id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16577	Crash in python_instances_of_class	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-14.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 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 0x00000001dd3b5ec0 (most recent call first):
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 44 in python_instances_of_class
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 176 in _copy_custom_attrs
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 162 in copy
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py"", line 65 in combine_cmd
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2904 in run
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 319 in execute
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 280 in event_loop
  File ""/Applications/ChimeraX_Daily.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_Daily.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.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, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.segment._segment, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 63)


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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Capsid/Corndog-Head-
> Cap-C5-2_96A/00-C5-Head-Cap-pdbs part 2.pdb"" format pdb

Chain information for 00-C5-Head-Cap-pdbs part 2.pdb  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A 1.24/A 1.25/A 1.26/A 1.27/A 1.28/A 1.29/A 1.30/A 1.31/A 1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B 1.11/B 1.12/B 1.13/B 1.14/B 1.15/B 1.16/B 1.17/B 1.18/B 1.19/B 1.20/B 1.21/B 1.22/B 1.23/B 1.24/B 1.25/B 1.26/B 1.27/B 1.28/B 1.29/B 1.30/B 1.31/B 1.1/C 1.7/C 1.8/C 1.9/C 1.10/C 1.11/C 1.12/C 1.13/C 1.14/C 1.15/C 1.16/C 1.1/D 1.2/D 1.3/D 1.4/D 1.5/D 1.6/D 1.7/D 1.8/D 1.9/D 1.10/D 1.11/D 1.12/D 1.13/D 1.14/D 1.15/D 1.16/D 1.17/D 1.18/D 1.19/D 1.20/D 1.21/D 1.22/D 1.23/D 1.24/D 1.25/D 1.26/D 1.27/D 1.28/D 1.29/D 1.30/D 1.31/D 1.1/E 1.7/E 1.8/E 1.9/E 1.10/E 1.11/E 1.12/E 1.13/E 1.14/E 1.15/E 1.16/E 1.12/F 1.13/F 1.14/F 1.15/F 1.16/F 1.17/F 1.18/F 1.19/F 1.20/F 1.21/F 1.22/F 1.23/F 1.24/F 1.25/F 1.26/F 1.27/F 1.28/F 1.29/F 1.30/F 1.31/F | No description available  
1.2/C 1.3/C 1.4/C 1.5/C 1.6/C 1.17/C 1.18/C 1.19/C 1.20/C 1.21/C 1.22/C 1.23/C 1.24/C 1.25/C 1.26/C 1.27/C 1.28/C 1.29/C 1.30/C 1.31/C 1.2/E 1.3/E 1.4/E 1.5/E 1.6/E 1.17/E 1.18/E 1.19/E 1.20/E 1.21/E 1.22/E 1.23/E 1.24/E 1.25/E 1.26/E 1.27/E 1.28/E 1.29/E 1.30/E 1.31/E 1.2/F 1.3/F 1.4/F 1.5/F 1.6/F | No description available  
  

> close

> open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/Protein Face Session.cxs"" format session

opened ChimeraX session  

> close #10,12-13#11

> close #9

> view #8 clip false

> hide #7 models

> show #7 models

> lighting flat

> set bgColor white

> lighting soft

> lighting flat

> save ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Connector/AlphaDifference/Portal_12mer.png"" width 1104 height 742
> supersample 3 transparentBackground true

> hide #7 models

> hide #8 models

> show #6 models

> show #5 models

> view #6 clip false

> color #6 darkgrey

> color #6 black

> save ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Connector/AlphaDifference/Adaptor_12mer.png"" width 1104 height 742
> supersample 3 transparentBackground true

> hide #6 models

> hide #5 models

> show #4 models

> show #3 models

> view #3 clip false

> color #4 #919191ff

> save ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Connector/AlphaDifference/Terminator.png"" width 1104 height 742 supersample
> 3 transparentBackground true

> hide #3 models

> hide #4 models

> show #2 models

> show #1 models

> view #1 clip false

> color #2 #797979ff

> color #2 #d6d6d6ff

> color #2 white

> color #2 #941751ff

> color #2 #005493ff

> color #2 #945200ff

> color #2 #4f8f00ff

> color #2 #008f00ff

> color #2 #ff8ad8ff

> color #2 #ff40ffff

> color #2 #ff2f92ff

> color #2 #5e5e5eff

> save ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Connector/AlphaDifference/Stopper.png"" width 1104 height 742 supersample 3
> transparentBackground true

> hide #1 models

> hide #2 models

> show #5 models

> show #6 models

> view #5 clip false

Already setting window visible!  

