Restoring new session in old version

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202109100619 (2021-09-10 06:19:11 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3.dev202109100619 (2021-09-10)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> /Users/whenriques/Dropbox/wiedenheft/projects/capsid.Hs/pnma.family.analysis.1025/chimera.sessions/pnma1.7lma7.TERT.p65.RNA.bound.cxs

Log from Tue Dec 14 17:20:04 2021UCSF ChimeraX version: 1.3.dev202109100619
(2021-09-10)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> /Users/whenriques/Dropbox/wiedenheft/projects/capsid.Hs/context.analysis/pnma-
> ntd/RBD.tertp65.pnma1.cxs

Log from Wed Nov 17 11:31:31 2021UCSF ChimeraX version: 1.3.dev202109100619
(2021-09-10)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/whenriques/Downloads/7lma.pdb

7lma.pdb title:  
Tetrahymena telomerase T3D2 structure At 3.3 angstrom [more info...]  
  
Chain information for 7lma.pdb #1  
---  
Chain | Description | UniProt  
A | telomerase reverse transcriptase | TERT_TETTH  
B | telomerase RNA |  
C | telomere DNA |  
D | telomerase holoenzyme TEB1 subunit | D2CVN6_TETTH  
E | telomerase holoenzyme TEB2 subunit |  
F | telomerase holoenzyme TEB3 subunit |  
G | P50 | TAP50_TETTS  
H | telomerase La-related protein P65 | LARP7_TETTS  
  
Non-standard residues in 7lma.pdb #1  
---  
ZN — zinc ion  
  

> select #1/H

1367 atoms, 1381 bonds, 3 pseudobonds, 199 residues, 2 models selected  

> show sel cartoons

> show sel atoms

> style sel stick

Changed 1367 atom styles  

> hide sel atoms

> select #1/B

3293 atoms, 3679 bonds, 156 residues, 1 model selected  

> style sel stick

Changed 3293 atom styles  

> open
> /Users/whenriques/Dropbox/wiedenheft/bioinformatics/20211025-1108/capsid/pnma.family.analysis/pdbs/pnma1.hs.alphafold.NTD.pdb

pnma1.hs.alphafold.NTD.pdb title:  
Alphafold V2.0 prediction for paraneoplastic antigen MA1 (Q8ND90) [more
info...]  
  
Chain information for pnma1.hs.alphafold.NTD.pdb #2  
---  
Chain | Description | UniProt  
A | paraneoplastic antigen MA1 | PNMA1_HUMAN  
  

> mmaker #2 to #1/H

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 7lma.pdb, chain H (#1) with pnma1.hs.alphafold.NTD.pdb, chain A
(#2), sequence alignment score = 59.1  
RMSD between 4 pruned atom pairs is 1.329 angstroms; (across all 115 pairs:
29.111)  
  

> mmaker #2:1-100 to #1/H

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 7lma.pdb, chain H (#1) with pnma1.hs.alphafold.NTD.pdb, chain A
(#2), sequence alignment score = 45.1  
RMSD between 42 pruned atom pairs is 1.221 angstroms; (across all 90 pairs:
33.622)  
  

> mmaker #2:1-100 to #1/H

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 7lma.pdb, chain H (#1) with pnma1.hs.alphafold.NTD.pdb, chain A
(#2), sequence alignment score = 45.1  
RMSD between 42 pruned atom pairs is 1.221 angstroms; (across all 90 pairs:
33.622)  
  

> hide ~ #1/H #1/B #2

> select #1

18672 atoms, 19367 bonds, 12 pseudobonds, 2008 residues, 3 models selected  

> ~select #1

Nothing selected  

> view clip false

> color pink #2

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color pink #2 'All'

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color pink #2:'All'

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> hide #!1 models

> show #!1 models

> select #2

1257 atoms, 1290 bonds, 158 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel pink

> ~select #2

Nothing selected  

> mmaker #2:1-100 to #1/H

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 7lma.pdb, chain H (#1) with pnma1.hs.alphafold.NTD.pdb, chain A
(#2), sequence alignment score = 45.1  
RMSD between 42 pruned atom pairs is 1.221 angstroms; (across all 90 pairs:
33.622)  
  

> mmaker #2:1-90 to #1/H

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 7lma.pdb, chain H (#1) with pnma1.hs.alphafold.NTD.pdb, chain A
(#2), sequence alignment score = 35.8  
RMSD between 40 pruned atom pairs is 1.212 angstroms; (across all 81 pairs:
35.073)  
  

> mmaker #2:1-90 to #1/H:412-513

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 7lma.pdb, chain H (#1) with pnma1.hs.alphafold.NTD.pdb, chain A
(#2), sequence alignment score = 16.2  
RMSD between 10 pruned atom pairs is 0.927 angstroms; (across all 40 pairs:
15.550)  
  

