Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-12.6.1-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 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 0x0000000204518600 (most recent call first):
  Garbage-collecting
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/orderedset.py", line 53 in __iter__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 294 in list_handlers
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 489 in trigger_handlers
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1027 in _fire_trigger
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1017 in _cpp_rename
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 120 in set_prop
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 98 in clone_seq
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 60 in matches_to_gapped_seqs
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 55 in nw
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/match.py", line 78 in align
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/match.py", line 406 in match
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/match.py", line 742 in cmd_match
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/Applications/ChimeraX-1.7.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.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.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.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.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, chimerax.pdb_lib._load_libs, 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.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, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 59)


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{
  "uptime" : 2500000,
  "procLaunch" : "2024-03-06 15:58:56.0898 +0000",
  "procRole" : "Foreground",
  "version" : 2,
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  "deployVersion" : 210,
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  "captureTime" : "2024-03-06 22:25:43.2527 +0000",
  "incident" : "E0E6D6FC-4127-41C5-AB59-314D49484930",
  "bug_type" : "309",
  "pid" : 99064,
  "procExitAbsTime" : 61444439770151,
  "translated" : true,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
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  "storeInfo" : {"deviceIdentifierForVendor":"EDD8B610-D200-5890-8C1B-29D609195B52","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "ECED8795-F73E-B1B9-01B1-947CFD465E40",
  "wakeTime" : 899,
  "sleepWakeUUID" : "E8228FAE-CC34-4AA8-8150-4528EDDC8D8A",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 140722568036183\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc86ae0000-7ffc8711c000 [ 6384K] r-x\/r-x SM=COW  ...t_id=1f3bc26f",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 140722568036183\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc86ae0000-7ffc8711c000 [ 6384K] r-x\/r-x SM=COW  ...t_id=1f3bc26f",
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  "faultingThread" : 0,
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===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/sean/Downloads/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/sean/Downloads/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb

Chain information for
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/sean/Downloads/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb

Chain information for
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb
#3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/sean/Downloads/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb
#4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/sean/Downloads/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb

Chain information for
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb
#5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-5 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
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#2), sequence alignment score = 1245.7  
RMSD between 236 pruned atom pairs is 0.344 angstroms; (across all 243 pairs:
0.541)  
  
Matchmaker
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain B (#3), sequence alignment score = 1243.9  
RMSD between 239 pruned atom pairs is 0.373 angstroms; (across all 243 pairs:
0.494)  
  
Matchmaker
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#4), sequence alignment score = 1256.5  
RMSD between 242 pruned atom pairs is 0.343 angstroms; (across all 243 pairs:
0.375)  
  
Matchmaker
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#5), sequence alignment score = 1247.5  
RMSD between 241 pruned atom pairs is 0.311 angstroms; (across all 243 pairs:
0.365)  
  

> color bfactor

10460 atoms, 1290 residues, atom bfactor range 17.3 to 98.9  

> open
> /Users/sean/Downloads/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#6  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/sean/Downloads/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb

Chain information for
HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb
#7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/sean/Downloads/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb

Chain information for
HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb
#8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/sean/Downloads/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb

Chain information for
HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb
#9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/sean/Downloads/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb
#10  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-10 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
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#2), sequence alignment score = 1245.7  
RMSD between 236 pruned atom pairs is 0.344 angstroms; (across all 243 pairs:
0.541)  
  
Matchmaker
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain B (#3), sequence alignment score = 1243.9  
RMSD between 239 pruned atom pairs is 0.373 angstroms; (across all 243 pairs:
0.494)  
  
Matchmaker
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#4), sequence alignment score = 1256.5  
RMSD between 242 pruned atom pairs is 0.343 angstroms; (across all 243 pairs:
0.375)  
  
Matchmaker
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#5), sequence alignment score = 1247.5  
RMSD between 241 pruned atom pairs is 0.311 angstroms; (across all 243 pairs:
0.365)  
  
Matchmaker
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#6), sequence alignment score = 1249.3  
RMSD between 235 pruned atom pairs is 0.523 angstroms; (across all 243 pairs:
0.869)  
  
Matchmaker
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain B (#7), sequence alignment score = 1243.9  
RMSD between 237 pruned atom pairs is 0.385 angstroms; (across all 243 pairs:
0.635)  
  
Matchmaker
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#8), sequence alignment score = 1252.9  
RMSD between 238 pruned atom pairs is 0.379 angstroms; (across all 243 pairs:
0.514)  
  
Matchmaker
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#9), sequence alignment score = 1243.9  
RMSD between 240 pruned atom pairs is 0.340 angstroms; (across all 243 pairs:
0.428)  
  
Matchmaker
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#10), sequence alignment score = 1227.7  
RMSD between 235 pruned atom pairs is 0.324 angstroms; (across all 243 pairs:
0.858)  
  