> close #1-4

> split #5

Split fold_corndog_43_adaptor_model_0.cif (#5) into 12 models  
Chain information for fold_corndog_43_adaptor_model_0.cif A #5.1  
---  
Chain | Description  
A | No description available  
  
Chain information for fold_corndog_43_adaptor_model_0.cif B #5.2  
---  
Chain | Description  
B | No description available  
  
Chain information for fold_corndog_43_adaptor_model_0.cif C #5.3  
---  
Chain | Description  
C | No description available  
  
Chain information for fold_corndog_43_adaptor_model_0.cif D #5.4  
---  
Chain | Description  
D | No description available  
  
Chain information for fold_corndog_43_adaptor_model_0.cif E #5.5  
---  
Chain | Description  
E | No description available  
  
Chain information for fold_corndog_43_adaptor_model_0.cif F #5.6  
---  
Chain | Description  
F | No description available  
  
Chain information for fold_corndog_43_adaptor_model_0.cif G #5.7  
---  
Chain | Description  
G | No description available  
  
Chain information for fold_corndog_43_adaptor_model_0.cif H #5.8  
---  
Chain | Description  
H | No description available  
  
Chain information for fold_corndog_43_adaptor_model_0.cif I #5.9  
---  
Chain | Description  
I | No description available  
  
Chain information for fold_corndog_43_adaptor_model_0.cif J #5.10  
---  
Chain | Description  
J | No description available  
  
Chain information for fold_corndog_43_adaptor_model_0.cif K #5.11  
---  
Chain | Description  
K | No description available  
  
Chain information for fold_corndog_43_adaptor_model_0.cif L #5.12  
---  
Chain | Description  
L | No description available  
  

> hide #5.1 models

> hide #5.2 models

> hide #5.3 models

> show #5.3 models

> hide #5.4 models

> hide #5.5 models

> hide #5.6 models

> hide #5.7 models

> hide #5.9 models

> show #5.9 models

> hide #5.8 models

> hide #5.9 models

> hide #5.10 models

> hide #5.11 models

> hide #5.12 models

> split #6

Split 00-Portal-12mers-Adaptor-12mers.pdb (#6) into 12 models  
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb M #6.1  
---  
Chain | Description  
M | No description available  
  
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb N #6.2  
---  
Chain | Description  
N | No description available  
  
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb O #6.3  
---  
Chain | Description  
O | No description available  
  
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb P #6.4  
---  
Chain | Description  
P | No description available  
  
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb Q #6.5  
---  
Chain | Description  
Q | No description available  
  
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb R #6.6  
---  
Chain | Description  
R | No description available  
  
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb S #6.7  
---  
Chain | Description  
S | No description available  
  
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb T #6.8  
---  
Chain | Description  
T | No description available  
  
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb U #6.9  
---  
Chain | Description  
U | No description available  
  
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb V #6.10  
---  
Chain | Description  
V | No description available  
  
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb W #6.11  
---  
Chain | Description  
W | No description available  
  
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb X #6.12  
---  
Chain | Description  
X | No description available  
  

> hide #6.1 models

> hide #6.2 models

> hide #6.3 models

> hide #6.4 models

> hide #6.5 models

> hide #6.6 models

> hide #6.7 models

> hide #6.8 models

> hide #6.9 models

> hide #6.10 models

> hide #6.12 models

> view #6.11 clip false

> save ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Connector/AlphaDifference/Adaptor.png"" width 1104 height 742 supersample 3
> transparentBackground true

Cell requested for row 1 is out of bounds for table with 16 rows! Resizing
table model.  

> hide #!6 models

> hide #!5 models

> show #7 models

> show #8 models

> view #7 clip false

> split #7

Split fold_corndog_34_portal_model_0.cif (#7) into 12 models  
Chain information for fold_corndog_34_portal_model_0.cif A #7.1  
---  
Chain | Description  
A | No description available  
  
Chain information for fold_corndog_34_portal_model_0.cif B #7.2  
---  
Chain | Description  
B | No description available  
  
Chain information for fold_corndog_34_portal_model_0.cif C #7.3  
---  
Chain | Description  
C | No description available  
  
Chain information for fold_corndog_34_portal_model_0.cif D #7.4  
---  
Chain | Description  
D | No description available  
  
Chain information for fold_corndog_34_portal_model_0.cif E #7.5  
---  
Chain | Description  
E | No description available  
  
Chain information for fold_corndog_34_portal_model_0.cif F #7.6  
---  
Chain | Description  
F | No description available  
  
Chain information for fold_corndog_34_portal_model_0.cif G #7.7  
---  
Chain | Description  
G | No description available  
  
Chain information for fold_corndog_34_portal_model_0.cif H #7.8  
---  
Chain | Description  
H | No description available  
  
Chain information for fold_corndog_34_portal_model_0.cif I #7.9  
---  
Chain | Description  
I | No description available  
  
Chain information for fold_corndog_34_portal_model_0.cif J #7.10  
---  
Chain | Description  
J | No description available  
  
Chain information for fold_corndog_34_portal_model_0.cif K #7.11  
---  
Chain | Description  
K | No description available  
  
Chain information for fold_corndog_34_portal_model_0.cif L #7.12  
---  
Chain | Description  
L | No description available  
  

> split #8

Split Portal_12mer_Coot.pdb (#8) into 12 models  
Chain information for Portal_12mer_Coot.pdb A #8.1  
---  
Chain | Description  
A | No description available  
  
