Session restore: 'FeatureBrowser' object has no attribute 'sel_check_box'

[blemire@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Saved session unable to be restored.(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/blemire/Googledrive/C_albicans_F6/XP_711446_TSC2/XP_711446_TSC2_modeller+6SSH+3brw.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 713, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 688, in restore_snapshot  
inst.show_feature_browser(seq, state=fb_data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 652, in show_feature_browser  
self._feature_browsers[seq] = FeatureBrowser(self, seq, state,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/feature_browser.py", line 74, in __init__  
feature_chooser.set_state(state['feature_chooser'])  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/feature_browser.py", line 316, in set_state  
self.set_features(state['features'], selected_rows=set(state['selected
rows']))  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/feature_browser.py", line 313, in set_features  
self._fb._update_residue_display(shown_regions)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/feature_browser.py", line 270, in
_update_residue_display  
if self.sel_check_box.isChecked():  
AttributeError: 'FeatureBrowser' object has no attribute 'sel_check_box'  
  
Log from Fri Jun 25 16:12:11 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/blemire/Googledrive/C_albicans_F6/XP_711446_TSC2/PHYRE_XP_711446_TSC2_normal/_XP_711446_TSC2_6sshA.pdb

Chain information for _XP_711446_TSC2_6sshA.pdb #1  
---  
Chain | Description  
? | No description available  
  

> open
> /Users/blemire/Googledrive/C_albicans_F6/XP_711446_TSC2/PHYRE_XP_711446_TSC2_normal/_XP_711446_TSC2_7dl2B.pdb

Chain information for _XP_711446_TSC2_7dl2B.pdb #2  
---  
Chain | Description  
? | No description available  
  

> select /?:1236-1460

3245 atoms, 3320 bonds, 1 pseudobond, 374 residues, 3 models selected  

> select #2/?:134-1477

8231 atoms, 8410 bonds, 4 pseudobonds, 1013 residues, 2 models selected  

> select clear

> mmaker #1 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 _XP_711446_TSC2_7dl2B.pdb, chain (blank) (#2) with
_XP_711446_TSC2_6sshA.pdb, chain (blank) (#1), sequence alignment score =
734.8  
RMSD between 130 pruned atom pairs is 1.041 angstroms; (across all 177 pairs:
2.649)  
  

> view

> open
> /Users/blemire/Googledrive/C_albicans_F6/XP_711446_TSC2/XP_711446_TSC2.fasta

Summary of feedback from opening
/Users/blemire/Googledrive/C_albicans_F6/XP_711446_TSC2/XP_711446_TSC2.fasta  
---  
note | Alignment identifier is XP_711446_TSC2.fasta  
  
Opened 1 sequences from XP_711446_TSC2.fasta  

> sequence associate #2/? XP_711446_TSC2.fasta:1

Associated _XP_711446_TSC2_7dl2B.pdb chain (blank) to XP_711446.2 Tsc2p
[Candida albicans SC5314] with 3 mismatches and/or gaps  

> sequence associate #1/? XP_711446_TSC2.fasta:1

Associated _XP_711446_TSC2_6sshA.pdb chain (blank) to XP_711446.2 Tsc2p
[Candida albicans SC5314] with 0 mismatches and/or gaps  

> open
> /Users/blemire/Googledrive/C_albicans_F6/XP_711446_TSC2/XP_711446_TSC2.fasta
> format fasta

Summary of feedback from opening
/Users/blemire/Googledrive/C_albicans_F6/XP_711446_TSC2/XP_711446_TSC2.fasta  
---  
note | Alignment identifier is XP_711446_TSC2.fasta  
  
Opened 1 sequences from XP_711446_TSC2.fasta  

> sequence associate #1/? XP_711446_TSC2.fasta:1

Associated _XP_711446_TSC2_6sshA.pdb chain (blank) to XP_711446.2 Tsc2p
[Candida albicans SC5314] with 0 mismatches and/or gaps  

> select #2:1325-1334

Nothing selected  

> ui tool show "Modeller Comparative"

<QNSWindow: 0x7fda97a6fc50; contentView=<QNSView: 0x7fda97a76a30;
QCocoaWindow(0x60000238d4a0, window=QWidgetWindow(0x6000030a1080,
name="AlignSeqMenuButtonClassWindow"))>> has active key-value observers (KVO)!
These will stop working now that the window is recreated, and will result in
exceptions when the observers are removed. Break in
QCocoaWindow::recreateWindowIfNeeded to debug.  

