close session set_pbgroup_py_instance: symbol not found

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> /Users/heejongkim/Dropbox/heejong_and_kenji/hir_asf1_h3h4/model/figure4_h3h4asf1_XL_HJK1.cxs
> format session

Opened 21run_it126_class001.mrc as #1, grid size 160,160,160, pixel 1.36,
shown at level 0.0066, step 1, values float32  
Opened 21run_it126_class001.mrc 0 as #3.1, grid size 160,160,160, pixel 1.36,
shown at level 0.0066, step 1, values float32  
Opened 21run_it126_class001.mrc 1 as #3.2, grid size 160,160,160, pixel 1.36,
shown at level 0.00612, step 1, values float32  
Log from Fri Sep 16 03:54:47 2022UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> /Users/heejongkim/Dropbox/heejong_and_kenji/hir_asf1_h3h4/model/figure5_bottom_histone_centric_map_HJK1.cxs
> format session

Opened 21run_it126_class001.mrc as #1, grid size 160,160,160, pixel 1.36,
shown at level 0.0066, step 1, values float32  
Opened 21run_it126_class001.mrc 0 as #3.1, grid size 160,160,160, pixel 1.36,
shown at level 0.0066, step 1, values float32  
Opened 21run_it126_class001.mrc 1 as #3.2, grid size 160,160,160, pixel 1.36,
shown at level 0.00612, step 1, values float32  
Log from Wed Sep 14 07:17:29 2022UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/heejongkim/Dropbox/heejong_and_kenji/hir_asf1_h3h4/maps_for_composite_220910/21run_it126_class001.mrc

Opened 21run_it126_class001.mrc as #1, grid size 160,160,160, pixel 1.36,
shown at level 0.0131, step 1, values float32  

> open
> /Users/heejongkim/Dropbox/heejong_and_kenji/hir_asf1_h3h4/maps_for_composite_220910/yeasth3h4_asf1_to21_it126_cls1.pdb

Chain information for yeasth3h4_asf1_to21_it126_cls1.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> hide atoms

> show cartoons

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 7130 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> transparency 50

> volume #1 level 0.0066

> ui tool show "Color Zone"

> color zone #1 near #2 distance 8.16

> color single #1

Need to color zone map before it can be split  

> color zone #1 near #2 distance 8.16

> volume splitbyzone #1

Opened 21run_it126_class001.mrc 0 as #3.1, grid size 160,160,160, pixel 1.36,
shown at level 0.0066, step 1, values float32  
Opened 21run_it126_class001.mrc 1 as #3.2, grid size 160,160,160, pixel 1.36,
shown at level 0.0066, step 1, values float32  
Opened 21run_it126_class001.mrc 2 as #3.3, grid size 160,160,160, pixel 1.36,
shown at level 0.0066, step 1, values float32  
Opened 21run_it126_class001.mrc 3 as #3.4, grid size 160,160,160, pixel 1.36,
shown at level 0.0066, step 1, values float32  
Opened 21run_it126_class001.mrc 4 as #3.5, grid size 160,160,160, pixel 1.36,
shown at level 0.0066, step 1, values float32  
Opened 21run_it126_class001.mrc 5 as #3.6, grid size 160,160,160, pixel 1.36,
shown at level 0.0066, step 1, values float32  

> close #3

> show #!1 models

> color single #1

> select #2

7130 atoms, 7186 bonds, 442 residues, 1 model selected  

> color sel gray

> select clear

> color zone #1 near #2 distance 8.16

> volume splitbyzone #1

Opened 21run_it126_class001.mrc 0 as #3.1, grid size 160,160,160, pixel 1.36,
shown at level 0.0066, step 1, values float32  
Opened 21run_it126_class001.mrc 1 as #3.2, grid size 160,160,160, pixel 1.36,
shown at level 0.0066, step 1, values float32  

> hide #!3.1 models

> transparency #3.2.1 50

> volume #3.2 level 0.005617

> volume #3.2 level 0.006122

> ui tool show "Model Panel"

> open
> /Users/heejongkim/Dropbox/heejong_and_kenji/hir_asf1_h3h4/model/model_v12pt1_aligned.pdb

Chain information for model_v12pt1_aligned.pdb #4  
---  
Chain | Description  
1 | No description available  
3 | No description available  
4 | No description available  
A B | No description available  
C E | No description available  
D F | No description available  
G L | No description available  
H M | No description available  
I N | No description available  
J P | No description available  
K R | No description available  
O S | No description available  
Q T | No description available  
U | No description available  
  

> hide atoms

> show cartoons

> ui tool show Matchmaker

> matchmaker #!4 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 yeasth3h4_asf1_to21_it126_cls1.pdb, chain E (#2) with
model_v12pt1_aligned.pdb, chain 1 (#4), sequence alignment score = 972.6  
RMSD between 188 pruned atom pairs is 0.001 angstroms; (across all 188 pairs:
0.001)  
  

> hide #2 models

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 117320 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> color /C,G #ffd500

> color /N,D #9fa0ff

> color /S #dab6fc

> color /E,L #f8961e

> color /I,F #8187dc

> color /O #bbadff

> color /T,M #98c9a3

> color /Q,H #77bfa3

> color /A,B #027da9

> color /J,P #01baef

> color /3 #004bff

> color /4 #04e762

> color /1 hotpink

> color /K #f8961e

> select #4/J:502

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

368 atoms, 368 bonds, 22 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #4/J:510