Chain information for Portal_12mer_Coot.pdb B #8.2  
---  
Chain | Description  
B | No description available  
  
Chain information for Portal_12mer_Coot.pdb C #8.3  
---  
Chain | Description  
C | No description available  
  
Chain information for Portal_12mer_Coot.pdb D #8.4  
---  
Chain | Description  
D | No description available  
  
Chain information for Portal_12mer_Coot.pdb E #8.5  
---  
Chain | Description  
E | No description available  
  
Chain information for Portal_12mer_Coot.pdb F #8.6  
---  
Chain | Description  
F | No description available  
  
Chain information for Portal_12mer_Coot.pdb G #8.7  
---  
Chain | Description  
G | No description available  
  
Chain information for Portal_12mer_Coot.pdb H #8.8  
---  
Chain | Description  
H | No description available  
  
Chain information for Portal_12mer_Coot.pdb I #8.9  
---  
Chain | Description  
I | No description available  
  
Chain information for Portal_12mer_Coot.pdb J #8.10  
---  
Chain | Description  
J | No description available  
  
Chain information for Portal_12mer_Coot.pdb K #8.11  
---  
Chain | Description  
K | No description available  
  
Chain information for Portal_12mer_Coot.pdb L #8.12  
---  
Chain | Description  
L | No description available  
  

> hide #7.1 models

> hide #7.2 models

> hide #7.3 models

> hide #7.4 models

> hide #7.5 models

> hide #7.6 models

> hide #7.7 models

> hide #7.8 models

> hide #7.9 models

> hide #7.10 models

> show #7.10 models

> hide #7.11 models

> hide #7.12 models

> hide #8.1 models

> hide #8.3 models

> hide #8.2 models

> hide #8.4 models

> hide #8.5 models

> hide #8.6 models

> hide #8.7 models

> hide #8.8 models

> hide #8.9 models

> hide #8.10 models

> hide #8.11 models

> view #8.12 clip false

> ui tool show ""Show Sequence Viewer""

> sequence chain #8.1/A #8.2/B #8.3/C #8.4/D #8.5/E #8.6/F #8.7/G #8.8/H
> #8.9/I #8.10/J #8.11/K #8.12/L

Alignment identifier is 1  

> select #8.1/A:76 #8.2/B:76 #8.3/C:76 #8.4/D:76 #8.5/E:76 #8.6/F:76 #8.7/G:76
> #8.8/H:76 #8.9/I:76 #8.10/J:76 #8.11/K:76 #8.12/L:76

84 atoms, 72 bonds, 12 residues, 12 models selected  

> select #8.1/A:76-77 #8.2/B:76-77 #8.3/C:76-77 #8.4/D:76-77 #8.5/E:76-77
> #8.6/F:76-77 #8.7/G:76-77 #8.8/H:76-77 #8.9/I:76-77 #8.10/J:76-77
> #8.11/K:76-77 #8.12/L:76-77

180 atoms, 168 bonds, 24 residues, 12 models selected  
1 [ID: 1] region 12 chains [1-2] RMSD: 63.143  
  

> ui tool show ""Show Sequence Viewer""

> sequence chain #7.1/A #7.2/B #7.3/C #7.4/D #7.5/E #7.6/F #7.7/G #7.8/H
> #7.9/I #7.10/J #7.11/K #7.12/L

Alignment identifier is 1  

> select #7.1/A:75-76 #7.2/B:75-76 #7.3/C:75-76 #7.4/D:75-76 #7.5/E:75-76
> #7.6/F:75-76 #7.7/G:75-76 #7.8/H:75-76 #7.9/I:75-76 #7.10/J:75-76
> #7.11/K:75-76 #7.12/L:75-76

216 atoms, 204 bonds, 24 residues, 12 models selected  

> select #7.1/A:69-76 #7.2/B:69-76 #7.3/C:69-76 #7.4/D:69-76 #7.5/E:69-76
> #7.6/F:69-76 #7.7/G:69-76 #7.8/H:69-76 #7.9/I:69-76 #7.10/J:69-76
> #7.11/K:69-76 #7.12/L:69-76

756 atoms, 744 bonds, 96 residues, 12 models selected  
1 [ID: 1] region 12 chains [69-76] RMSD: 75.160  
  

> select #7.1/A:74 #7.2/B:74 #7.3/C:74 #7.4/D:74 #7.5/E:74 #7.6/F:74 #7.7/G:74
> #7.8/H:74 #7.9/I:74 #7.10/J:74 #7.11/K:74 #7.12/L:74

96 atoms, 84 bonds, 12 residues, 12 models selected  

> select #7.1/A:70-74 #7.2/B:70-74 #7.3/C:70-74 #7.4/D:70-74 #7.5/E:70-74
> #7.6/F:70-74 #7.7/G:70-74 #7.8/H:70-74 #7.9/I:70-74 #7.10/J:70-74
> #7.11/K:70-74 #7.12/L:70-74

