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

[fzyzz180409@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
When I am trying to run a matchmaker alignment between two specific chains (chain A of model 1 and chain E of model 2) of two models, an error processing as:
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted

File "D:\Chimera\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "D:/learning/Imperial College London/Project 1/Structures/Protein
> Structure/ATR-Mec1 Alignment.cxs"

Log from Wed Jan 13 17:09:00 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:/learning/Imperial College London/Project 1/Structures/Protein
> Structure/Activated Mec1-Ddc2 (F2244L_StateII).pdb"

Summary of feedback from opening D:/learning/Imperial College London/Project
1/Structures/Protein Structure/Activated Mec1-Ddc2 (F2244L_StateII).pdb  
---  
warnings | Ignored bad PDB record found on line 20  
  
  
Ignored bad PDB record found on line 21  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 22  
BOND : 0.007 0.090 47552  
  
Ignored bad PDB record found on line 23  
ANGLE : 1.075 16.637 64388  
  
Ignored bad PDB record found on line 24  
CHIRALITY : 0.061 0.344 7382  
  
17 messages similar to the above omitted  
  
Chain information for Activated Mec1-Ddc2 (F2244L_StateII).pdb #1  
---  
Chain | Description  
C D | No description available  
E F | No description available  
  

> open "D:/learning/Imperial College London/Project 1/Structures/Protein
> Structure/ATR-ATRIP Complex.pdb"

ATR-ATRIP Complex.pdb title:  
Cryo-em structure of human atr-atrip complex [more info...]  
  
Chain information for ATR-ATRIP Complex.pdb #2  
---  
Chain | Description  
A B | serine/threonine-protein kinase atr  
C D | ATM AND RAD3-related-interacting protein  
  

> ui tool show Matchmaker

> matchmaker #1/E & sel to #2/A & sel pairing ss

No 'to' chains specified  

> close #2

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select /E

18692 atoms, 19078 bonds, 12 pseudobonds, 2325 residues, 2 models selected  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> delete ~sel

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select clear

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> open "D:/learning/Imperial College London/Project 1/Structures/Protein
> Structure/ATR-ATRIP Complex.pdb"

ATR-ATRIP Complex.pdb title:  
Cryo-em structure of human atr-atrip complex [more info...]  
  
Chain information for ATR-ATRIP Complex.pdb #2  
---  
Chain | Description  
A B | serine/threonine-protein kinase atr  
C D | ATM AND RAD3-related-interacting protein  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select #2

33371 atoms, 33739 bonds, 32 pseudobonds, 5404 residues, 2 models selected  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A #2/B

Alignment identifier is 1  

> select /A

15007 atoms, 15192 bonds, 16 pseudobonds, 2362 residues, 2 models selected  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select /B

15007 atoms, 15192 bonds, 16 pseudobonds, 2362 residues, 2 models selected  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> delete ~sel

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Undo failed, probably because structures have been modified.  

> select clear

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> open "D:/learning/Imperial College London/Project 1/Structures/Protein
> Structure/Activated Mec1-Ddc2 (F2244L_StateII).pdb"

Summary of feedback from opening D:/learning/Imperial College London/Project
1/Structures/Protein Structure/Activated Mec1-Ddc2 (F2244L_StateII).pdb  
---  
warnings | Ignored bad PDB record found on line 20  
  
  
Ignored bad PDB record found on line 21  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 22  
BOND : 0.007 0.090 47552  
  
Ignored bad PDB record found on line 23  
ANGLE : 1.075 16.637 64388  
  
Ignored bad PDB record found on line 24  
CHIRALITY : 0.061 0.344 7382  
  
17 messages similar to the above omitted  
  
Chain information for Activated Mec1-Ddc2 (F2244L_StateII).pdb #1  
---  
Chain | Description  
C D | No description available  
E F | No description available  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select #1 /E

18692 atoms, 19078 bonds, 12 pseudobonds, 2325 residues, 2 models selected  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select #1 /E & #2

Nothing selected  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select /e & /a

Nothing selected  

> select #1 /A, #2

Expected a keyword  

> select #1 /A & #2

Nothing selected  

> select #1 /E & #2

Nothing selected  

> select #1 /E, #2

Expected a keyword  

> select #1 /E

18692 atoms, 19078 bonds, 12 pseudobonds, 2325 residues, 2 models selected  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> ui tool show "Show Sequence Viewer"

> select #1 /C&/D&/F

Nothing selected  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select #1 /C,/D,/F

Expected a keyword  

> select #1 /C, /D, /F

Expected a keyword  

> select #1 /C & /D & /F

Nothing selected  

> select #1 /C & #1 /D & #1 /F

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/E #1/F

Alignment identifier is 1  

> sequence chain #1/C #1/D

Alignment identifier is 2  

> delete /c

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> delete /d

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> delete /f

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select clear

Drag select of 1 atoms  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Drag select of 33 atoms, 33 bonds  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Drag select of 34 atoms, 33 bonds  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> delete sel

