id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
6512	Calling _cpp_modified failed	davis797@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202203290305 (2022-03-29 03:05:53 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x000070001099e000 (most recent call first):
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1284 in run
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap

Current thread 0x00000001172d2600 (most recent call first):
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molobject.py"", line 1407 in delete
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/structure.py"", line 124 in delete
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/models.py"", line 898 in close
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/std_commands/close.py"", line 32 in close
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897 in run
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py"", line 38 in run
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/model_panel/tool.py"", line 397 in close
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/model_panel/tool.py"", line 87 in 
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 318 in event_loop
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 867 in init
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1018 in 
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main


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    }
  ],
  ""experiments"" : [

  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202203290305 (2022-03-29)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/barrettdavis/Library/CloudStorage/Box-
> Box/TKU_Lab/Lab_Members/Barrett Davis/Koehn/Barrett/zz_Eva/asdf.mol2""

Chain information for combination #1  
---  
Chain | Description  
B | No description available  
  
Opened asdf.mol2 containing 1 structures (6284 atoms, 6336 bonds)  

> save ""/Users/barrettdavis/Library/CloudStorage/Box-
> Box/TKU_Lab/Lab_Members/Barrett Davis/Koehn/Barrett/zz_Eva/turboid_pdp1.cif""
> relModel #1

Not saving entity_poly_seq for non-authoritative sequences  

> open ""/Users/barrettdavis/Library/CloudStorage/Box-
> Box/TKU_Lab/Lab_Members/Barrett Davis/Koehn/Barrett/zz_Eva/turboid_pdp1.cif""

Summary of feedback from opening /Users/barrettdavis/Library/CloudStorage/Box-
Box/TKU_Lab/Lab_Members/Barrett Davis/Koehn/Barrett/zz_Eva/turboid_pdp1.cif  
---  
warnings | Unknown polymer entity '1' near line 114  
Atom H is not in the residue template for SER /B:1  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for turboid_pdp1.cif #2  
---  
Chain | Description  
B | ?  
  

> close #1

> rainbow

> open 7PNN

7pnn title:  
mVenus released from fusion protein. [more info...]  
  
Chain information for 7pnn #1  
---  
Chain | Description | UniProt  
A | mVenus | GFP_AEQVI  
  
Non-standard residues in 7pnn #1  
---  
CL — chloride ion  
CR2 —
{(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid (chromophore (gly-tyr-gly))  
  

> matchmaker #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 turboid_pdp1.cif, chain B (#2) with 7pnn, chain A (#1), sequence
alignment score = 147.9  
RMSD between 29 pruned atom pairs is 0.620 angstroms; (across all 29 pairs:
0.620)  
  

> select #1:36-end

3390 atoms, 3152 bonds, 471 residues, 1 model selected  

> select #2:36-end

5733 atoms, 5781 bonds, 368 residues, 1 model selected  

> select #2:40-end

5676 atoms, 5723 bonds, 364 residues, 1 model selected  

> ui mousemode right ""translate selected atoms""

> select #2:48-end

5599 atoms, 5646 bonds, 356 residues, 1 model selected  

> undo

> ui tool show Matchmaker

> matchmaker #2 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 7pnn, chain A (#1) with turboid_pdp1.cif, chain B (#2), sequence
alignment score = 147.9  
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: 7pnn #1/A, turboid_pdp1.cif
#2/B  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  
RMSD between 29 pruned atom pairs is 0.620 angstroms; (across all 29 pairs:
0.620)  
  

> select #1/A:229

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:229 #2/B:29

28 atoms, 26 bonds, 2 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region 7pnn, chain A..turboid_pdp1.cif, chain B
[229] RMSD: 1.557  
  

> select #1/A:201

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

> select #1/A:201-229 #2/B:1-29

922 atoms, 928 bonds, 58 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region 7pnn, chain A..turboid_pdp1.cif, chain B
[201-229] RMSD: 0.620  
  