468 atoms, 456 bonds, 60 residues, 12 models selected  
1 [ID: 1] region 12 chains [70-74] RMSD: 76.576  
  

> select #7.1/A:75-76 #7.2/B:75-76 #7.3/C:75-76 #7.4/D:75-76 #7.5/E:75-76
> #7.6/F:75-76 #7.7/G:75-76 #7.8/H:75-76 #7.9/I:75-76 #7.10/J:75-76
> #7.11/K:75-76 #7.12/L:75-76

216 atoms, 204 bonds, 24 residues, 12 models selected  

> select #7.1/A:73-76 #7.2/B:73-76 #7.3/C:73-76 #7.4/D:73-76 #7.5/E:73-76
> #7.6/F:73-76 #7.7/G:73-76 #7.8/H:73-76 #7.9/I:73-76 #7.10/J:73-76
> #7.11/K:73-76 #7.12/L:73-76

420 atoms, 408 bonds, 48 residues, 12 models selected  
1 [ID: 1] region 12 chains [73-76] RMSD: 70.467  
  

> select #7.1/A:1 #7.2/B:1 #7.3/C:1 #7.4/D:1 #7.5/E:1 #7.6/F:1 #7.7/G:1
> #7.8/H:1 #7.9/I:1 #7.10/J:1 #7.11/K:1 #7.12/L:1

96 atoms, 84 bonds, 12 residues, 12 models selected  

> select #7.1/A:1-75 #7.2/B:1-75 #7.3/C:1-75 #7.4/D:1-75 #7.5/E:1-75
> #7.6/F:1-75 #7.7/G:1-75 #7.8/H:1-75 #7.9/I:1-75 #7.10/J:1-75 #7.11/K:1-75
> #7.12/L:1-75

7152 atoms, 7464 bonds, 900 residues, 12 models selected  
1 [ID: 1] region 12 chains [1-75] RMSD: 89.598  
  

> save ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Connector/AlphaDifference/Portal.png"" width 1104 height 742 supersample 3
> transparentBackground true

> close #8

> close

> open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted Models/Current
> Connector Assembly.pdb""

Chain information for Current Connector Assembly.pdb #1  
---  
Chain | Description  
A B C D E F | No description available  
G H I J K L Y Z a b c d e | No description available  
M N O P Q R S T U V W X | No description available  
f g h i j k | No description available  
  

> close

> open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Combined_C6_C12_Connector.mrc""

Opened Combined_C6_C12_Connector.mrc as #1, grid size 536,536,684, pixel
1.06,1.06,1.06, shown at level 0.275, step 4, values float32  

> surface dust #1 size 10.6

> volume #1 step 1

> volume #1 level 0.3

> lighting soft

> ui mousemode right ""map eraser""

> ui tool show ""Segment Map""

Segmenting Combined_C6_C12_Connector.mrc, density threshold 0.300000  
Only showing 60 of 2449 regions.  
Showing 60 of 2449 region surfaces  
143784 watershed regions, grouped to 2449 regions  
Showing Combined_C6_C12_Connector.seg - 2449 regions, 60 surfaces  

> close #2

> undo

Undo failed, probably because structures have been modified.  

> ui tool show ""Map Eraser""

> volume erase #1 center 214.42,245.66,109.82 radius 68.636

Opened Combined_C6_C12_Connector.mrc copy as #3, grid size 536,536,684, pixel
1.06,1.06,1.06, shown at step 1, values float32  

> surface dust #3 size 10.6

> close #3

> show #!1 models

> volume erase #1 center 177.79,242.66,94.807 radius 107.77

Opened Combined_C6_C12_Connector.mrc copy as #3, grid size 536,536,684, pixel
1.06,1.06,1.06, shown at step 1, values float32  

> close #3

> show #!1 models

> volume erase #1 center 162.42,242.35,95.667 radius 107.77

Opened Combined_C6_C12_Connector.mrc copy as #3, grid size 536,536,684, pixel
1.06,1.06,1.06, shown at step 1, values float32  

> volume erase #3 center 149.61,244.28,192.02 radius 107.77

> hide #2 models

> surface dust #3 size 10.6

> undo

> volume erase #3 center 156.89,256.09,27.046 radius 107.77

> hide #2 models

> open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted Models/Current
> Connector Assembly.pdb""

Chain information for Current Connector Assembly.pdb #4  
---  
Chain | Description  
A B C D E F | No description available  
G H I J K L Y Z a b c d e | No description available  
M N O P Q R S T U V W X | No description available  
f g h i j k | No description available  
  

> hide atoms

> show cartoons

> ui tool show ""Color Zone""

> color zone #3 near #4 distance 6.37

> hide #4 models

> ui tool show ""Modeller Comparative""

> ui tool show ""Show Sequence Viewer""

> sequence chain /A /B /C /D /E /F

Alignment identifier is 1  

> select /A-F:2

42 atoms, 42 bonds, 6 residues, 1 model selected  

> select /A-F

5448 atoms, 5586 bonds, 708 residues, 1 model selected  

> show #4 models

> color sel magenta

> ui tool show ""Show Sequence Viewer""