> mmaker #2:1-90 to #1/H

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 7lma.pdb, chain H (#1) with pnma1.hs.alphafold.NTD.pdb, chain A
(#2), sequence alignment score = 35.8  
RMSD between 40 pruned atom pairs is 1.212 angstroms; (across all 81 pairs:
35.073)  
  

> view clip false

[Repeated 1 time(s)]

> center #2

Unknown command: center #2  

> view #2 clip false

> lighting full

> lighting simple

> lighting soft

[Repeated 1 time(s)]

> lighting full

> lighting simple

> lighting soft

> save
> /Users/whenriques/Dropbox/wiedenheft/bioinformatics/20211025-1108/capsid/context.analysis/pnma-
> ntd/pnma1.7lma-H.RNA.intxn.png width 864 height 670 supersample 3
> transparentBackground true

> select #1:121

69 atoms, 68 bonds, 6 residues, 1 model selected  

> select #1:121 #1:122

122 atoms, 124 bonds, 11 residues, 1 model selected  

> hide ~#2 #1/H #1:121 #1:122

> center #1:122

Unknown command: center #1:122  

> view #1:122

> view #2 clip false

> view #2:50

> lighting full

> lighting soft

> select #1:460-470

176 atoms, 177 bonds, 22 residues, 1 model selected  

> select #1:460-467

132 atoms, 132 bonds, 16 residues, 1 model selected  

> show sel atoms

> view #2

> select #1:405-411

130 atoms, 133 bonds, 14 residues, 1 model selected  

> show sel atoms

> view #1:405-411

> view #1/H:405-411

> style sel stick

Changed 130 atom styles  

> style sel stick

Changed 130 atom styles  

> color sel byhetero

> select #1:121

69 atoms, 68 bonds, 6 residues, 1 model selected  

> color sel byhetero

> select #1:121 #1:122

122 atoms, 124 bonds, 11 residues, 1 model selected  

> color sel byhetero

> select #2:465-467

Nothing selected  

> select #1/H:465-467

31 atoms, 31 bonds, 3 residues, 1 model selected  

> color sel byhetero

> view #1/B

> view #1:100-120

> view #2

> save
> /Users/whenriques/Dropbox/wiedenheft/bioinformatics/20211025-1108/capsid/context.analysis/pnma-
> ntd/RBD.tertp65.pnma1.cxs

——— End of log from Wed Nov 17 11:31:31 2021 ———

opened ChimeraX session  

> hide #!1 models

> show #!1 models

> open /Users/whenriques/Downloads/7lma.pdb

7lma.pdb title:  
Tetrahymena telomerase T3D2 structure At 3.3 angstrom [more info...]  
  
Chain information for 7lma.pdb #3  
---  
Chain | Description | UniProt  
A | telomerase reverse transcriptase | TERT_TETTH  
B | telomerase RNA |  
C | telomere DNA |  
D | telomerase holoenzyme TEB1 subunit | D2CVN6_TETTH  
E | telomerase holoenzyme TEB2 subunit |  
F | telomerase holoenzyme TEB3 subunit |  
G | P50 | TAP50_TETTS  
H | telomerase La-related protein P65 | LARP7_TETTS  
  
Non-standard residues in 7lma.pdb #3  
---  
ZN — zinc ion  
  

> select #1

18672 atoms, 19367 bonds, 12 pseudobonds, 2008 residues, 3 models selected  

> color (#!1 & sel) gray

> preset cartoons/nucleotides cylinders/stubs

Changed 32618 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 (#!1 & sel) gray

> ~select #1

Nothing selected  

> select #3

18672 atoms, 19367 bonds, 12 pseudobonds, 2008 residues, 3 models selected  

> color (#!3 & sel) gray

> show sel surfaces

> color (#!3 & sel) gray

> select #1/B

3293 atoms, 3679 bonds, 156 residues, 1 model selected  

> rainbow sel

> show sel cartoons

> hide sel surfaces

[Repeated 1 time(s)]

> select #3/B

3293 atoms, 3679 bonds, 156 residues, 1 model selected  

> hide sel surfaces

> select #3/H

1367 atoms, 1381 bonds, 3 pseudobonds, 199 residues, 2 models selected  

> preset cartoons/nucleotides cylinders/stubs

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
    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

  