> select #1/A:229

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:229 #2/B:29

28 atoms, 26 bonds, 2 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region 7pnn, chain A..turboid_pdp1.cif, chain B
[229] RMSD: 1.557  
  

> select #2/B:28

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

> select #2/B:13-28

257 atoms, 258 bonds, 16 residues, 1 model selected  

> select #2/B:30-31

26 atoms, 25 bonds, 2 residues, 1 model selected  

> select #2/B:30-40

153 atoms, 153 bonds, 11 residues, 1 model selected  

> select #1/A:229

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:201-229

460 atoms, 463 bonds, 29 residues, 1 model selected  

> select #2/B:29

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:201-229 #2/B:1-29

922 atoms, 928 bonds, 58 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region 7pnn, chain A..turboid_pdp1.cif, chain B
[201-229] RMSD: 0.620  
  

> select #2/B:29

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #2/B:11-29

300 atoms, 301 bonds, 19 residues, 1 model selected  

> select #2/B:11-end

6122 atoms, 6172 bonds, 393 residues, 1 model selected  

> select #2/B:1-29

462 atoms, 465 bonds, 29 residues, 1 model selected  

> Del #2/B:1-29

Unknown command: Del #2/B:1-29  

> delete #2/B:1-29

> combine #1 #2

Associated combination chain B to turboid_pdp1.cif, chain B with 0 mismatches  
Associated combination chain A to 7pnn, chain A with 0 mismatches  
Chains used in RMSD evaluation for alignment 1: 7pnn #1/A, turboid_pdp1.cif
#2/B, combination #3/A  

> hide #1 models

> hide #2 models

> select #3/B:30

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

> select #3/B:30 #3/A:229

33 atoms, 31 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> show sel atoms

> color sel wihte

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color sel white

> color sel byhetero

> select #3/B:30 #3/A:229@c

20 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/B:30@n #3/A:229@c

2 atoms, 2 residues, 1 model selected  

> ui tool show Matchmaker

> ui tool show ""Build Structure""

> bond sel

Created 0 bonds  

> select #3/A

3899 atoms, 3665 bonds, 506 residues, 1 model selected  

> select #3/B:30@n #3/A:229@c

2 atoms, 2 residues, 1 model selected  

> select #3/A

3899 atoms, 3665 bonds, 506 residues, 1 model selected  

> select #3/B:30@n #3/A:229@c

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select all

19442 atoms, 19071 bonds, 1760 residues, 3 models selected  

> hide sel & #3 atoms

> show sel & #3 cartoons

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/triggerset.py"", line 134, in invoke  
return self._func(self._name, data)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/rmsd.py"", line 200, in _atomic_changes_cb  
self.reevaluate()  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/rmsd.py"", line 112, in reevaluate  
by_struct.setdefault(chain.structure, []).append(chain)  
AttributeError: 'Sequence' object has no attribute 'structure'  
  

Populating font family aliases took 1109 ms. Replace uses of missing font
family "".AppleSystemUIFont"" with one that exists to avoid this cost.  

Error processing trigger ""changes"":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/rmsd.py"", line 112, in reevaluate  
by_struct.setdefault(chain.structure, []).append(chain)  
  
See log for complete Python traceback.  
  
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/triggerset.py"", line 134, in invoke  
return self._func(self._name, data)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/rmsd.py"", line 200, in _atomic_changes_cb  
self.reevaluate()  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/rmsd.py"", line 112, in reevaluate  
by_struct.setdefault(chain.structure, []).append(chain)  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
Error processing trigger ""changes"":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/rmsd.py"", line 112, in reevaluate  
by_struct.setdefault(chain.structure, []).append(chain)  
  
See log for complete Python traceback.  
  