> sequence chain /G /H /I /J /K /L /Y /Z /a /b /c /d /e

Alignment identifier is 2  

> select /G-L,Y-e:374-408

3341 atoms, 3367 bonds, 455 residues, 1 model selected  

> select /G-L,Y-e

33852 atoms, 34658 bonds, 4329 residues, 1 model selected  

> ui tool show ""Color Actions""

> ui tool show ""Show Sequence Viewer""

> sequence chain /M /N /O /P /Q /R /S /T /U /V /W /X

Alignment identifier is 2  

> select /M-X:2

60 atoms, 48 bonds, 12 residues, 1 model selected  

> select /M-X

18708 atoms, 19092 bonds, 2400 residues, 1 model selected  

> color sel yellow

> ui tool show ""Show Sequence Viewer""

> sequence chain /f /g /h /i /j /k

Alignment identifier is 2  

> select /f-k:1

48 atoms, 42 bonds, 6 residues, 1 model selected  

> select /f-k

7296 atoms, 7452 bonds, 900 residues, 1 model selected  

> color sel orange

> color zone #3 near #4 distance 6.37

> hide #4 models

> show #2 models

> volume erase #3 center 150.62,247.75,141.42 radius 107.77

> volume erase #3 center 151.86,247.47,142.68 radius 107.77

> volume erase #3 center 154.99,247.06,146.2 radius 107.77

> volume erase #3 center 157.8,247.23,149.86 radius 107.77

> volume erase #3 center 161.04,247.12,152.59 radius 107.77

> volume erase #3 center 160.85,246.84,180.76 radius 107.77

> hide #2 models

> color zone #3 near #4 distance 6.27

> color zone #3 near #4 distance 6.17

> color zone #3 near #4 distance 6.07

> color zone #3 near #4 distance 5.97

> color zone #3 near #4 distance 5.87

> color zone #3 near #4 distance 5

> color zone #3 near #4 distance 4.9

> color zone #3 near #4 distance 4.8

> color zone #3 near #4 distance 4.7

> color zone #3 near #4 distance 4.6

> color zone #3 near #4 distance 4.5

> color zone #3 near #4 distance 4.4

> color zone #3 near #4 distance 4.3

> color zone #3 near #4 distance 4.2

> color zone #3 near #4 distance 4.1

> color zone #3 near #4 distance 4

> color zone #3 near #4 distance 3.9

> color zone #3 near #4 distance 3.8

> color zone #3 near #4 distance 3.7

> color zone #3 near #4 distance 3.6

> color zone #3 near #4 distance 3.5

> color zone #3 near #4 distance 3.4

> color zone #3 near #4 distance 3.3

> color zone #3 near #4 distance 3.2

> color zone #3 near #4 distance 3.1

> color zone #3 near #4 distance 3

> color zone #3 near #4 distance 2.9

> color zone #3 near #4 distance 2.8

> color zone #3 near #4 distance 2.7

> color zone #3 near #4 distance 2.6

> color zone #3 near #4 distance 2.5

> color zone #3 near #4 distance 2.4

> color zone #3 near #4 distance 2.5

> color zone #3 near #4 distance 2.6

> color zone #3 near #4 distance 2.7

> color zone #3 near #4 distance 2.8

> color zone #3 near #4 distance 2.9

> color zone #3 near #4 distance 3

> color zone #3 near #4 distance 3.1

> color zone #3 near #4 distance 3.2

> color zone #3 near #4 distance 3.3

> color zone #3 near #4 distance 3.4

> color zone #3 near #4 distance 3.5

> color zone #3 near #4 distance 3.6

> color zone #3 near #4 distance 3.7

> color zone #3 near #4 distance 3.8

> color zone #3 near #4 distance 3.9

> color zone #3 near #4 distance 4

> color zone #3 near #4 distance 4.1

> color zone #3 near #4 distance 4.2

> color zone #3 near #4 distance 4.3

> color zone #3 near #4 distance 4.4

> color zone #3 near #4 distance 4.5

> color zone #3 near #4 distance 4.6

> color zone #3 near #4 distance 4.7

> color zone #3 near #4 distance 4.8

> color zone #3 near #4 distance 4.9

> color zone #3 near #4 distance 5

> color zone #3 near #4 distance 5.1

> color zone #3 near #4 distance 5.2

> color zone #3 near #4 distance 5.3

> color zone #3 near #4 distance 5.4

> color zone #3 near #4 distance 6

> show #2 models

> volume erase #3 center 155.71,244.1,255.24 radius 107.77

> volume erase #3 center 158.67,244.12,250.64 radius 107.77

> volume erase #3 center 160.27,244.62,246.49 radius 107.77

> volume erase #3 center 160.35,244.82,239.65 radius 107.77

> hide #2 models

> show #2 models

> volume erase #3 center 160.76,244.92,236.32 radius 107.77

> hide #2 models

> show #2 models

> volume erase #3 center 160.79,245.18,233.14 radius 107.77

> volume erase #3 center 160.71,246.53,227.42 radius 107.77

> hide #2 models

> show #4 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> ui tool show ""Show Sequence Viewer""