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

> select up

57 atoms, 56 bonds, 4 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #4/P:510

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

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #4/P:491

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

> select up

368 atoms, 368 bonds, 22 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> close #4

> open
> /Users/heejongkim/Dropbox/heejong_and_kenji/hir_asf1_h3h4/model/model_v12pt1_aligned.pdb

Chain information for model_v12pt1_aligned.pdb #4  
---  
Chain | Description  
1 | No description available  
3 | No description available  
4 | No description available  
A B | No description available  
C E | No description available  
D F | No description available  
G L | No description available  
H M | No description available  
I N | No description available  
J P | No description available  
K R | No description available  
O S | No description available  
Q T | No description available  
U | No description available  
  

> hide #!4 atoms

> show #!4 cartoons

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 117320 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> ui tool show Matchmaker

> matchmaker #!4 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 yeasth3h4_asf1_to21_it126_cls1.pdb, chain E (#2) with
model_v12pt1_aligned.pdb, chain 1 (#4), sequence alignment score = 972.6  
RMSD between 188 pruned atom pairs is 0.001 angstroms; (across all 188 pairs:
0.001)  
  

> show #2 models

> hide #2 models

> color /C,G #ffd500

> color /N,D #9fa0ff

> color /S #dab6fc

> color /E,L #f8961e

> color /I,F #8187dc

> color /O #bbadff

> color /T,M #98c9a3

> color /Q,H #77bfa3

> color /A,B #027da9

> color /J,P #01baef

> color /3 #004bff

> color /4 #04e762

> color /1 hotpink

> color /K #f8961e

> select #4/3,4,1

6254 atoms, 6306 bonds, 389 residues, 1 model selected  

> select ~sel

118196 atoms, 119378 bonds, 4 pseudobonds, 7295 residues, 10 models selected  

> transparency sel 80 target c

> select clear

> graphics silhouettes true width 1

[Repeated 1 time(s)]

> select clear

> save
> /Users/heejongkim/Dropbox/heejong_and_kenji/hir_asf1_h3h4/model/figure5_bottom_histone_centric_map_HJK1.cxs

——— End of log from Wed Sep 14 07:17:29 2022 ———

opened ChimeraX session  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> hide #!3 models

> select #4/3,4,1

6254 atoms, 6306 bonds, 389 residues, 1 model selected  

> select ~sel

118196 atoms, 119378 bonds, 4 pseudobonds, 7295 residues, 10 models selected  

> hide sel target c

> select clear

> ui tool show XMAS

> show #2 models

> hide #2 models

> hide #!4 models

> show #2 models

> hide #2 models

> show #!4 models

Please check one or more files  
  
Peptide pair mapping of Xi evidence file:
/Users/heejongkim/Dropbox/heejong_and_kenji/hir_asf1_h3h4/XLMS/dsbu/combined_between_05HAHH_HConly/Asf1H3H4_associated_XMAS.csv  
Unique peptide pairs: 267 out of 267  
Unique peptide pairs with pseudobonds: 169  
Pseudobonds are stored in
/Users/heejongkim/Dropbox/heejong_and_kenji/hir_asf1_h3h4/XLMS/dsbu/combined_between_05HAHH_HConly/Asf1H3H4_associated_XMAS_2,4.pb  
Mapping information is stored in
/Users/heejongkim/Dropbox/heejong_and_kenji/hir_asf1_h3h4/XLMS/dsbu/combined_between_05HAHH_HConly/Asf1H3H4_associated_XMAS_2,4.tsv  

> hide #5 models

> select clear

[Repeated 3 time(s)]

> select #4/4:4

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

> select up

388 atoms, 388 bonds, 25 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> save /Users/heejongkim/Desktop/image1.png supersample 3

> save
> /Users/heejongkim/Dropbox/heejong_and_kenji/hir_asf1_h3h4/model/figure4_h3h4asf1_XL_HJK1.cxs

——— End of log from Fri Sep 16 03:54:47 2022 ———

opened ChimeraX session  

> close session

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1051, in <lambda>  
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 700, in file_close_cb  
run(session, 'close session')  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/close.py", line 60, in close_session  
session.reset()  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 588, in reset_state  
for pbg in list(self.group_map.values()):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 536, in group_map  
f = c_function('set_pbgroup_py_instance',  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 31, in c_function  
f = getattr(self._c_lib, func_name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 387, in __getattr__  
func = self.__getitem__(name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 392, in __getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
AttributeError: dlsym(0x600002151b20, set_pbgroup_py_instance): symbol not
found  
  

Populating font family aliases took 743 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

AttributeError: dlsym(0x600002151b20, set_pbgroup_py_instance): symbol not
found  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 392, in __getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.6.21
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16064.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.6.8 (20G730)
      Kernel Version: Darwin 20.6.0
      Time since boot: 17 days 19:46

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    biopython: 1.79
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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-RIBFIND: 0.2
    ChimeraX-RMF: 0.11
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-XMAS: 1.1.2
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    et-xmlfile: 1.1.0
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openpyxl: 3.0.10
    openvr: 1.16.802
    packaging: 21.0
    pandas: 1.4.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    QtRangeSlider: 0.1.5
    RandomWords: 0.3.0
    requests: 2.27.1
    ribfind: 2.0.2
    scipy: 1.7.3
    seaborn: 0.11.2
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0