> select~ #3/H #3/B #2

Unknown command: select~ #3/H #3/B #2  

> select ~ #3/H #3/B #2

32684 atoms, 33674 bonds, 21 pseudobonds, 3661 residues, 19 models selected  

> show sel surfaces

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

> view #2 clip false

> select #3/B

3293 atoms, 3679 bonds, 156 residues, 1 model selected  

> nucleotides sel slab

> style nucleic & sel stick

Changed 3293 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel fill

> style nucleic & sel stick

Changed 3293 atom styles  

> select #3

18672 atoms, 19367 bonds, 12 pseudobonds, 2008 residues, 3 models selected  

> ~select #3

8 models selected  

> select #3/B

3293 atoms, 3679 bonds, 156 residues, 1 model selected  

> color (#!3 & sel) cornflower blue

> select #3

18672 atoms, 19367 bonds, 12 pseudobonds, 2008 residues, 3 models selected  

> ~select #3

8 models selected  

> select #3/B #3/H #2

5917 atoms, 6350 bonds, 3 pseudobonds, 513 residues, 3 models selected  

> select ~ #3/B #3/H #2

32684 atoms, 33674 bonds, 21 pseudobonds, 3661 residues, 6 models selected  

> show sel surfaces

> color (#!1,3 & sel) gray

> ~select #1

14012 atoms, 14307 bonds, 9 pseudobonds, 1653 residues, 17 models selected  

> close #1

> color (#!3 & sel) #ffffff80

> lighting soft

> select #3

18672 atoms, 19367 bonds, 12 pseudobonds, 2008 residues, 3 models selected  

> ~select #3

8 models selected  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> mmaker #1:1-100 to #2/H

No 'to' model specified  

> mmaker #2:1-100 to #3/H

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 7lma.pdb, chain H (#3) with pnma1.hs.alphafold.NTD.pdb, chain A
(#2), sequence alignment score = 45.1  
RMSD between 42 pruned atom pairs is 1.221 angstroms; (across all 90 pairs:
33.622)  
  

> mmaker #2:1-100 to #3/H:378-512

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 7lma.pdb, chain H (#3) with pnma1.hs.alphafold.NTD.pdb, chain A
(#2), sequence alignment score = 47.7  
RMSD between 41 pruned atom pairs is 1.222 angstroms; (across all 73 pairs:
6.393)  
  

> save
> /Users/whenriques/Dropbox/wiedenheft/projects/capsid.Hs/pnma.family.analysis.1025/chimera.sessions/pnma1.7lma7.TERT.p65.RNA.bound.cxs

——— End of log from Tue Dec 14 17:20:04 2021 ———

opened ChimeraX session  

> open "/Users/whenriques/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/19038004-4585-4194-BEDF-99D30636DB2A/PNMA8B-3_codingStrand.primatesBLAT.aln3.fa"

Summary of feedback from opening
/Users/whenriques/Library/Containers/com.apple.mail/Data/Library/Mail
Downloads/19038004-4585-4194-BEDF-99D30636DB2A/PNMA8B-3_codingStrand.primatesBLAT.aln3.fa  
---  
notes | Alignment identifier is PNMA8B-3_codingStrand.primatesBLAT.aln3.fa  
Showing conservation header ("seq_conservation" residue attribute) for
alignment PNMA8B-3_codingStrand.primatesBLAT.aln3.fa  
  
Opened 25 sequences from PNMA8B-3_codingStrand.primatesBLAT.aln3.fa  

> hbonds reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 7lma.pdb #3/H PRO 149 N; 7lma.pdb #3/H PRO 234 N  

1792 hydrogen bonds found  

> hide #!3 models

> show #!3 models

> hide #3.10 models

> show #3.10 models

> hide #!3 models

> show #!3 models

> close session

> open
> /Users/whenriques/Dropbox/wiedenheft/output/proposals/grants/F31_Comps/translation_review/tRNA_synthetase.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 717, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1336, in restore_snapshot  
s.set_state_from_snapshot(session, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1343, in set_state_from_snapshot  
Structure.set_state_from_snapshot(self, session, data['structure state'])  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 212, in set_state_from_snapshot  
StructureData.set_state_from_snapshot(self, session, data['structure state'])  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1795, in set_state_from_snapshot  
f(self._c_pointer, data['version'], tuple(data['ints']),
tuple(data['floats']), tuple(data['misc']))  
TypeError: Don't know how to restore new session data; update your version of
ChimeraX  
  
opened ChimeraX session  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache: 8 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 31 days 18:25

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        BenQ GW2760HS:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    charset-normalizer: 2.0.4
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.29.1
    ChimeraX-AtomicLibrary: 4.1.4
    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: 2.5.3
    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: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.4.1
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202109100619
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    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: 2.1.1
    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
    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: 2.0.1
    ChimeraX-MDcrds: 2.5
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.1.2
    ChimeraX-ModelPanel: 1.1.1
    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: 2.6.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    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
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    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: 2.4.3
    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
    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: 1.12
    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: 0.10.0
    Cython: 0.29.23
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.6.2
    numexpr: 2.7.3
    numpy: 1.21.0
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.2.1
    qtconsole: 5.1.0
    QtPy: 1.11.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    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
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0