ChimeraX bug report submission

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-06-29)
Description
Traceback upon "close" after opening map, atomic structure, making molmap, moving atomic structure with translate-selection mouse mode, and starting some tools, as shown in Command History below.  I tried a few times to reproduce this traceback with fewer actions (like just opening the map and structure) but was not successful.  I did reproduce it by doing all the steps again.

open 5020 format ccp4 fromDatabase emdb
open 1gc1 format mmCIF fromDatabase pdb
rainbow chain
select /G:465
molmap /h,l 8
toolshed show "Segment Map"
toolshed show "Fit in Map"
close


Log:
UCSF ChimeraX version: 0.91 (2019-06-29)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5020 format ccp4 fromDatabase emdb

Opened emd_5020.map, grid size 100,100,100, pixel 4.1, shown at level 1.83,
step 1, values float32  

> open 1gc1 format mmCIF fromDatabase pdb

1gc1 title:  
Hiv-1 GP120 core complexed with CD4 and A neutralizing human antibody [more
info...]  
  
Chain information for 1gc1 #2  
---  
Chain | Description  
C | CD4  
G | envelope protein GP120  
H | antibody 17B  
L | antibody 17B  
  
Non-standard residues in 1gc1 #2  
---  
FUC — α-L-fucose  
NAG — N-acetyl-D-glucosamine  
NDG — 2-(acetylamino)-2-deoxy-A-D-glucopyranose  
  
  

> close

> open 5020 format ccp4 fromDatabase emdb

Opened emd_5020.map, grid size 100,100,100, pixel 4.1, shown at level 1.83,
step 1, values float32  

> open 1gc1 format mmCIF fromDatabase pdb

1gc1 title:  
Hiv-1 GP120 core complexed with CD4 and A neutralizing human antibody [more
info...]  
  
Chain information for 1gc1 #2  
---  
Chain | Description  
C | CD4  
G | envelope protein GP120  
H | antibody 17B  
L | antibody 17B  
  
Non-standard residues in 1gc1 #2  
---  
FUC — α-L-fucose  
NAG — N-acetyl-D-glucosamine  
NDG — 2-(acetylamino)-2-deoxy-A-D-glucopyranose  
  
  

> select /C:152

9 atoms, 8 bonds, 1 model selected  

> ui mousemode rightMode "translate selected models"

> rainbow chains

> close

> open 5020 format ccp4 fromDatabase emdb

Opened emd_5020.map, grid size 100,100,100, pixel 4.1, shown at level 1.83,
step 1, values float32  

> open 1gc1 format mmCIF fromDatabase pdb

1gc1 title:  
Hiv-1 GP120 core complexed with CD4 and A neutralizing human antibody [more
info...]  
  
Chain information for 1gc1 #2  
---  
Chain | Description  
C | CD4  
G | envelope protein GP120  
H | antibody 17B  
L | antibody 17B  
  
Non-standard residues in 1gc1 #2  
---  
FUC — α-L-fucose  
NAG — N-acetyl-D-glucosamine  
NDG — 2-(acetylamino)-2-deoxy-A-D-glucopyranose  
  
  

> rainbow chains

> select clear

> select clear

> select clear

> select clear

> select /G:465

6 atoms, 5 bonds, 1 model selected  

> molmap /h,l 8

> toolshed show "Segment Map"

> toolshed show "Fit in Map"

> close

Traceback (most recent call last):  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 297, in _items_change  
self.value = (list(self.value_map.keys()) + self._special_items)[0]  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 262, in value  
or (val is not None and self.value == val):  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 255, in value  
return self.item_map[text]  
KeyError: '1gc1 #2'  
  
Error processing trigger "remove models": '1gc1 #2':  
KeyError: '1gc1 #2'  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 255, in value  
return self.item_map[text]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation