Opened 4 years ago

Closed 4 years ago

#4769 closed defect (duplicate)

MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted

Reported by: chimerax-bug-report@… Owned by: pett
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:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2 (2021-04-27 05:33:30 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2 (2021-04-27)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed MolecularDynamicsViewer-1.2  
Installed MolecularDynamicsViewer (1.2)  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2217, in float_changed  
self.main_window._float_changed(self.tool_window, floating)  
AttributeError: 'NoneType' object has no attribute '_float_changed'  
  
AttributeError: 'NoneType' object has no attribute '_float_changed'  
  
File
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2217, in float_changed  
self.main_window._float_changed(self.tool_window, floating)  
  
See log for complete Python traceback.  
  

> open /Users/yuliia/Desktop/Yuliia/200319_phLUZ/Tail.pdb

Chain information for Tail.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L | No description available  
M N O P Q R S T U V W X | No description available  
Y Z a b c d | No description available  
  

> select #A-Z,a-d

Expected an objects specifier or a keyword  

> select #J

Expected an objects specifier or a keyword  

> select #1/J

1055 atoms, 1078 bonds, 159 residues, 1 model selected  

> select ~sel

76495 atoms, 77624 bonds, 84 pseudobonds, 12051 residues, 2 models selected  

> hide sel atoms

> select #1/J

1055 atoms, 1078 bonds, 159 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> set bgColor white

> view

> select #1

77550 atoms, 78702 bonds, 84 pseudobonds, 12210 residues, 2 models selected  

> ~select #1

Nothing selected  

> view

> select #1/J

1055 atoms, 1078 bonds, 159 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel #2332a4ff

> lighting flat

> color sel #2331a4ff

> color sel #2238a4ff

> color sel #2239a4ff

> color sel #253da4ff

> color sel #2b46a4ff

> color sel #3251a4ff

> color sel #3656a4ff

> color sel #385aa4ff

> color sel #3a5da4ff

> color sel #3a5ea4ff

> color sel #3b5ea4ff

> color sel #3c61a4ff

> color sel #4065a4ff

> color sel #4167a4ff

> color sel #4268a4ff

> color sel #4369a4ff

> color sel #4469a4ff

> color sel #4369a4ff

> color sel #4368a4ff

> color sel #4368a4ff

> color sel #4368a4ff

> color sel #4367a4ff

> select #1

77550 atoms, 78702 bonds, 84 pseudobonds, 12210 residues, 2 models selected  

> ~select #1

Nothing selected  

> select #1/J:165-184

159 atoms, 161 bonds, 20 residues, 1 model selected  

> color sel #2432a5ff

> color sel #2431a5ff

> color sel #2331a5ff

> color sel #2230a0ff

> color sel #222f9cff

> color sel #212e9aff

> color sel #202d96ff

> color sel #1f2b90ff

> color sel #1e298aff

> color sel #1d2885ff

> color sel #1c2781ff

> color sel #1b2680ff

> color sel #1a257bff

> color sel #182270ff

> color sel #17206dff

> color sel #17206cff

> color sel #17206cff

> color sel #17206cff

> color sel #17206bff

> color sel #17206bff

> color sel #17206aff

> color sel #161f68ff

> color sel #161f68ff

> color sel #161f67ff

> color sel #161f67ff

> color sel #161f67ff

> color sel #161f68ff

> color sel #171f69ff

> color sel #17206aff

> color sel #17206aff

> color sel #17206cff

> color sel #17206cff

> color sel #17206cff

> color sel #17206cff

> color sel #17216dff

> color sel #17216dff

> color sel #18216eff

> color sel #18216eff

> color sel #18216eff

> select #1/J:51-110

445 atoms, 459 bonds, 60 residues, 1 model selected  

> color sel cornflower blue

> select #1

77550 atoms, 78702 bonds, 84 pseudobonds, 12210 residues, 2 models selected  

> ~select #1

Nothing selected  

> select #1/J:51-110

445 atoms, 459 bonds, 60 residues, 1 model selected  

> color sel #74adffff

> color sel #74b5ffff

> color sel #74b5ffff

> color sel #75b6ffff

> color sel #75b6ffff

> color sel #75b7ffff

> color sel #76b8ffff

> color sel #77baffff

> color sel #78bcffff

> color sel #79beffff

> color sel #79bfffff

> color sel #7ac0ffff

> color sel #7ac1ffff

> color sel #7ac1ffff

> color sel #7ac2ffff

> color sel #7ac2ffff

> color sel #7bc2ffff

> color sel #7bc3ffff

> color sel #7bc3ffff

> color sel #7bc4ffff

> color sel #7bc4ffff

> color sel #7cc5ffff

> color sel #7cc6ffff

> color sel #7cc7ffff

> color sel #7dc8ffff

> color sel #7dc8ffff

> color sel #7dc9ffff

> color sel #7dc9ffff

> color sel #7ec9ffff

> color sel #7ecaffff

> color sel #7ecaffff

> color sel #7ecbffff

> color sel #7dcbffff

> color sel #7dcbffff

> color sel #7dcbffff

> color sel #7dcbffff

> select #1

77550 atoms, 78702 bonds, 84 pseudobonds, 12210 residues, 2 models selected  

> ~select #1

Nothing selected  

> select #1/J:165-184

159 atoms, 161 bonds, 20 residues, 1 model selected  

> color sel #2332a4ff

> color sel #2331a4ff

> color sel #2331a4ff

> color sel #2332a6ff

> color sel #2433a8ff

> color sel #2433a9ff

> color sel #2433a9ff

> color sel #2433aaff

> color sel #2434acff

> color sel #2534aeff

> color sel #2535afff

> color sel #2535afff

> color sel #2535b0ff

> color sel #2535b1ff

> color sel #2636b3ff

> color sel #2636b4ff

> color sel #2636b4ff

> color sel #2636b5ff

> color sel #2637b6ff

> color sel #2737b6ff

> color sel #2737b7ff

> color sel #2737b7ff

> color sel #2737b8ff

> color sel #2738bbff

> color sel #2839bdff

> color sel #2839bdff

> color sel #2839bdff

> color sel #2839bdff

> color sel #2839beff

> color sel #2839beff

> color sel #2839beff

> color sel #2839beff

> color sel #2839bfff

> color sel #283ac0ff

> color sel #293ac0ff

> color sel #293ac1ff

> color sel #2a3bc6ff

> color sel #2a3cc8ff

> color sel #2a3cc8ff

> color sel #2a3cc8ff

> color sel #303ec8ff

> color sel #303ec8ff

> color sel #303ec8ff

> color sel #313ec8ff

> color sel #343dc8ff

> color sel #383dc8ff

> color sel #3c3ec8ff

> color sel #403fc8ff

> color sel #4340c8ff

> color sel #4641c8ff

> color sel #4742c8ff

> color sel #4842c8ff

> color sel #4942c8ff

> color sel #4a43c8ff

> color sel #4a43c8ff

> color sel #4b43c8ff

> color sel #4d44c8ff

> color sel #5045c8ff

> color sel #5246c8ff

> color sel #5447c8ff

> color sel #5648c8ff

> color sel #5748c8ff

> color sel #5848c8ff

> color sel #5849c8ff

> color sel #5949c8ff

> color sel #5949c8ff

> color sel #5a49c8ff

> color sel #5a49c8ff

> color sel #5a49c8ff

> color sel #5a49c8ff

> color sel #5a48c8ff

> color sel #5a48c8ff

> color sel #5a47c8ff

> color sel #5a46c8ff

> color sel #5a46c8ff

> color sel #5a45c8ff

> color sel #5a45c8ff

> color sel #5a45c8ff

> color sel #5b45c8ff

> color sel #5b45c8ff

> color sel #5b45c8ff

> color sel #5c46c8ff

> color sel #5c46c8ff

> color sel #5d47c8ff

> color sel #5e48c8ff

> color sel #5f49c8ff

> color sel #604ac8ff

> color sel #604ac8ff

> color sel #604ac8ff

> color sel #624ec8ff

> color sel #6453c8ff

> color sel #6657c8ff

> color sel #675ac8ff

> color sel #685cc8ff

> color sel #695cc8ff

> color sel #685cc8ff

> color sel #685cc8ff

> color sel #665ac8ff

> color sel #6459c8ff

> color sel #6157c8ff

> color sel #5e55c8ff

> color sel #5952c8ff

> color sel #5650c8ff

> color sel #534ec8ff

> color sel #514dc8ff

> color sel #504dc8ff

> color sel #4f4dc8ff

> color sel #4e4cc8ff

> color sel #4d4cc8ff

> color sel #4c4cc8ff

> color sel #4c4bc8ff

> color sel #4b4bc8ff

> color sel #4b4bc8ff

> color sel #4a4cc8ff

> color sel #4a4cc8ff

> color sel #494cc8ff

> color sel #484cc8ff

> color sel #474ac8ff

> color sel #4549c8ff

> color sel #4246c8ff

> color sel #3f43c8ff

> color sel #3b3fc8ff

> color sel #3538c8ff

> color sel #2f30c8ff

> color sel #2a29c8ff

> color sel #2826c8ff

> color sel #2723c8ff

> color sel #2722c8ff

> color sel #2622c8ff

> color sel #2823c8ff

> color sel #2a23c8ff

> color sel #2c24c8ff

> color sel #2f25c8ff

> color sel #3226c8ff

> color sel #3527c8ff

> color sel #3828c8ff

> color sel #3b29c8ff

> color sel #3f2ac8ff

> color sel #412bc8ff

> color sel #432bc8ff

> color sel #452cc8ff

> color sel #462cc8ff

> color sel #472dc8ff

> color sel #482dc8ff

> color sel #492dc8ff

> color sel #4a2dc8ff

> color sel #4a2dc8ff

> color sel #4a2dc8ff

> color sel #4a2dc8ff

> color sel #4a2cc8ff

> color sel #4a2ac8ff

> color sel #4a28c8ff

> color sel #4925c8ff

> color sel #4822c8ff

> color sel #471fc8ff

> color sel #471cc8ff

> color sel #461ac8ff

> color sel #4519c8ff

> color sel #4518c8ff

> color sel #4517c8ff

> color sel #4417c8ff

> color sel #4416c8ff

> color sel #4415c8ff

> color sel #4314c8ff

> color sel #4314c8ff

> color sel #4313c8ff

> color sel #4212c8ff

> color sel #4112c8ff

> color sel #4011c8ff

> color sel #3f10c8ff

> color sel #3f10c8ff

> color sel #3e0fc8ff

> color sel #3d0fc8ff

> color sel #3d0fc8ff

> color sel #3d0fc8ff

> color sel #3c0fc8ff

> color sel #3a0ec8ff

> color sel #390ec8ff

> color sel #380ec8ff

> color sel #370ec8ff

> color sel #360dc8ff

> color sel #360dc8ff

> color sel #350dc8ff

> color sel #340dc8ff

> color sel #330dc8ff