> sequence chain /G /H /I /J /K /L /Y /Z /a /b /c /d /e

Alignment identifier is 2  

> select /G-L,Y-e:163-204

4277 atoms, 4342 bonds, 546 residues, 1 model selected  

> select /G-L,Y-e:163-252

9178 atoms, 9321 bonds, 1170 residues, 1 model selected  

> select /G-L,Y-e:158

91 atoms, 78 bonds, 13 residues, 1 model selected  

> select /G-L,Y-e:158-165

845 atoms, 884 bonds, 104 residues, 1 model selected  

> select /G-L,Y-e:242

78 atoms, 65 bonds, 13 residues, 1 model selected  

> select /G-L,Y-e:242-330

8788 atoms, 8957 bonds, 1157 residues, 1 model selected  

> select /G-L,Y-e:326

143 atoms, 143 bonds, 13 residues, 1 model selected  

> select /G-L,Y-e:326-329

494 atoms, 520 bonds, 52 residues, 1 model selected  

> select /G-L,Y-e:266-267

195 atoms, 182 bonds, 26 residues, 1 model selected  

> select /G-L,Y-e:266-271

455 atoms, 442 bonds, 78 residues, 1 model selected  

> select /G-L,Y-e:275-276

182 atoms, 169 bonds, 26 residues, 1 model selected  

> select /G-L,Y-e:224-275

5226 atoms, 5330 bonds, 676 residues, 1 model selected  

> select /G-L,Y-e:277-278

195 atoms, 182 bonds, 26 residues, 1 model selected  

> select /G-L,Y-e:277-286

949 atoms, 936 bonds, 130 residues, 1 model selected  

> select /G-L,Y-e:277

117 atoms, 104 bonds, 13 residues, 1 model selected  

> select /G-L,Y-e:277-301

2535 atoms, 2535 bonds, 325 residues, 1 model selected  

> show #!3 models

> select /G-L,Y-e:303

91 atoms, 78 bonds, 13 residues, 1 model selected  

> select /G-L,Y-e:303-312

910 atoms, 949 bonds, 130 residues, 1 model selected  

> select /G-L,Y-e:303

91 atoms, 78 bonds, 13 residues, 1 model selected  

> select /G-L,Y-e:303-323

1950 atoms, 2002 bonds, 273 residues, 1 model selected  

> delete sel

> color zone #3 near #4 distance 6

> select /G-L,Y-e:324

117 atoms, 104 bonds, 13 residues, 1 model selected  

> select /G-L,Y-e:324-335

1365 atoms, 1391 bonds, 156 residues, 1 model selected  

> delete sel

> color zone #3 near #4 distance 6

> hide #!4 models

> undo

> hide #!4 models

> hide #4.1 models

> show #4.1 models

> hide #4.1 models

> hide #!4 models

> show #4.1 models

> color zone #3 near #4 distance 6

> close #4

> open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Combined_C6_C12_Connector.mrc""

Opened Combined_C6_C12_Connector.mrc as #4, grid size 536,536,684, pixel
1.06,1.06,1.06, shown at level 0.275, step 4, values float32  

> close #4

> open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted Models/Current
> Connector Assembly.pdb""

Chain information for Current Connector Assembly.pdb #4  
---  
Chain | Description  
A B C D E F | No description available  
G H I J K L Y Z a b c d e | No description available  
M N O P Q R S T U V W X | No description available  
f g h i j k | No description available  
  

> hide atoms

> show cartoons

> ui tool show ""Show Sequence Viewer""

> sequence chain /A /B /C /D /E /F

Alignment identifier is 1  

> select /A-F:119

30 atoms, 24 bonds, 6 residues, 1 model selected  

> select /A-F

5448 atoms, 5586 bonds, 708 residues, 1 model selected  

> color sel magenta

> ui tool show ""Show Sequence Viewer""

> sequence chain /M /N /O /P /Q /R /S /T /U /V /W /X

Alignment identifier is 1  

> select /M-X:2

60 atoms, 48 bonds, 12 residues, 1 model selected  

> select /M-X

18708 atoms, 19092 bonds, 2400 residues, 1 model selected  

> color sel yellow

> ui tool show ""Show Sequence Viewer""

> sequence chain /f /g /h /i /j /k

Alignment identifier is 1  

> select /f-k:1

48 atoms, 42 bonds, 6 residues, 1 model selected  

> select /f-k

7296 atoms, 7452 bonds, 900 residues, 1 model selected  

> color sel orange

> color zone #3 near #4 distance 6

> hide #4 models

> save ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/SnapShot of Interior Connector.png"" width 977 height 742 supersample
> 3 transparentBackground true

> open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /3D/Capsid Assembled.mrc""

Opened Capsid Assembled.mrc as #5, grid size 894,894,1747, pixel
1.06,1.06,1.06, shown at step 1, values float32  