> close #1-2

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/triggerset.py"", line 134, in invoke  
return self._func(self._name, data)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py"", line 458, in _delay_disassoc  
self._notify_observers(self.NOTE_DEL_ASSOC, data)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py"", line 681, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py"", line 431, in
alignment_notification  
self.notify_alignment(self.alignment.NOTE_HDR_RELEVANCE)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py"", line 152, in
notify_alignment  
self.alignment.notify(note_name, note_data)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py"", line 549, in notify  
if hdr.shown and not hdr.relevant:  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py"", line 441, in relevant  
return len(set([x.structure  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py"", line 441, in
  
return len(set([x.structure  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
Error processing trigger ""changes done"":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py"", line 441, in  
return len(set([x.structure  
  
See log for complete Python traceback.  
  
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/triggerset.py"", line 134, in invoke  
return self._func(self._name, data)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py"", line 458, in _delay_disassoc  
self._notify_observers(self.NOTE_DEL_ASSOC, data)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py"", line 681, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py"", line 431, in
alignment_notification  
self.notify_alignment(self.alignment.NOTE_HDR_RELEVANCE)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py"", line 152, in
notify_alignment  
self.alignment.notify(note_name, note_data)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py"", line 549, in notify  
if hdr.shown and not hdr.relevant:  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py"", line 441, in relevant  
return len(set([x.structure  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py"", line 441, in
  
return len(set([x.structure  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
Error processing trigger ""changes done"":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py"", line 441, in  
return len(set([x.structure  
  
See log for complete Python traceback.  
  

> save ""/Users/barrettdavis/Library/CloudStorage/Box-
> Box/TKU_Lab/Lab_Members/Barrett
> Davis/Koehn/Barrett/zz_Eva/mvenus_turboid_pdp1.mol2""

> open ""/Users/barrettdavis/Library/CloudStorage/Box-
> Box/TKU_Lab/Lab_Members/Barrett
> Davis/Koehn/Barrett/zz_Eva/mvenus_turboid_pdp1.mol2""

Chain information for combination #1  
---  
Chain | Description  
A | No description available  
  
Opened mvenus_turboid_pdp1.mol2 containing 1 structures (9721 atoms, 9536
bonds)  

> hide #3 models

> show #3 models

> hide #1 models

> show #1 models

> hide #3 models

> close #3


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

Log:
UCSF ChimeraX version: 1.4.dev202203290305 (2022-03-29)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/barrettdavis/Library/CloudStorage/Box-
> Box/TKU_Lab/Lab_Members/Barrett
> Davis/Koehn/Barrett/zz_Eva/mvenus_turboid_pdp1.mol2""

Chain information for combination #1  
---  
Chain | Description  
A | No description available  
  
Opened mvenus_turboid_pdp1.mol2 containing 1 structures (9721 atoms, 9536
bonds)  




OpenGL version: 4.1 INTEL-18.4.6
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.9.6
Locale: UTF-8
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,4
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.8 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 428.60.3.0.0
      OS Loader Version: 540.80.2~11
      SMC Version (system): 2.29f24

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 6 days 21:27

Graphics/Displays:

    Intel Iris Pro:

      Chipset Model: Intel Iris Pro
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0d26
      Revision ID: 0x0008
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        E2411:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: 107NDEZ58868
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
        E2411:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: 107NDQA58884
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.5.30
    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: 2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.36.3
    ChimeraX-AtomicLibrary: 6.1.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    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-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.dev202203290305
    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-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-ItemsInspection: 1.0
    ChimeraX-Label: 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: 1.8
    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-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: 2.5
    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
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.3
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.31.2
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    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: 4.9.2
    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: 1.5.4
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    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: 3.0.28
    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: 3.0.7
    PyQt6-commercial: 6.2.3
    PyQt6-sip: 13.2.0
    PyQt6-WebEngine-commercial: 6.2.1
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 22.3.0
    qtconsole: 5.3.0
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    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

}}}
"	defect	closed	normal		Sequence		duplicate						all	ChimeraX