> color sel #330cc8ff

> color sel #320cc8ff

> color sel #320cc8ff

> color sel #310cc8ff

> color sel #310cc8ff

> color sel #310cc8ff

> color sel #300cc8ff

> color sel #300cc8ff

> color sel #2f0bc8ff

> color sel #2e0bc8ff

> color sel #2d0bc8ff

> color sel #2d0bc8ff

> color sel #2d0bc8ff

> color sel #2c0bc8ff

> color sel #2c0bc8ff

> color sel #2c0cc8ff

> color sel #2c0cc8ff

> color sel #2c0dc8ff

> color sel #2c0ec8ff

> color sel #2d0fc8ff

> color sel #2d10c8ff

> color sel #2d10c8ff

> color sel #2d11c8ff

> color sel #2d12c8ff

> color sel #2e13c8ff

> color sel #2d13c8ff

> color sel #2d13c8ff

> color sel #2e13c9ff

> color sel #2f14d0ff

> color sel #3014d5ff

> color sel #3014d5ff

> color sel #3014d5ff

> color sel #3014d4ff

> color sel #3014d4ff

> color sel #3014d4ff

> color sel #3014d4ff

> color sel #3014d3ff

> select #1

77550 atoms, 78702 bonds, 84 pseudobonds, 12210 residues, 2 models selected  

> ~select #1

Nothing selected  

> select #1/J:51-110

445 atoms, 459 bonds, 60 residues, 1 model selected  

> color sel #3718d3ff

> color sel #3819d3ff

> color sel #381ad3ff

> color sel #3a1ed3ff

> color sel #3c22d3ff

> color sel #3e26d3ff

> color sel #412cd3ff

> color sel #4434d3ff

> color sel #4739d3ff

> color sel #4a3fd3ff

> color sel #4c43d3ff

> color sel #4e47d3ff

> color sel #504cd3ff

> color sel #5352d3ff

> color sel #585bd3ff

> color sel #5e64d3ff

> color sel #646ed3ff

> color sel #6876d3ff

> color sel #6d7ed3ff

> color sel #7084d3ff

> color sel #738bd3ff

> color sel #7693d3ff

> color sel #7898d3ff

> color sel #7a9dd3ff

> color sel #7aa0d3ff

> color sel #7ba2d3ff

> color sel #7ba3d3ff

> color sel #7aa4d3ff

> color sel #79a4d3ff

> color sel #78a4d3ff

> color sel #77a4d3ff

> color sel #75a4d3ff

> color sel #73a3d3ff

> color sel #71a4d3ff

> color sel #6ea4d3ff

> color sel #6aa4d3ff

> color sel #67a4d3ff

> color sel #64a4d3ff

> color sel #63a4d3ff

> color sel #63a4d3ff

> color sel #63a5d3ff

> color sel #63a5d3ff

> color sel #64a6d3ff

> color sel #64a6d3ff

> color sel #64a6d3ff

> color sel #67afd3ff

> color sel #67afd3ff

> color sel #67afd3ff

> color sel #68afd3ff

> color sel #69afd3ff

> color sel #6aafd3ff

> color sel #6aafd3ff

> color sel #6aafd3ff

> color sel #6bafd3ff

> color sel #6bafd3ff

> color sel #6bafd3ff

> color sel #6bafd3ff

> color sel #6aadd3ff

> color sel #69aad3ff

> color sel #66a4d3ff

> color sel #619ed3ff

> color sel #5c99d3ff

> color sel #5694d3ff

> color sel #5191d3ff

> color sel #4e90d3ff

> color sel #4a8fd3ff

> color sel #478fd3ff

> color sel #448fd3ff

> color sel #418fd3ff

> color sel #418fd3ff

> color sel #408fd3ff

> color sel #408fd3ff

> color sel #408fd3ff

> color sel #3f8ed3ff

> color sel #3e8bd3ff

> color sel #3b88d3ff

> color sel #3783d3ff

> color sel #347fd3ff

> color sel #317bd3ff

> color sel #3079d3ff

> color sel #2f78d3ff

> color sel #2f77d3ff

> color sel #2e77d3ff

> color sel #2e77d3ff

> color sel #2e77d3ff

> color sel #2d77d3ff

> color sel #2d77d3ff

> color sel #2d77d3ff

> color sel #2c77d3ff

> color sel #2c77d3ff

> select #1

77550 atoms, 78702 bonds, 84 pseudobonds, 12210 residues, 2 models selected  

> ~select #1

Nothing selected  

> select #1/J

1055 atoms, 1078 bonds, 159 residues, 1 model selected  

> color sel cornflower blue

> select #1/J:165-184

159 atoms, 161 bonds, 20 residues, 1 model selected  

> color sel #2432a6ff

> select #1/J:51-110

445 atoms, 459 bonds, 60 residues, 1 model selected  

> color sel #2634a6ff

> color sel #2634a6ff

> color sel #2635a6ff

> color sel #2838a6ff

