Opened 3 years ago

Closed 3 years ago

#8754 closed defect (duplicate)

MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Comparison Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-21.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/yurishibata/Library/CloudStorage/OneDrive-
> wehi.edu.au/FAM115A/Data/Structures/M60-like/Figures/FAM115A M60-like
> superposed with ZmpB 5kdn/FAM115A M60_5kdn.cxs" format session

Log from Thu May 13 13:14:58 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/shibata.y/OneDrive - wehi.edu.au/FAM115A
> paper/Data/Structures/M60-like/Figures/FAM115A M60-like
> overall/highlight/FAM115A M60-like highlight.cxs"

Log from Wed May 12 21:42:00 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/shibata.y/OneDrive - wehi.edu.au/FAM115A
> paper/Data/Structures/M60-like/Figures/FAM115A M60-like
> overall/highlight/FAM115A M60-like highlight.cxs"

Log from Wed May 12 18:03:49 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/shibata.y/OneDrive - wehi.edu.au/FAM115A
> paper/Data/Structures/M60-like/Figures/SeMet_FAM115A_M60_refine_120-coot-8.pdb"

Summary of feedback from opening /Users/shibata.y/OneDrive -
wehi.edu.au/FAM115A
paper/Data/Structures/M60-like/Figures/SeMet_FAM115A_M60_refine_120-coot-8.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2020-04-16 Time 02:46:11 AEST +1000 (1586969171.17 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name : /Users/shibata.y/Desktop/Structures/FAM115A_M60/FAM115  
  
33 messages similar to the above omitted  
  
Chain information for SeMet_FAM115A_M60_refine_120-coot-8.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> set bgColor white

> hide all

> hide /b cartoons

> color cadet blue

> select /A:753-763

174 atoms, 177 bonds, 11 residues, 1 model selected  

> color sel salmon

> select /A:527-636

1669 atoms, 1686 bonds, 110 residues, 1 model selected  

> color sel khaki

> save "./FAM115A M60-like highlight.cxs"

opened ChimeraX session  

> cartoon style width 3

> cartoon style thickness 0.4

> save "./FAM115A M60-like highlight.cxs"

opened ChimeraX session  

> open "/Users/shibata.y/OneDrive - wehi.edu.au/FAM115A
> paper/Data/Structures/M60-like/Bacterial M60/ZmpB/5KDN M60-like/5kdn.pdb"

5kdn.pdb title:  
ZMPB metallopeptidase from clostridium perfringens [more info...]  
  
Chain information for 5kdn.pdb #2  
---  
Chain | Description  
A | metallopeptidase  
  
Non-standard residues in 5kdn.pdb #2  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
ZN — zinc ion  
  