> volume #5 region 0,0,0,893,893,1746 step 8

> volume #5 level 0.3

> volume #5 change image level -0.03476,0 level 0.4075,0.8 level 1.094,1

> select add #5

7296 atoms, 7452 bonds, 900 residues, 4 models selected  

> select add #4

65304 atoms, 66788 bonds, 8337 residues, 4 models selected  

> select subtract #4

3 models selected  

> select add #5

3 models selected  

> select add #5

3 models selected  

> select add #5

3 models selected  

> select add #5

3 models selected  

> hide #!5 models

> show #!5 models

> select add #5

3 models selected  

> show #5.1 models

> hide #5.1 models

> select add #5.1

3 models selected  

> select subtract #5.2

2 models selected  

> select add #5.2

3 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #5,1,0,0,-70.528,0,1,0,46.331,0,0,1,-1212.9

> view matrix models #5,1,0,0,0.69037,0,1,0,26.699,0,0,1,-1636.6

> ui tool show ""Fit in Map""

> fitmap #5 inMap #1

Fit map Capsid Assembled.mrc in map Combined_C6_C12_Connector.mrc using 63456
points  
correlation = 0.1725, correlation about mean = 0.05023, overlap = 215.2  
steps = 2000, shift = 87.3, angle = 5.65 degrees  
  
Position of Capsid Assembled.mrc (#5) relative to
Combined_C6_C12_Connector.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99997487 -0.00677646 -0.00208067 3.22227426  
0.00694798 0.99514666 0.09815723 -150.89967529  
0.00140542 -0.09816922 0.99516874 -1600.93767666  
Axis -0.99740902 -0.01771060 0.06972507  
Axis point 0.00000000 -16265.34711247 753.33259850  
Rotation angle (degrees) 5.64809186  
Shift along axis -112.16690043  
  

> view matrix models
> #5,0.99982,-0.006119,0.018016,-15.506,0.0057294,0.99975,0.021603,-80.987,-0.018144,-0.021496,0.9996,-1620.4

> view matrix models
> #5,0.99982,-0.006119,0.018016,-25.925,0.0057294,0.99975,0.021603,-41.203,-0.018144,-0.021496,0.9996,-1621.7

> fitmap #5 inMap #1

Fit map Capsid Assembled.mrc in map Combined_C6_C12_Connector.mrc using 63456
points  
correlation = 0.1818, correlation about mean = 0.05149, overlap = 211.5  
steps = 2000, shift = 4.86, angle = 1.07 degrees  
  
Position of Capsid Assembled.mrc (#5) relative to
Combined_C6_C12_Connector.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99966976 0.01003685 0.02365673 -39.48477494  
-0.01071090 0.99953525 0.02854056 -40.40017321  
-0.02335928 -0.02878452 0.99931266 -1618.61035989  
Axis -0.74459834 0.61069345 -0.26949362  
Axis point 0.00000000 -52342.50621595 9998.01944798  
Rotation angle (degrees) 2.20608622  
Shift along axis 440.93334282  
  

> fitmap #5 inMap #1

Fit map Capsid Assembled.mrc in map Combined_C6_C12_Connector.mrc using 63456
points  
correlation = 0.1824, correlation about mean = 0.05215, overlap = 212.1  
steps = 2000, shift = 0.297, angle = 0.0203 degrees  
  
Position of Capsid Assembled.mrc (#5) relative to
Combined_C6_C12_Connector.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99966305 0.01016542 0.02388417 -39.67991622  
-0.01085156 0.99952699 0.02877570 -40.86540763  
-0.02358035 -0.02902518 0.99930051 -1618.51715268  
Axis -0.74400617 0.61095774 -0.27052811  
Axis point 0.00000000 -51879.09421691 9960.47141491  
Rotation angle (degrees) 2.22617779  
Shift along axis 442.40944528  
  

> view matrix models
> #5,0.99991,0.012592,-0.004378,-14.256,-0.012472,0.99958,0.026309,-38.156,0.0047074,-0.026252,0.99964,-1627.3

> view matrix models
> #5,0.99991,0.012592,-0.004378,-1.2187,-0.012472,0.99958,0.026309,-36.831,0.0047074,-0.026252,0.99964,-1630.7

> fitmap #5 inMap #1

Fit map Capsid Assembled.mrc in map Combined_C6_C12_Connector.mrc using 63456
points  
correlation = 0.1845, correlation about mean = 0.05574, overlap = 215.5  
steps = 2000, shift = 13.7, angle = 1.82 degrees  
  
Position of Capsid Assembled.mrc (#5) relative to
Combined_C6_C12_Connector.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99993928 -0.01097185 0.00102488 1.35965289  
0.01096583 0.99992360 0.00570527 -10.93514426  
-0.00108740 -0.00569369 0.99998320 -1632.73298348  
Axis -0.45940413 0.08512975 0.88413844  
Axis point -10641.82269394 -60325.94094752 0.00000000  
Rotation angle (degrees) 0.71084383  
Shift along axis -1445.11752196  
  