> modeller comparative XP_711446_TSC2.fasta:1 multichain true numModels 5 fast
> false hetPreserve false hydrogens false tempPath
> /Users/blemire/Desktop/untitled_folder waterPreserve false

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service1624649018927490463772  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1624649018927490463772  
stdout.txt = standard output  
stderr.txt = standard error  

> open 6ssh

Summary of feedback from opening 6ssh fetched from pdb  
---  
note | Fetching compressed mmCIF 6ssh from
http://files.rcsb.org/download/6ssh.cif  
  
6ssh title:  
Structure of the TSC2 GAP domain [more info...]  
  
Chain information for 6ssh #3  
---  
Chain | Description  
A | GTPase activator-like protein  
  
Non-standard residues in 6ssh #3  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
  

> log metadata #3

Metadata for 6ssh #3  
---  
Title | Structure of the TSC2 GAP domain  
Citation | Hansmann, P., Bruckner, A., Kiontke, S., Berkenfeld, B., Seebohm,
G., Brouillard, P., Vikkula, M., Jansen, F.E., Nellist, M., Oeckinghaus, A.,
Kummel, D. (2020). Structure of the TSC2 GAP Domain: Mechanistic Insight into
Catalysis and Pathogenic Mutations. Structure, 28, 933-942.e4. PMID: 32502382.
DOI: 10.1016/j.str.2020.05.008  
Non-standard residue | EDO — 1,2-ethanediol (ethylene glycol)  
Gene source | Chaetomium thermophilum  
Experimental method | X-ray diffraction  
Resolution | 1.4Å  
  
> mmaker #3 to #1 showalignment true

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 _XP_711446_TSC2_6sshA.pdb, chain (blank) (#1) with 6ssh, chain A
(#3), sequence alignment score = 535.8  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: _XP_711446_TSC2_6sshA.pdb
#1/?, 6ssh #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 184 pruned atom pairs is 0.217 angstroms; (across all 191 pairs:
0.770)  
  

> sequence header 1 rmsd hide

Hiding rmsd header for alignment 1  

> select #2

8231 atoms, 8410 bonds, 4 pseudobonds, 1013 residues, 2 models selected  

> ~select #2

Nothing selected  

> hide #!2 models

> view

> select #3

3228 atoms, 3109 bonds, 2 pseudobonds, 350 residues, 2 models selected  

> hide sel atoms

> select clear

> select #1:1320-1337

34 atoms, 33 bonds, 4 residues, 1 model selected  

> open G0SFF5 fromDatabase uniprot

Summary of feedback from opening G0SFF5 fetched from uniprot  
---  
notes | Fetching G0SFF5 UniProt info from
https://www.uniprot.org/uniprot/G0SFF5.xml  
Alignment identifier is G0SFF5  
Associated 6ssh chain A to G0SFF5 with 0 mismatches  
  
Opened UniProt G0SFF5  
Modeller job ID appModeller9v8Service1624649018927490463772 finished  
Parameters  
---  
Chain pairing | ss  
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 _XP_711446_TSC2_6sshA.pdb, chain (blank) (#1) with
XP_711446.2_Tsc2, chain (blank) (#), sequence alignment score = 973.8  
RMSD between 191 pruned atom pairs is 0.341 angstroms; (across all 197 pairs:
1.135)  
  
Parameters  
---  
Chain pairing | ss  
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 _XP_711446_TSC2_6sshA.pdb, chain (blank) (#1) with
XP_711446.2_Tsc2, chain (blank) (#), sequence alignment score = 973.8  
RMSD between 192 pruned atom pairs is 0.276 angstroms; (across all 197 pairs:
1.136)  
  