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select #1/B:2@MG

1 atom, 1 residue, 1 model selected  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select up

4 atoms, 1 bond, 3 residues, 1 model selected  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select up

33 atoms, 33 bonds, 3 residues, 1 model selected  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> delete sel

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select #1/Z:3@ZN

1 atom, 1 residue, 1 model selected  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> delete sel

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> ui tool show Matchmaker

> matchmaker #1/E to #2/B 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 ATR-ATRIP Complex.pdb, chain B (#2) with Activated Mec1-Ddc2
(F2244L_StateII).pdb, chain E (#1), sequence alignment score = 2040.7  
RMSD between 311 pruned atom pairs is 1.219 angstroms; (across all 1933 pairs:
31.172)  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/E

Alignment identifier is 1/E  

> sequence chain #2/B

Alignment identifier is 2/B  

> show surfaces

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> hide surfaces

> view matrix camera
> 0.61031,-0.69322,0.38336,211.73,0.1209,0.55978,0.81977,276.88,-0.7829,-0.45396,0.42544,158.1

> save "D:/learning/Imperial College London/Project 1/Structures/Protein
> Structure/ATR-Mec1 Alignment.cxs"

> close session

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> open "D:/learning/Imperial College London/Project 1/Structures/Protein
> Structure/ATR-ATRIP Complex.pdb"

ATR-ATRIP Complex.pdb title:  
Cryo-em structure of human atr-atrip complex [more info...]  
  
Chain information for ATR-ATRIP Complex.pdb #1  
---  
Chain | Description  
A B | serine/threonine-protein kinase atr  
C D | ATM AND RAD3-related-interacting protein  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> ui tool show "Show Sequence Viewer"

> select /a :1521-2644

8565 atoms, 8752 bonds, 12 pseudobonds, 1065 residues, 2 models selected  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> delete ~sel

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select clear

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> open "D:/learning/Imperial College London/Project 1/Structures/Protein
> Structure/Kinase Domain with AMP-PNP with Mg.pdb"

Summary of feedback from opening D:/learning/Imperial College London/Project
1/Structures/Protein Structure/Kinase Domain with AMP-PNP with Mg.pdb  
---  
warnings | Ignored bad PDB record found on line 46  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 47  
MOLPROBITY STATISTICS.  
  
Ignored bad PDB record found on line 3248  
END  
  
Chain information for Kinase Domain with AMP-PNP with Mg.pdb #2  
---  
Chain | Description  
E | No description available  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> ui tool show Matchmaker

> matchmaker #2/E 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 ATR-ATRIP Complex.pdb, chain A (#1) with Kinase Domain with AMP-PNP
with Mg.pdb, chain E (#2), sequence alignment score = 811.7  
RMSD between 247 pruned atom pairs is 1.072 angstroms; (across all 377 pairs:
5.029)  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> view matrix camera
> 0.61031,-0.69322,0.38336,211.73,0.1209,0.55978,0.81977,276.88,-0.7829,-0.45396,0.42544,158.1

> save "D:/learning/Imperial College London/Project 1/Structures/Protein
> Structure/ATR-Mec1 Alignment.cxs"

opened ChimeraX session  

> select #2/E:2313

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

24 atoms, 23 bonds, 3 residues, 1 model selected  

> select up

3090 atoms, 3152 bonds, 388 residues, 1 model selected  

> select down

24 atoms, 23 bonds, 3 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #2/E

Alignment identifier is 2/E  

> name sel PRD-I-Mec1

"sel" is reserved and cannot be redefined  

> name sel PRD-I-Mec1

"sel" is reserved and cannot be redefined  

> color sel purple

> select clear

> select #1/A:2586

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel purple

> select clear

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color sel orchid

> select clear

> select clear

> select #1/A:2380

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

> select clear

> ui tool show Matchmaker

> close session

> open "D:/learning/Imperial College London/Project 1/Structures/Protein
> Structure/ATR-ATRIP Complex.pdb"

ATR-ATRIP Complex.pdb title:  
Cryo-em structure of human atr-atrip complex [more info...]  
  
Chain information for ATR-ATRIP Complex.pdb #1  
---  
Chain | Description  
A B | serine/threonine-protein kinase atr  
C D | ATM AND RAD3-related-interacting protein  
  

> open "D:/learning/Imperial College London/Project 1/Structures/Protein
> Structure/Activated Mec1-Ddc2 (F2244L_StateII).pdb"

Summary of feedback from opening D:/learning/Imperial College London/Project
1/Structures/Protein Structure/Activated Mec1-Ddc2 (F2244L_StateII).pdb  
---  
warnings | Ignored bad PDB record found on line 20  
  
  
Ignored bad PDB record found on line 21  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 22  
BOND : 0.007 0.090 47552  
  
Ignored bad PDB record found on line 23  
ANGLE : 1.075 16.637 64388  
  
Ignored bad PDB record found on line 24  
CHIRALITY : 0.061 0.344 7382  
  
17 messages similar to the above omitted  
  
Chain information for Activated Mec1-Ddc2 (F2244L_StateII).pdb #2  
---  
Chain | Description  
C D | No description available  
E F | No description available  
  