> Load FAM115A M60-like hi light

Unknown command: Load FAM115A M60-like hi light  

> Load 5kdn pdb

Unknown command: Load 5kdn pdb  

> hide #2 atoms

> show :ZN

> show #2 :756, 757, 760, 771 atoms

> color #2 /A medium purple

> select O

2712 atoms, 2086 residues, 2 models selected  

> color sel crimson

> select N

1742 atoms, 1290 residues, 2 models selected  

> color sel medium blue

> select S

42 atoms, 42 residues, 2 models selected  

> color sel gold

> color #2 /A medium purple target c

> color #2 /A dim gray target p

> color :ZN gray

> select #1 /A:753-763

174 atoms, 177 bonds, 11 residues, 1 model selected  

> color sel salmon

> select #1 /A:527-636

1669 atoms, 1686 bonds, 110 residues, 1 model selected  

> color sel khaki

> cartoon style width 3

> cartoon style thickness 0.4

> hide #2 atoms

> show :ZN

> show #2 :756, 757, 760, 771 atoms

> color #2 /A medium purple

> select O

2712 atoms, 2086 residues, 2 models selected  

> color sel crimson

> select N

1742 atoms, 1290 residues, 2 models selected  

> color sel medium blue

> select S

42 atoms, 42 residues, 2 models selected  

> color sel gold

> color #2 /A medium purple target c

> color #2 /A dim gray target p

> color :ZN gray

> color #1 cadet blue

> select #1 /A:753-763

174 atoms, 177 bonds, 11 residues, 1 model selected  

> color sel salmon

> select #1 /A:527-636

1669 atoms, 1686 bonds, 110 residues, 1 model selected  

> color sel khaki

> cartoon style width 3

> cartoon style thickness 0.44

> hide #2 atoms

> show :ZN

> show #2 :756, 757, 760, 771 atoms

> color #2 /A navy

> select O

2712 atoms, 2086 residues, 2 models selected  

> color sel crimson

> select N

1742 atoms, 1290 residues, 2 models selected  

> color sel medium blue

> select S

42 atoms, 42 residues, 2 models selected  

> color sel gold

> color #2 /A navy target c

> color #2 /A dim gray target p

> color :ZN gray

> color #1 cadet blue

> select #1 /A:753-763

174 atoms, 177 bonds, 11 residues, 1 model selected  

> color sel salmon

> select #1 /A:527-636

1669 atoms, 1686 bonds, 110 residues, 1 model selected  

> color sel khaki

> cartoon style width 3

> cartoon style thickness 0.4

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> matchmaker #2 to sel

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 SeMet_FAM115A_M60_refine_120-coot-8.pdb, chain A (#1) with
5kdn.pdb, chain A (#2), sequence alignment score = 190.4  
RMSD between 60 pruned atom pairs is 1.144 angstroms; (across all 160 pairs:
6.058)  
  

> select #1

12536 atoms, 12551 bonds, 952 residues, 1 model selected  

> ~select #1

Nothing selected  

> save /Users/shibata.y/Desktop/image2.png supersample 3

> save "/Users/shibata.y/OneDrive - wehi.edu.au/FAM115A
> paper/Data/Structures/M60-like/Figures/FAM115A M60_5kdn.cxs"

opened ChimeraX session  

> hide #!2 models

> open /Users/yurishibata/Downloads/4rkk.pdb

4rkk.pdb title:  
Structure of A product bound phosphatase [more info...]  
  
Chain information for 4rkk.pdb #3  
---  
Chain | Description  
A C | laforin  
  
Non-standard residues in 4rkk.pdb #3  
---  
GLC — α-D-glucopyranose  
PO4 — phosphate ion  
  

> ui tool show Matchmaker

> matchmaker #1 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 4rkk.pdb, chain A (#3) with
SeMet_FAM115A_M60_refine_120-coot-8.pdb, chain A (#1), sequence alignment
score = 107.3  
RMSD between 9 pruned atom pairs is 1.557 angstroms; (across all 262 pairs:
28.466)  
  

> ui tool show Matchmaker

> matchmaker #1 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 4rkk.pdb, chain A (#3) with
SeMet_FAM115A_M60_refine_120-coot-8.pdb, chain A (#1), sequence alignment
score = 107.3  
RMSD between 9 pruned atom pairs is 1.557 angstroms; (across all 262 pairs:
28.466)  
  

> ui tool show Matchmaker

> matchmaker #!3 to #1

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 SeMet_FAM115A_M60_refine_120-coot-8.pdb, chain A (#1) with
4rkk.pdb, chain A (#3), sequence alignment score = 107.3  
RMSD between 9 pruned atom pairs is 1.557 angstroms; (across all 262 pairs:
28.466)  
  

> hide #!3 models

> show #!3 models

> ui tool show Matchmaker

> matchmaker #!2-3 to #1/A pairing bs

Parameters  
---  
Chain pairing | bs  
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 SeMet_FAM115A_M60_refine_120-coot-8.pdb, chain A (#1) with
5kdn.pdb, chain A (#2), sequence alignment score = 328.7  
RMSD between 90 pruned atom pairs is 1.317 angstroms; (across all 350 pairs:
7.771)  
  
Matchmaker SeMet_FAM115A_M60_refine_120-coot-8.pdb, chain A (#1) with
4rkk.pdb, chain A (#3), sequence alignment score = 107.3  
RMSD between 9 pruned atom pairs is 1.557 angstroms; (across all 262 pairs:
28.466)  
  

> ui tool show Matchmaker

> matchmaker #3/A to #1/A pairing ss

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 SeMet_FAM115A_M60_refine_120-coot-8.pdb, chain A (#1) with
4rkk.pdb, chain A (#3), sequence alignment score = 107.3  
RMSD between 9 pruned atom pairs is 1.557 angstroms; (across all 262 pairs:
28.466)  
  
Traceback (most recent call last):  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File
"/private/var/folders/1w/mrn_sv4501794v6__7sx74c00000gn/T/AppTranslocation/3C5F95CC-2C0F-4CB0-A13F-5189E527EC1A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
      OS Loader Version: 540.120.3~22

Software:

    System Software Overview:

      System Version: macOS 12.6.3 (21G419)
      Kernel Version: Darwin 21.6.0
      Time since boot: 11 days 9:49

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: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5300M:

      Chipset Model: AMD Radeon Pro 5300M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0043
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32207P1-019
      Option ROM Version: 113-D32207P1-019
      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

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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: 0.29.20
    decorator: 4.4.2
    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: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Structure Comparison
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted

comment:2 by Eric Pettersen, 3 years ago

Resolution: → duplicate
Status: accepted → closed
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