Parameters  
---  
Chain pairing | ss  
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 _XP_711446_TSC2_6sshA.pdb, chain (blank) (#1) with
XP_711446.2_Tsc2, chain (blank) (#), sequence alignment score = 973.8  
RMSD between 192 pruned atom pairs is 0.330 angstroms; (across all 197 pairs:
1.158)  
  
Parameters  
---  
Chain pairing | ss  
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 _XP_711446_TSC2_6sshA.pdb, chain (blank) (#1) with
XP_711446.2_Tsc2, chain (blank) (#), sequence alignment score = 973.8  
RMSD between 189 pruned atom pairs is 0.288 angstroms; (across all 197 pairs:
1.148)  
  
Parameters  
---  
Chain pairing | ss  
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 _XP_711446_TSC2_6sshA.pdb, chain (blank) (#1) with
XP_711446.2_Tsc2, chain (blank) (#), sequence alignment score = 977.4  
RMSD between 192 pruned atom pairs is 0.327 angstroms; (across all 197 pairs:
1.094)  
  
Associated XP_711446.2_Tsc2 chain (blank) to XP_711446.2 Tsc2p [Candida
albicans SC5314] with 0 mismatches  
Associated XP_711446.2_Tsc2 chain (blank) to XP_711446.2 Tsc2p [Candida
albicans SC5314] with 0 mismatches  
Associated XP_711446.2_Tsc2 chain (blank) to XP_711446.2 Tsc2p [Candida
albicans SC5314] with 0 mismatches  
Associated XP_711446.2_Tsc2 chain (blank) to XP_711446.2 Tsc2p [Candida
albicans SC5314] with 0 mismatches  
Associated XP_711446.2_Tsc2 chain (blank) to XP_711446.2 Tsc2p [Candida
albicans SC5314] with 0 mismatches  
Chain information for XP_711446.2_Tsc2  
---  
Chain | Description  
4.1/? 4.2/? 4.3/? 4.4/? 4.5/? | No description available  
  

> select #4:1-1235

49560 atoms, 50560 bonds, 6175 residues, 5 models selected  

> delete #4:1-1235

> select #4:1461-end

1165 atoms, 1180 bonds, 150 residues, 5 models selected  

> delete #4:1461-end

> modeller scores #4.1-5 refresh false

> modeller scores #4.1-5 refresh true

> hide #1 models

> select #4:1320-1337

715 atoms, 710 bonds, 90 residues, 5 models selected  

> ui tool show "Color Actions"

> color sel red

> mmaker # 4.1 to #3 showalignment true

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 6ssh, chain A (#3) with XP_711446.2_Tsc2, chain (blank) (#4.1),
sequence alignment score = 505.7  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: 6ssh #3/A, XP_711446.2_Tsc2
#4.1/?  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 176 pruned atom pairs is 0.377 angstroms; (across all 191 pairs:
2.559)  
  

> sequence header 2 rmsd hide

Hiding rmsd header for alignment 2  
Drag select of 13 residues  

> color sel blue

> select clear

> show #!2 models

> hide #!3 models

> select clear

> hide #!4 models

> show #!4 models

> select #2

8231 atoms, 8410 bonds, 4 pseudobonds, 1013 residues, 2 models selected  

> show sel cartoons

> select clear

> select #3:1643

Nothing selected  

> select #2:1643

Nothing selected  

> hide #!2 models

> show #!3 models

> hide #4.1 models

> select #2

8231 atoms, 8410 bonds, 4 pseudobonds, 1013 residues, 2 models selected  

> select #3

3228 atoms, 3109 bonds, 2 pseudobonds, 350 residues, 2 models selected  

> rainbow sel

> select clear

> select #3

3228 atoms, 3109 bonds, 2 pseudobonds, 350 residues, 2 models selected  
Alignment identifier is 3/A  

> select #3:4

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #3

3228 atoms, 3109 bonds, 2 pseudobonds, 350 residues, 2 models selected  

> renumber

Unknown command: renumber  

> open 3BRW

Summary of feedback from opening 3BRW fetched from pdb  
---  
warnings | Unknown polymer entity '5' near line 10835  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
note | Fetching compressed mmCIF 3brw from
http://files.rcsb.org/download/3brw.cif  
  
3brw title:  
Structure of the Rap-RapGAP complex [more info...]  
  