> hide #5 models

> hide #4 models

> hide #3 models

> hide #2 models

> color #1,6-10 bychain

> color bfactor #1,6-10

12257 atoms, 1523 residues, atom bfactor range 16.9 to 98.9  

> show #2 models

> show #3 models

> show #4 models

> show #5 models

> select #1/B#2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B

19640 atoms, 19950 bonds, 2430 residues, 10 models selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_B
SES surface #1.1: minimum, -14.25, mean -0.67, maximum 13.96  
Coulombic values for
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb_B
SES surface #2.1: minimum, -18.46, mean -0.67, maximum 13.67  
Coulombic values for
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb_B
SES surface #3.1: minimum, -14.29, mean -0.64, maximum 14.99  
Coulombic values for
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb_B
SES surface #4.1: minimum, -13.81, mean -0.59, maximum 14.25  
Coulombic values for
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb_B
SES surface #5.1: minimum, -17.36, mean -0.66, maximum 14.37  
Coulombic values for
HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb_B
SES surface #6.1: minimum, -14.90, mean -0.53, maximum 13.49  
Coulombic values for
HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb_B
SES surface #7.1: minimum, -13.99, mean -0.60, maximum 13.50  
Coulombic values for
HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb_B
SES surface #8.1: minimum, -14.14, mean -0.69, maximum 13.50  
Coulombic values for
HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb_B
SES surface #9.1: minimum, -14.46, mean -0.64, maximum 14.71  
Coulombic values for
HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb_B
SES surface #10.1: minimum, -17.43, mean -0.71, maximum 14.57  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!5 models

> show #!5 models

> hide #!7 models

> hide #!6 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> show #!10 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> hide #!10 models

> hide #!5 models

> close #6-10

Alignment identifier is 1  

> select clear

Alignment identifier is 2  
Alignment identifier is 3  

> select #1/A:2 #2/A:2 #3/A:2 #4/A:2 #5/A:2

55 atoms, 50 bonds, 5 residues, 5 models selected  

> select #1/A:2 #2/A:2 #3/A:2 #4/A:2 #5/A:2

55 atoms, 50 bonds, 5 residues, 5 models selected  
2 [ID: 2] region 5 chains [2] RMSD: 3.967  
  

> select #1/A:2,4-5 #2/A:2,4-5 #3/A:2,4-5 #4/A:2,4-5 #5/A:2,4-5

165 atoms, 155 bonds, 15 residues, 5 models selected  
2 [ID: 2] region 5 chains [2] + 1 other block RMSD: 3.652  
  

> select #1/A:2,4-5,9-10 #2/A:2,4-5,9-10 #3/A:2,4-5,9-10 #4/A:2,4-5,9-10
> #5/A:2,4-5,9-10

260 atoms, 245 bonds, 25 residues, 5 models selected  
2 [ID: 2] region 5 chains [2] + 2 other blocks RMSD: 3.026  
  

> select #1/A:12 #2/A:12 #3/A:12 #4/A:12 #5/A:12

55 atoms, 50 bonds, 5 residues, 5 models selected  

> select #1/A:12-13 #2/A:12-13 #3/A:12-13 #4/A:12-13 #5/A:12-13

110 atoms, 105 bonds, 10 residues, 5 models selected  
2 [ID: 2] region 5 chains [12-13] RMSD: 1.724  
  

> select #1/A:9,12-13 #2/A:9,12-13 #3/A:9,12-13 #4/A:9,12-13 #5/A:9,12-13

165 atoms, 155 bonds, 15 residues, 5 models selected  
2 [ID: 2] region 5 chains [12-13] + 1 other block RMSD: 1.787  
  

> select #1/A:4-5,9,12-13 #2/A:4-5,9,12-13 #3/A:4-5,9,12-13 #4/A:4-5,9,12-13
> #5/A:4-5,9,12-13

275 atoms, 260 bonds, 25 residues, 5 models selected  
2 [ID: 2] region 5 chains [12-13] + 2 other blocks RMSD: 2.602  
  

> select #1/A:2,4-5,9,12-13 #2/A:2,4-5,9,12-13 #3/A:2,4-5,9,12-13
> #4/A:2,4-5,9,12-13 #5/A:2,4-5,9,12-13

330 atoms, 310 bonds, 30 residues, 5 models selected  
2 [ID: 2] region 5 chains [12-13] + 3 other blocks RMSD: 2.875  
  

> show sel & #!1-4 atoms

> color (#!1-4 & sel) orange

> select #1/A:7 #2/A:7 #3/A:7 #4/A:7 #5/A:7

40 atoms, 35 bonds, 5 residues, 5 models selected  

> select #1/A:7-8 #2/A:7-8 #3/A:7-8 #4/A:7-8 #5/A:7-8

80 atoms, 75 bonds, 10 residues, 5 models selected  
2 [ID: 2] region 5 chains [7-8] RMSD: 3.111  
  

> select #1/A:7-8,10 #2/A:7-8,10 #3/A:7-8,10 #4/A:7-8,10 #5/A:7-8,10

120 atoms, 110 bonds, 15 residues, 5 models selected  
2 [ID: 2] region 5 chains [7-8] + 1 other block RMSD: 2.678  
  