> color sel #2a3aa6ff

> color sel #2c3da6ff

> color sel #2d3fa6ff

> color sel #2f41a6ff

> color sel #3043a6ff

> color sel #3144a6ff

> color sel #3245a6ff

> color sel #3448a6ff

> color sel #364aa6ff

> color sel #374ba6ff

> color sel #394ca6ff

> color sel #394ca6ff

> color sel #394da6ff

> color sel #3b4ea6ff

> color sel #3c50a6ff

> color sel #3e53a6ff

> color sel #4156a6ff

> color sel #4358a6ff

> color sel #4459a6ff

> color sel #455aa6ff

> color sel #465ba6ff

> color sel #475da6ff

> color sel #495ea6ff

> color sel #4b60a6ff

> color sel #4d63a6ff

> color sel #4f66a6ff

> color sel #5169a6ff

> color sel #546da6ff

> color sel #5670a6ff

> color sel #5874a6ff

> color sel #5a77a6ff

> color sel #5b7aa6ff

> color sel #5c7ca6ff

> color sel #5d7da6ff

> color sel #5d7fa6ff

> color sel #5d80a6ff

> color sel #5d82a6ff

> color sel #5e84a6ff

> color sel #5f87a6ff

> color sel #5f8aa6ff

> color sel #608da6ff

> color sel #608fa6ff

> color sel #6190a6ff

> color sel #6192a6ff

> color sel #6192a6ff

> color sel #6293a6ff

> color sel #6294a6ff

> color sel #6295a6ff

> color sel #6396a6ff

> color sel #6397a6ff

> color sel #6398a6ff

> color sel #6398a6ff

> color sel #6398a6ff

> color sel #6399a6ff

> color sel #639aa6ff

> color sel #639ba6ff

> color sel #649ca6ff

> color sel #659ea6ff

> color sel #659fa6ff

> color sel #66a0a6ff

> color sel #67a2a6ff

> color sel #67a4a6ff

> color sel #68a6a6ff

> color sel #69a6a4ff

> color sel #69a6a1ff

> color sel #69a6a0ff

> color sel #69a69eff

> color sel #69a69dff

> color sel #69a69bff

> color sel #69a69bff

> color sel #69a69aff

> color sel #69a69bff

> color sel #69a69bff

> color sel #69a69cff

> color sel #69a69cff

> color sel #69a69dff

> color sel #69a69eff

> color sel #6aa69fff

> color sel #6aa6a0ff

> color sel #6aa6a2ff

> color sel #6aa6a3ff

> color sel #6aa6a5ff

> color sel #6aa6a5ff

> color sel #6aa5a6ff

> color sel #6aa4a6ff

> color sel #6aa4a6ff

> color sel #6aa3a6ff

> color sel #6aa3a6ff

> color sel #6aa2a6ff

> color sel #6aa2a6ff

> color sel #6aa1a6ff

> color sel #6aa0a6ff

> color sel #6a9fa6ff

> color sel #6a9ea6ff

> color sel #6a9ea6ff

> color sel #6a9da6ff

> color sel #699aa6ff

> color sel #6998a6ff

> color sel #6895a6ff

> color sel #6790a6ff

> color sel #668ca6ff

> color sel #6487a6ff

> color sel #6282a6ff

> color sel #607ea6ff

> color sel #5f7ba6ff

> color sel #5e78a6ff

> color sel #5c76a6ff

> color sel #5b74a6ff

> color sel #5b73a6ff

> color sel #5a72a6ff

> color sel #5a71a6ff

> color sel #5970a6ff

> color sel #5970a6ff

> color sel #5970a6ff

> color sel #596fa6ff

> color sel #596fa6ff

> color sel #596fa6ff

> color sel #5a6fa6ff

> color sel #5a6fa6ff

> color sel #5a6fa6ff

> color sel #5a6fa6ff

> color sel #5b6fa6ff

> color sel #5b6fa6ff

> color sel #5b6fa6ff

> color sel #5c6fa6ff

> color sel #5c6fa6ff

> color sel #5c6fa6ff

> color sel #5d6fa6ff

> color sel #5d6fa6ff

> color sel #5d6fa6ff

> color sel #5d6fa6ff

> color sel #5d6ea6ff

> color sel #5d6ea6ff

> color sel #5d6ea6ff

> color sel #5d6da6ff

> color sel #5d6da6ff

> color sel #5d6da6ff

> color sel #5d6ea6ff

> select #1

77550 atoms, 78702 bonds, 84 pseudobonds, 12210 residues, 2 models selected  

> ~select #1

Nothing selected  

> save /Users/yuliia/Desktop/image153.png supersample 3

> turn y 180

> save /Users/yuliia/Desktop/image154.png supersample 3

> select #1

77550 atoms, 78702 bonds, 84 pseudobonds, 12210 residues, 2 models selected  

> close #1

> open /Users/yuliia/Documents/Documents_off/Building/gp32/mcp_hexamer.pdb
> format pdb

