Crash in intra_bonds

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.21.3.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f5ae594b700 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 316 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 574 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 1284 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007f5c18d58740 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 622 in intra_bonds
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1113 in add_implied_bonds
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1100 in evaluate
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1275 in parse
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 889 in parse
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2447 in _parse_arg
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2588 in _process_positional_arguments
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2812 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/model_panel/tool.py", line 241 in set_model_color
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/widgets/color_button.py", line 132 in _color_changed_cb
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/widgets/color_button.py", line 47 in _make_color_callback
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> set selectionWidth 4

UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/home/rodolpho/Desktop/Paper Figures/ycf1_pka_valid.pdb"

Chain information for ycf1_pka_valid.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open "/home/rodolpho/Projects/Initial Models/1st-model_ycf1-pka-rdomain.pdb"

Chain information for 1st-model_ycf1-pka-rdomain.pdb #2  
---  
Chain | Description  
A | No description available  
  

> select #2

24337 atoms, 24589 bonds, 1515 residues, 1 model selected  

> hide sel cartoons

> show #2:859-880 target c

> select clear

> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1

> licorice

> alias licorice car style protein modeh default arrows f xsect oval width 2
> thick 1

> licorice

> select clear

> color #1 lightgrey transparency 0

> lighting soft

> set bgColor white

> color #2 #8ae234 transparency 0

> color #1:855-935 darkmagenta

> select clear

> select #2:872

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2:872, 874, 875

51 atoms, 49 bonds, 3 residues, 1 model selected  

> show sel atoms

> select clear

> hide H

> select #1:907, 908, 910, 912, 914, 920, 927, 928, 934

127 atoms, 121 bonds, 9 residues, 1 model selected  

> show sel atoms

> size stickRadius 0.5

Changed 48588 bond radii  

> color byhetero

> hide H

> select clear

> ui tool show Distances

> select #2/A:874@CB

1 atom, 1 residue, 1 model selected  

> select #2/A:872@CB

1 atom, 1 residue, 1 model selected  

> select #2/A:872@CB

1 atom, 1 residue, 1 model selected  

> set bgColor black

> select #1/A:912@CB

1 atom, 1 residue, 1 model selected  

> select add #2/A:872@CB

2 atoms, 2 residues, 2 models selected  

> distance #1/A:912@CB #2/A:872@CB

Distance between ycf1_pka_valid.pdb #1/A LEU 912 CB and 1st-model_ycf1-pka-
rdomain.pdb #2/A SER 872 CB: 57.932Å  

> select clear

> select #2/A:872@CB

1 atom, 1 residue, 1 model selected  

> select #1/A:909

12 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/A:909@CB

1 atom, 1 residue, 1 model selected  

> select add #2/A:872@CB

2 atoms, 2 residues, 2 models selected  

> distance #1/A:909@CB #2/A:872@CB

Distance between ycf1_pka_valid.pdb #1/A ASP 909 CB and 1st-model_ycf1-pka-
rdomain.pdb #2/A SER 872 CB: 52.561Å  

> select clear

> select #2/A:874@CB

1 atom, 1 residue, 1 model selected  

> select #2/A:874@CB

1 atom, 1 residue, 1 model selected  

> select add #1/A:909@CB

2 atoms, 2 residues, 2 models selected  

> distance #2/A:874@CB #1/A:909@CB

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A VAL 874 CB and
ycf1_pka_valid.pdb #1/A ASP 909 CB: 51.572Å  

> select clear

> select #2/A:874@CB

1 atom, 1 residue, 1 model selected  

> select add #1/A:910@CB

2 atoms, 2 residues, 2 models selected  

> distance #2/A:874@CB #1/A:910@CB

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A VAL 874 CB and
ycf1_pka_valid.pdb #1/A ALA 910 CB: 52.124Å  

> select #2/A:875

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #2/A:875@CG

1 atom, 1 residue, 1 model selected  

> select add #1/A:907@CB

2 atoms, 2 residues, 2 models selected  

> distance #2/A:875@CG #1/A:907@CB

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A ARG 875 CG and
ycf1_pka_valid.pdb #1/A ALA 907 CB: 44.818Å  

