traceback when closing seq viewer with multiple chains associated

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-05)
Description
Closed sequence panel using the close button on its title bar.sa

Log:
UCSF ChimeraX version: 0.91 (2019-09-05)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6h6b format mmCIF fromDatabase pdb

6h6b title:  
Structure of alpha-synuclein fibrils [more info...]  
  
Chain information for 6h6b #1  
---  
Chain | Description  
A B C D E F G H I J | Alpha-synuclein  
  
  

> hide atoms

> show cartoons

> set bgColor white

> lighting simple

> graphics silhouettes true

> save /Users/goddard/Desktop/image1.png supersample 3

> close

> open 6h6b format mmCIF fromDatabase pdb

6h6b title:  
Structure of alpha-synuclein fibrils [more info...]  
  
Chain information for 6h6b #1  
---  
Chain | Description  
A B C D E F G H I J | Alpha-synuclein  
  
  

> save /Users/goddard/Desktop/image1.png supersample 3

> hide atoms

> show ribbons

> save /Users/goddard/Desktop/image1.png supersample 3

> show /A only

> show /A ribbons only

> hide /A

> show ribbons

> show /A ribbons only

> show ribbons

> save /Users/goddard/Desktop/image1.png supersample 3

> select clear

> color /D,E,F,I,J tan

> color /A,B,C,G,H pink

> save /Users/goddard/Desktop/image1.png supersample 3

> select /A

806 atoms, 808 bonds, 1 model selected  

> show /A ribbons only

> select clear

> save /Users/goddard/Desktop/image1.png supersample 3

> show /A atoms

> style stick

Changed 8060 atom styles  

> color byhetero

> save /Users/goddard/Desktop/image1.png supersample 3

> log metadata #1

Metadata for 6h6b #1  
---  
Title | Structure of alpha-synuclein fibrils  
Citation | Guerrero-Ferreira, R., Taylor, N.M., Mona, D., Ringler, P., Lauer,
M.E., Riek, R., Britschgi, M., Stahlberg, H. (2018). Cryo-EM structure of
alpha-synuclein fibrils. Elife, 7. PMID: 29969391. DOI: 10.7554/eLife.36402  
Gene source | Homo sapiens  
Experimental method | Electron microscopy  
Resolution | 3.4Å  
  
> sequence chain #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H#1/I#1/J

Alignment identifier is 1  

> select clear

> color sel orange

> color /D,E,F,I,J tan

> color /A,B,C,G,H pink

> color byhetero

> select clear

Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1666, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 549, in close_request  
tool_instance.delete()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 495, in delete  
self.alignment.detach_viewer(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 325, in detach_viewer  
self.session.alignments.destroy_alignment(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 110, in destroy_alignment  
alignment._destroy()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 498, in _destroy  
aseq.match_maps[sseq].mod_handler.remove()  
KeyError: <chimerax.atomic.molobject.Chain object at 0x129c06550>  
  
KeyError:  
  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 498, in _destroy  
aseq.match_maps[sseq].mod_handler.remove()  
  
See log for complete Python traceback.  
  

> save /Users/goddard/Desktop/seqbug.cxs




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
File attachment: seqbug.cxs

seqbug.cxs​

[goddard@…]

Added by email2trac

[Eric Pettersen]

Happens when closing any sequence viewer where there are multiple chains associated with the sequence.

[Eric Pettersen]

A previous fix to stop a memory leak resulting in some data structures begin cleared before they were finished being used. Code now uses better timing for clearing them.