> fitmap #5 inMap #1

Fit map Capsid Assembled.mrc in map Combined_C6_C12_Connector.mrc using 63456
points  
correlation = 0.1857, correlation about mean = 0.05607, overlap = 215.4  
steps = 2000, shift = 1.99, angle = 0.122 degrees  
  
Position of Capsid Assembled.mrc (#5) relative to
Combined_C6_C12_Connector.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99993582 -0.01122589 0.00152902 0.17810745  
0.01121371 0.99990704 0.00775715 -14.70762357  
-0.00161596 -0.00773951 0.99996874 -1632.05272742  
Axis -0.56451504 0.11456571 0.81743346  
Axis point -12892.72075132 -67087.65701707 0.00000000  
Rotation angle (degrees) 0.78644610  
Shift along axis -1335.88004462  
  

> ui tool show ""Volume Viewer""

> volume #5 step 1

> select subtract #5.2

2 models selected  

> close #5

> show #4 models

> hide #4 models

> open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/A_Portal/Portal_12mer_Coot.pdb""

Summary of feedback from opening /Users/melvinshen/Desktop/Sinica /Protein
Purification/New Phage Proteins/Structure/CryoEM/cryosparc/Corndog
/Connector/Fitted Models/A_Portal/Portal_12mer_Coot.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 169 169 GLU M 6 PHE M 12 1 7  
Start residue of secondary structure not found: HELIX 170 170 GLY M 22 CYS M
39 1 18  
Start residue of secondary structure not found: HELIX 171 171 LEU M 84 LYS M
86 1 3  
Start residue of secondary structure not found: HELIX 172 172 ALA M 133 THR M
149 1 17  
Start residue of secondary structure not found: HELIX 173 173 GLU M 156 ASP M
158 1 3  
175 messages similar to the above omitted  
  
Chain information for Portal_12mer_Coot.pdb #2  
---  
Chain | Description  
A B C D E F G H I J K L | No description available  
  

> open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/A_Portal/Corndog_34_portal_12mer/fold_corndog_34_portal_model_0.cif""

Chain information for fold_corndog_34_portal_model_0.cif #5  
---  
Chain | Description  
A B C D E F G H I J K L | .  
  

> hide #5 models

> show #5 models

> select add #5

38496 atoms, 39564 bonds, 4908 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> color #5 #7a81ffff

> rainbow sel

> select subtract #5

Nothing selected  

> show #4 models

> hide #4 models

> select add #2

31248 atoms, 31992 bonds, 3996 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> color #2 #d783ffff

> color #2 #7a81ffff

> view matrix models #2,1,0,0,10.767,0,1,0,-136.19,0,0,1,147.03

> lighting flat

> ui tool show Matchmaker

> matchmaker #5 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Portal_12mer_Coot.pdb, chain A (#2) with
fold_corndog_34_portal_model_0.cif, chain A (#5), sequence alignment score =
1673.4  
RMSD between 319 pruned atom pairs is 0.601 angstroms; (across all 333 pairs:
1.035)  
  

> select add #5

69744 atoms, 71556 bonds, 8904 residues, 2 models selected  

> turn x 90 models #2

> turn x 90 models #5

> view matrix models
> #2,0.0024811,-0.053965,0.99854,225.83,-0.045532,0.9975,0.054022,-165.07,-0.99896,-0.0456,1.7775e-05,801.55,#5,-0.52869,0.63575,-0.56242,456.28,-0.43817,0.36308,0.8223,106.75,0.72698,0.68118,0.086613,517.79

> combine #2


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

Log:
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16U0000PTA/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.41.12
      OS Loader Version: 10151.41.12

Software:

    System Software Overview:

      System Version: macOS 14.1 (23B74)
      Kernel Version: Darwin 23.1.0
      Time since boot: 13 days, 1 hour, 14 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      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


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.1.1
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
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    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.56
    ChimeraX-AtomicLibrary: 14.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    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: 2.12.1
    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: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    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: 1.8.dev202403220040
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    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4.2
    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: 1.1.9
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
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    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-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
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    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
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    ChimeraX-Positions: 1.0
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    ChimeraX-PubChem: 2.1
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    ChimeraX-Registration: 1.1.2
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    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
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    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 1.0
    ChimeraX-SelInspector: 1.0
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    ChimeraX-Shape: 1.0.1
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    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
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    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
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    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
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    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
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    ChimeraX-vrml: 1.0
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    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
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    ChimeraX-Zone: 1.0.1
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    PyOpenGL: 3.1.7
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    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.2
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    PyQt6-WebEngine-commercial: 6.6.0
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    pytz: 2024.1
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    QtPy: 2.4.1
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    setuptools: 69.2.0
    setuptools-scm: 8.0.4
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    six: 1.16.0
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    sphinx-autodoc-typehints: 2.0.0
    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: 0.6.1
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.1
    typing-extensions: 4.10.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
}}}
"	defect	closed	normal		Core		duplicate						all	ChimeraX