> select clear

> select #2/A:875@CG

1 atom, 1 residue, 1 model selected  

> select add #1/A:908@CB

2 atoms, 2 residues, 2 models selected  

> select subtract #1/A:908@CB

1 atom, 1 residue, 1 model selected  

> select add #1/A:908@CB

2 atoms, 2 residues, 2 models selected  

> distance #2/A:875@CG #1/A:908@CB

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A ARG 875 CG and
ycf1_pka_valid.pdb #1/A SEP 908 CB: 49.673Å  

> select clear

> select #1/A:906

24 atoms, 23 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide H

> select #1/A:906@CB

1 atom, 1 residue, 1 model selected  

> select add #1/A:907@CB

2 atoms, 2 residues, 1 model selected  

> distance #1/A:906@CB #1/A:907@CB

Distance between ycf1_pka_valid.pdb #1/A ARG 906 CB and ALA 907 CB: 5.545Å  

> select clear

> select #1/A:906@CB

1 atom, 1 residue, 1 model selected  

> select add #1/A:908@CB

2 atoms, 2 residues, 1 model selected  

> distance #1/A:906@CB #1/A:908@CB

Distance between ycf1_pka_valid.pdb #1/A ARG 906 CB and SEP 908 CB: 7.913Å  

> select #1/A:906@CB

1 atom, 1 residue, 1 model selected  

> select add #1/A:909@CB

2 atoms, 2 residues, 1 model selected  

> distance #1/A:906@CB #1/A:909@CB

Distance between ycf1_pka_valid.pdb #1/A ARG 906 CB and ASP 909 CB: 8.997Å  

> select #1/A:906@CB

1 atom, 1 residue, 1 model selected  

> select add #1/A:910@CB

2 atoms, 2 residues, 1 model selected  

> distance #1/A:906@CB #1/A:910@CB

Distance between ycf1_pka_valid.pdb #1/A ARG 906 CB and ALA 910 CB: 13.187Å  

> select #1/A:906@CB

1 atom, 1 residue, 1 model selected  

> select #1/A:911

17 atoms, 16 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide H

> select #1/A:911@CB

1 atom, 1 residue, 1 model selected  

> select add #1/A:906@CG

2 atoms, 2 residues, 1 model selected  

> select add #1/A:906@CB

3 atoms, 2 residues, 1 model selected  

> select #1/A:906@CG

1 atom, 1 residue, 1 model selected  

> select #1/A:906@CB

1 atom, 1 residue, 1 model selected  

> select add #1/A:911@CB

2 atoms, 2 residues, 1 model selected  

> distance #1/A:906@CB #1/A:911@CB

Distance between ycf1_pka_valid.pdb #1/A ARG 906 CB and TPO 911 CB: 16.088Å  

> select clear

> select #1/A:914@CB

1 atom, 1 residue, 1 model selected  

> select add #1/A:920@CB

2 atoms, 2 residues, 1 model selected  

> distance #1/A:914@CB #1/A:920@CB

Distance between ycf1_pka_valid.pdb #1/A SEP 914 CB and ASP 920 CB: 17.564Å  

> select #1/A:914@CB

1 atom, 1 residue, 1 model selected  

> select #1/A:921

15 atoms, 14 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/A:921@CB

1 atom, 1 residue, 1 model selected  

> select add #1/A:928@CB

2 atoms, 2 residues, 1 model selected  

> distance #1/A:921@CB #1/A:928@CB

Distance between ycf1_pka_valid.pdb #1/A GLU 921 CB and HIS 928 CB: 15.194Å  

> select #1/A:927@CB

1 atom, 1 residue, 1 model selected  

> select add #1/A:934@CB

2 atoms, 2 residues, 1 model selected  

> distance #1/A:927@CB #1/A:934@CB

Distance between ycf1_pka_valid.pdb #1/A GLU 927 CB and VAL 934 CB: 17.833Å  

> select clear

> distance style decimalPlaces 0

> distance style dashes 1

> distance style radius 0.4

> distance style symbol false

> hide H

> distance save "/home/rodolpho/Desktop/Paper Figures/DISTANCES_COEV"