> show sel & #!1-4 atoms

> color (#!1-4 & sel) lime

> select clear

> hide #!4 models

> select #1/B:18 #2/B:18 #3/B:18 #4/B:18 #5/B:18

40 atoms, 35 bonds, 5 residues, 5 models selected  

> select #1/B:18 #2/B:18 #3/B:18 #4/B:18 #5/B:18

40 atoms, 35 bonds, 5 residues, 5 models selected  
1 [ID: 1] region 5 chains [18] RMSD: 0.535  
  

> select #1/B:18,20 #2/B:18,20 #3/B:18,20 #4/B:18,20 #5/B:18,20

85 atoms, 75 bonds, 10 residues, 5 models selected  
1 [ID: 1] region 5 chains [18] + 1 other block RMSD: 0.774  
  

> hide #!3 models

> hide #!2 models

> select #1/B#2/B#3/B#4/B#5/B

9820 atoms, 9975 bonds, 1215 residues, 5 models selected  

> mlp sel & #!1

Map values for surface
"HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_B
SES surface": minimum -28.78, mean -4.602, maximum 25.34  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel & #!1 surfaces

> open "/Users/sean/Documents/Projects/GOLPH3 paper/Briggs Kat
> Collaboration/ConFold/HsGOLPH3ConFold_b471d_weblogo.pdb"

Chain information for HsGOLPH3ConFold_b471d_weblogo.pdb #6  
---  
Chain | Description  
A | No description available  
  

> select #6/A

2370 atoms, 2401 bonds, 298 residues, 1 model selected  

> show sel surfaces

> ui tool show "Render by Attribute"

> color byattribute a:bfactor #!1-6 target cabs palette
> 0.04,#0fc7cf:25.1605,#b2b2b2:98.88,#9e205e

12830 atoms, 1588 residues, 6 surfaces, atom bfactor range 0.04 to 98.9  

> color byattribute a:bfactor #!6 target cabs palette
> 0.04,#0fc7cf:2.94081,#b2b2b2:5.09488,#9e205e

2370 atoms, 298 residues, 1 surfaces, atom bfactor range 0.04 to 17.3  

> color byattribute a:bfactor #!6 target cabs palette
> 0.04,#0fc7cf:2.94081,#b2b2b2:5.09488,#9e205e

2370 atoms, 298 residues, 1 surfaces, atom bfactor range 0.04 to 17.3  

> select clear

> ui tool show Matchmaker

> matchmaker #!2-6 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
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#2), sequence alignment score = 1245.7  
RMSD between 236 pruned atom pairs is 0.344 angstroms; (across all 243 pairs:
0.541)  
  
Matchmaker
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain B (#3), sequence alignment score = 1243.9  
RMSD between 239 pruned atom pairs is 0.373 angstroms; (across all 243 pairs:
0.494)  
  
Matchmaker
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#4), sequence alignment score = 1256.5  
RMSD between 242 pruned atom pairs is 0.343 angstroms; (across all 243 pairs:
0.375)  
  
Matchmaker
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#5), sequence alignment score = 1247.5  
RMSD between 241 pruned atom pairs is 0.311 angstroms; (across all 243 pairs:
0.365)  
  
Matchmaker
HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#1) with HsGOLPH3ConFold_b471d_weblogo.pdb, chain A (#6), sequence
alignment score = 1256.5  
RMSD between 224 pruned atom pairs is 0.689 angstroms; (across all 243 pairs:
1.083)  
  

> open
> /Users/sean/Downloads/HsGALNT2tail_GOLPH3_E_U_12_0_a277a/HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb

Chain information for
HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/sean/Downloads/HsGALNT2tail_GOLPH3_E_U_12_0_a277a/HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb
#8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/sean/Downloads/HsGALNT2tail_GOLPH3_E_U_12_0_a277a/HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb

Chain information for
HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb
#9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/sean/Downloads/HsGALNT2tail_GOLPH3_E_U_12_0_a277a/HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb

Chain information for
HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb
#10  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/sean/Downloads/HsGALNT2tail_GOLPH3_E_U_12_0_a277a/HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb
#11  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!1 models

> hide #!6 models

> ui tool show Matchmaker

> matchmaker #8-11#!2-6 to #7


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 76.3
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: MacBookPro18,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 32 GB

Software:

    System Software Overview:

      System Version: macOS 12.6.1 (21G217)
      Kernel Version: Darwin 21.6.0
      Time since boot: 55 days 4:00

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    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: 1.5.13
    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: 12.1.3
    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: 1.7
    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: 1.1.3
    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: 1.1.8
    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: 1.13.1
    ChimeraX-PDB: 2.7.3
    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: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    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: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
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    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: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
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    Pillow: 10.0.1
    pip: 23.0
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    platformdirs: 4.1.0
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    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
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    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: 25.1.2
    qtconsole: 5.4.3
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    RandomWords: 0.4.0
    requests: 2.31.0
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    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
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    sortedcontainers: 2.4.0
    soupsieve: 2.5
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    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: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    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