> ui tool show "Modeller Comparative"

No alignments chosen for modeling  
Drag select of 97 residues  

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #1/B

Alignment identifier is 1  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/E #2/F

Alignment identifier is 2  

> select clear

> select #

Expected an objects specifier or a keyword  

> ui mousemode right "translate selected models"

> select #2

46582 atoms, 47528 bonds, 28 pseudobonds, 5774 residues, 2 models selected  

> select clear

> ui mousemode right translate

> ui tool show Matchmaker

> select #1:2473-2499 & #2 2220-2265

Expected a keyword  

> select #1:2473-2499 & #2 :2220-2265

Nothing selected  

> select #1:2473-2499, #2 :2220-2265

Expected an objects specifier or a keyword  

> select #1:2473-2499 #2 :2220-2265

1156 atoms, 1176 bonds, 146 residues, 2 models selected  

> ui tool show Matchmaker

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  

> ui tool show Matchmaker

> matchmaker #!2 & sel to #1 & 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 ATR-ATRIP Complex.pdb, chain A (#1) with Activated Mec1-Ddc2
(F2244L_StateII).pdb, chain E (#2), sequence alignment score = 100.9  
RMSD between 27 pruned atom pairs is 0.864 angstroms; (across all 27 pairs:
0.864)  
  

> matchmaker #!2 & sel to #1 & 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 ATR-ATRIP Complex.pdb, chain A (#1) with Activated Mec1-Ddc2
(F2244L_StateII).pdb, chain E (#2), sequence alignment score = 100.9  
RMSD between 27 pruned atom pairs is 0.864 angstroms; (across all 27 pairs:
0.864)  
  

> select #1:2473-2499 #2 :2220-2265

1156 atoms, 1176 bonds, 146 residues, 2 models selected  

> select #1:2473-2515 #2 :2220-2265

1420 atoms, 1448 bonds, 178 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #2/E & sel to #1/A & sel 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 ATR-ATRIP Complex.pdb, chain A (#1) with Activated Mec1-Ddc2
(F2244L_StateII).pdb, chain E (#2), sequence alignment score = 158.1  
RMSD between 41 pruned atom pairs is 0.859 angstroms; (across all 43 pairs:
0.952)  
  

> help matchmaker

> undo

> undo

> select #1:2473-2515 #2 :2220-2265

1420 atoms, 1448 bonds, 178 residues, 2 models selected  

> select #1:2473-2515 #2 :2220-2265

1420 atoms, 1448 bonds, 178 residues, 2 models selected  

> select #1 /a #2 /e

33699 atoms, 34270 bonds, 28 pseudobonds, 4687 residues, 4 models selected  

> select #1:2473-2515 #2 :2220-2265

1420 atoms, 1448 bonds, 178 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #2/E 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 ATR-ATRIP Complex.pdb, chain A (#1) with Activated Mec1-Ddc2
(F2244L_StateII).pdb, chain E (#2), sequence alignment score = 1998.2  
RMSD between 307 pruned atom pairs is 1.231 angstroms; (across all 1898 pairs:
32.200)  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> matchmaker #2/E to #1/A pairing ss showAlignment true

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 ATR-ATRIP Complex.pdb, chain A (#1) with Activated Mec1-Ddc2
(F2244L_StateII).pdb, chain E (#2), sequence alignment score = 1998.2  
Alignment identifier is 3  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3  
Hiding conservation header for alignment 3  
Chains used in RMSD evaluation for alignment 3: ATR-ATRIP Complex.pdb #1/A,
Activated Mec1-Ddc2 (F2244L_StateII).pdb #2/E  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3  
RMSD between 307 pruned atom pairs is 1.231 angstroms; (across all 1898 pairs:
32.200)  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "D:\Chimera\ChimeraX 1.1\bin\lib\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 "D:\Chimera\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> save "D:/learning/Imperial College London/Project 1/Structures/Protein
> Structure/ATR-Mec1 Alignment.cxs"




OpenGL version: 3.3.0 NVIDIA 452.56
OpenGL renderer: GeForce GTX 1660 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 81Y6
OS: Microsoft Windows 10 Home (Build 18363)
Memory: 17,041,244,160
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz"
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
    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
    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
    gdcm: 2.8.8
    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+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    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
    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
    pywin32: 228
    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
    WMI: 1.5.1
File attachment: ATR-Mec1 Alignment.cxs

ATR-Mec1 Alignment.cxs​

[fzyzz180409@…]

Added by email2trac

[Eric Pettersen]

Hi Ziyi,

Thanks for reporting this problem. It has been fixed in the daily build, so you could use that to avoid this error. Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[fzyzz180409@…]

Hi Eric,

Thanks a lot.

Best wishes,
Ziyi

ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 于2021年1月19日周二 下午5:54写道：