> select #1/A:906@CB

1 atom, 1 residue, 1 model selected  

> select #1/A:906@CB

1 atom, 1 residue, 1 model selected  

> select add #1/A:912@CB

2 atoms, 2 residues, 1 model selected  

> distance #1/A:906@CB #1/A:912@CB

Distance between ycf1_pka_valid.pdb #1/A ARG 906 CB and LEU 912 CB: 18  

> distance style radius 0.4

> select clear

> select #1/A:790

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select clear

> distance style decimalPlaces 2

> distance style decimalPlaces 1

> distance save "/home/rodolpho/Desktop/Paper Figures/DISTANCES_COEV"

> distance style decimalPlaces 0

> distance monitor false

Missing or invalid "objects" argument: invalid objects specifier  

> distance #1 monitor false

Expected a keyword  

> distance #1, 2 monitor false

Expected a keyword  

> distance sel monitor false

Expected a keyword  

> distance delete

Undo failed, probably because structures have been modified.  

> undo

> select clear

> undo

> distance show

Missing or invalid "objects" argument: invalid objects specifier  

> distance

Missing or invalid "objects" argument: empty atom specifier  

> open "/home/rodolpho/Desktop/Paper Figures/DISTANCES_COEV"

'/home/rodolpho/Desktop/Paper Figures/DISTANCES_COEV' has no suffix  
Exactly two atoms must be selected!  

> select #2/A:872@CB

1 atom, 1 residue, 1 model selected  

> distance #2:872@cb #1:912@cb [signed false ] [ monitor false ]

Expected a keyword  

> distance #2:872@cb #1:912@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A SER 872 CB and
ycf1_pka_valid.pdb #1/A LEU 912 CB: 58  

> distance #2:872@cb #1:912@cb monitor false

Expected a keyword  

> distance #2:872@cb #1:912@cb monitor true

Expected a keyword  

> ~distance #2/A:872@CB #1/A:912@CB

> distance #2:872@cb #1:912@cb monitor false

Expected a keyword  

> distance #2:872@cb #1:912@cb [ monitor false ]

Expected a keyword  

> distance #2:872@cb #1:912@cb [monitor false]

Expected a keyword  

> distance #2:872@cb #1:912@cb [monitor false]

Expected a keyword  

> distance #2:872@cb #1:912@cb monitor false

Expected a keyword  

> distance #2:872@cb #1:912@cb true false

Expected a keyword  

> distance #2:872@cb #1:912@cb [true false]

Expected a keyword  

> distance #2:872@cb #1:912@cb [true] [false]

Expected a keyword  

> distance #2:872@cb #1:912@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A SER 872 CB and
ycf1_pka_valid.pdb #1/A LEU 912 CB: 58  

> select clear

> close #3.1

> distance #2:872@cb #1:909@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A SER 872 CB and
ycf1_pka_valid.pdb #1/A ASP 909 CB: 53  

> distance #2:874@cb #1:909@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A VAL 874 CB and
ycf1_pka_valid.pdb #1/A ASP 909 CB: 52  

> distance #2:874@cb #1:910@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A VAL 874 CB and
ycf1_pka_valid.pdb #1/A ALA 910 CB: 52  

> distance #2:875@cb #1:907@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A ARG 875 CB and
ycf1_pka_valid.pdb #1/A ALA 907 CB: 45  

> distance #2:875@cb #1:908@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A ARG 875 CB and
ycf1_pka_valid.pdb #1/A SEP 908 CB: 50  

> distance #2:906@cb #1:907@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A ARG 906 CB and
ycf1_pka_valid.pdb #1/A ALA 907 CB: 5  

> distance #2:906@cb #1:908@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A ARG 906 CB and
ycf1_pka_valid.pdb #1/A SEP 908 CB: 8  

> distance #2:906@cb #1:909@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A ARG 906 CB and
ycf1_pka_valid.pdb #1/A ASP 909 CB: 9  

> distance #2:906@cb #1:910@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A ARG 906 CB and
ycf1_pka_valid.pdb #1/A ALA 910 CB: 13  

> distance #2:906@cb #1:911@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A ARG 906 CB and
ycf1_pka_valid.pdb #1/A TPO 911 CB: 16  