Chain information for mcp_hexamer.pdb #1  
---  
Chain | Description  
A B C D F | No description available  
E | No description available  
  

> select #1/A

2643 atoms, 2692 bonds, 333 residues, 1 model selected  

> select ~sel

13210 atoms, 13455 bonds, 1664 residues, 1 model selected  

> hide sel atoms

> select #1/A

2643 atoms, 2692 bonds, 333 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> view

> close

> open /Users/yuliia/Documents/Documents_off/Building/gp32/mcp_chain_A.pdb

Chain information for mcp_chain_A.pdb #1  
---  
Chain | Description  
A | No description available  
  

> lighting flat

> rainbow

> save /Users/yuliia/Desktop/image155.png supersample 3

> close

> open
> /Users/yuliia/Desktop/Yuliia/sp_adapterNozzle/ref_post_automask3_zone_nozzle_monomer.mrc

Opened ref_post_automask3_zone_nozzle_monomer.mrc as #1, grid size 55,82,159,
pixel 1.06,1.06,1.06, shown at level 0.0802, step 1, values float32  

> volume #1 level 0.04825

> close #1

> open
> /Users/yuliia/Desktop/Yuliia/sp_adapterNozzle/ref_post_automask3_zone_nozzle.mrc

Opened ref_post_automask3_zone_nozzle.mrc as #1, grid size 159,148,159, pixel
1.06,1.06,1.06, shown at level 0.0828, step 1, values float32  

> open /Users/yuliia/Desktop/Yuliia/200319_phLUZ/Tail.pdb

Chain information for Tail.pdb #2  
---  
Chain | Description  
A B C D E F G H I J K L | No description available  
M N O P Q R S T U V W X | No description available  
Y Z a b c d | No description available  
  

> close #1

> close

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2149, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 620, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.toolshed_utils.tool.UpdateTool object at 0x7fc47a9379d0>  
  
KeyError:  
  
File
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 620, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  

> open /Users/yuliia/Downloads/3j7w.pdb

3j7w.pdb title:  
Capsid expansion mechanism of bacteriophage T7 revealed by multi-state atomic
models derived from cryo-em reconstructions [more info...]  
  
Chain information for 3j7w.pdb #1  
---  
Chain | Description  
A B C D E F G | major capsid protein 10A  
  

> open
> /Users/yuliia/Documents/Documents_off/Building/gp32/mcp_asym_unit_2xgp48_1xgp47.pdb
> format pdb

Chain information for mcp_asym_unit_2xgp48_1xgp47.pdb #2  
---  
Chain | Description  
A B C D F | No description available  
E | No description available  
G | No description available  
H I J K | No description available  
L M | No description available  
  

> ui tool show Matchmaker

> matchmaker #2/G to #1/G 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 3j7w.pdb, chain G (#1) with mcp_asym_unit_2xgp48_1xgp47.pdb, chain
G (#2), sequence alignment score = 322.7  
RMSD between 147 pruned atom pairs is 1.235 angstroms; (across all 314 pairs:
4.263)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 Metal - 71.0.7
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Processor Name: Unknown
      Processor Speed: 2,4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 4 MB
      Memory: 8 GB

Software:

    System Software Overview:

      System Version: macOS 11.2.3 (20D91)
      Kernel Version: Darwin 20.3.0
      Time since boot: 11 days 1:24

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

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: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    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: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.2
    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: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2
    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: 1.1.1
    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: 2.1
    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
    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
    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: 1.7.3
    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: 5.0.7
    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: 1.1.1
    matplotlib: 3.3.2
    MolecularDynamicsViewer: 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: 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: 2020.9.3
    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

Change History (2)

comment:1 by pett, 4 years ago

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

comment:2 by pett, 4 years ago

Resolution: → duplicate
Status: accepted → closed
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