 (2023-11-22)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGQ3LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2 (23C64)
Kernel Version: Darwin 23.2.0
Time since boot: 1 day, 1 hour, 45 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
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: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.13.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.12
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7rc202311220128
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.2
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: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
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: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
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: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.45.0
funcparserlib: 2.0.0a0
glfw: 2.6.3
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.0
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.7
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.0.0
prompt-toolkit: 3.0.41
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Mark,
--Eric