> distance #2:906@cb #1:912@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A ARG 906 CB and
ycf1_pka_valid.pdb #1/A LEU 912 CB: 18  

> distance #2:914@cb #1:920@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A SEP 914 CB and
ycf1_pka_valid.pdb #1/A ASP 920 CB: 17  

> distance #2:921@cb #1:928@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A GLU 921 CB and
ycf1_pka_valid.pdb #1/A HIS 928 CB: 13  

> distance #2:927@cb #1:934@cb

Distance between 1st-model_ycf1-pka-rdomain.pdb #2/A GLU 927 CB and
ycf1_pka_valid.pdb #1/A VAL 934 CB: 21  

> close #3.1

> select clear

> distance #1:906@cb #1:907@cb

Distance between ycf1_pka_valid.pdb #1/A ARG 906 CB and ALA 907 CB: 6  

> distance #1:906@cb #1:908@cb

Distance between ycf1_pka_valid.pdb #1/A ARG 906 CB and SEP 908 CB: 8  

> distance #1:906@cb #1:909@cb

Distance between ycf1_pka_valid.pdb #1/A ARG 906 CB and ASP 909 CB: 9  

> distance #1:906@cb #1:909@cb

Distance already exists; modify distance properties with 'distance style'  

> distance #1:906@cb #1:910@cb

Distance between ycf1_pka_valid.pdb #1/A ARG 906 CB and ALA 910 CB: 13  

> distance #1:906@cb #1:911@cb

Distance between ycf1_pka_valid.pdb #1/A ARG 906 CB and TPO 911 CB: 16  

> distance #1:906@cb #1:912@cb

Distance between ycf1_pka_valid.pdb #1/A ARG 906 CB and LEU 912 CB: 18  

> distance #1:914@cb #1:920@cb

Distance between ycf1_pka_valid.pdb #1/A SEP 914 CB and ASP 920 CB: 18  

> distance #1:921@cb #1:928@cb

Distance between ycf1_pka_valid.pdb #1/A GLU 921 CB and HIS 928 CB: 15  

> distance #1:927@cb #1:934@cb

Distance between ycf1_pka_valid.pdb #1/A GLU 927 CB and VAL 934 CB: 18  

> close #3.1

> select clear

> save "/home/rodolpho/Desktop/Paper Figures/Co-EV_Ycf1.cxs"

> cofr showPivot false

> set bgColor white

> distance style radius 0.5

> transparency #1 80 target c

> transparency #1 70 target c

> transparency #1 50 target c

> transparency #1 0 target c

> transparency #1 50 target c

> transparency #1 30 target c

> transparency #1 10 target c

> set bgColor black

> set bgColor white

> color #1 #d3d7cf transparency 0

> transparency #1 10 target c

> color #1 #babdb6 transparency 0

> transparency #1 10 target c

> color #1:855-935 darkmagenta

> color #1 #888a85 transparency 0

> color #1:855-935 darkmagenta

> transparency #1 10 target c

> transparency #1 20 target c

> color #1 #888a85 transparency 0

> transparency #1 20 target c

> lighting soft

> transparency #1 20 target c

> color #1 #eeeeec transparency 0

> transparency #1 20 target c

> color #1 #d3d7cf transparency 0

> transparency #1 20 target c

> color #1 #888a85 transparency 0

> transparency #1 20 target c

> transparency #1 30 target c

> transparency #1 50 target c

> transparency #1 80 target c

> transparency #1 70 target c

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

> lighting simple

> lighting soft

> lighting simple

> graphics silhouettes false

> lighting flat

> lighting soft

> graphics silhouettes false

> transparency #1 70 target c

> lighting flat

> graphics silhouettes false

> lighting soft

> transparency #1 0 target c

> color #1 #d3d7cf transparency 0


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

Log:
> set selectionWidth 4

UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 430.34
OpenGL renderer: GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7B09
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 AMD Ryzen Threadripper 2950X 16-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G         15G         22G        214M         87G        108G
	Swap:          4.0G        1.1G        2.9G

Graphics:
	0a:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104 [GeForce RTX 2080 Rev. A] [10de:1e87] (rev a1)	
	Subsystem: eVga.com. Corp. Device [3842:2183]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0