Chain information for 3brw #5  
---  
Chain | Description  
A B C | Rap1 GTPase-activating protein 1  
D | Ras-related protein Rap-1b  
  
Non-standard residues in 3brw #5  
---  
BEF — beryllium trifluoride ion  
MG — magnesium ion  
  
3brw mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  

> mmaker #5 to #3

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 6ssh, chain A (#3) with 3brw, chain A (#5), sequence alignment
score = 353.7  
RMSD between 116 pruned atom pairs is 0.938 angstroms; (across all 184 pairs:
2.810)  
  

> select clear

> log metadata #5

Metadata for 3brw #5  
---  
Title | Structure of the Rap-RapGAP complex  
Citation | Scrima, A., Thomas, C., Deaconescu, D., Wittinghofer, A. (2008).
The Rap-RapGAP complex: GTP hydrolysis without catalytic glutamine and
arginine residues. Embo J., 27, 1145-1153. PMID: 18309292. DOI:
10.1038/emboj.2008.30  
Non-standard residues | BEF — beryllium trifluoride ion  
MG — magnesium ion  
Gene source | Homo sapiens (human)  
Experimental method | X-ray diffraction  
Resolution | 3.400Å  
  
> show #4.1 models

> select #4:1345-1367

990 atoms, 1020 bonds, 115 residues, 5 models selected  

> select #3/A:125-184 #4.1/ :1372-1437

Expected a keyword  

> hide #!5 models

> hide #!3 models

> select #4:1351, 1346, 1252, 1348, 1374, 1376

290 atoms, 275 bonds, 30 residues, 5 models selected  

> show sel & #4.1 atoms

> color sel cyan

> color sel orange

> color sel byhetero

> select clear

> select #4:1289,1296, 1348

130 atoms, 120 bonds, 15 residues, 5 models selected  

> color sel magenta

> color sel byhetero

> show sel & #4.1 atoms

> select clear

> select #4:1442,1445

85 atoms, 80 bonds, 10 residues, 5 models selected  

> color sel goldenrod

> show sel & #4.1 atoms

> color sel brown

> select clear

> select #4.1

1851 atoms, 1892 bonds, 225 residues, 1 model selected  

> show sel surfaces

> color sel light green

> color sel pale green

> color sel aquamarine

> color sel light cyan

> color sel light green

> select #4:1442,1445

85 atoms, 80 bonds, 10 residues, 5 models selected  

> color sel gold

> color sel gold

> select #4:1289,1296, 1348

130 atoms, 120 bonds, 15 residues, 5 models selected  

> color sel magenta

> select #4:1351, 1346, 1252, 1348, 1374, 1376

290 atoms, 275 bonds, 30 residues, 5 models selected  

> color sel orange

> show #!5 models

> select #4:1345-1367

990 atoms, 1020 bonds, 115 residues, 5 models selected  

> select #4:1325-1334

385 atoms, 380 bonds, 50 residues, 5 models selected  

> color sel red

> select #4:1395-1407

510 atoms, 510 bonds, 65 residues, 5 models selected  

> color sel blue

> select clear

> save
> /Users/blemire/Googledrive/C_albicans_F6/XP_711446_TSC2/XP_711446_TSC2_modeller+6SSH+3brw.cxs

——— End of log from Fri Jun 25 16:12:11 2021 ———

opened ChimeraX session  




OpenGL version: 4.1 ATI-4.5.14
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 3.6 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: 64 GB
      System Firmware Version: 1554.120.15.0.0
      SMC Version (system): 2.46f12

Software:

    System Software Overview:

      System Version: macOS 11.4 (20F71)
      Kernel Version: Darwin 20.5.0
      Time since boot: 6 days 16:06

Graphics/Displays:

    Radeon Pro 580X:

      Chipset Model: Radeon Pro 580X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A1X-009
      EFI Driver Version: 01.B1.042
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        Thunderbolt Display:
          Display Type: LCD
          Resolution: 2048 x 1152
          UI Looks like: 2048 x 1152
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: C02MC33KF2GC
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort

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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    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: 2.0.1
    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: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    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: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

[Eric Pettersen]

Reported by Bernard Lemire