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#2151 closed defect (fixed)

'FitSegmentsDialog' object has no attribute 'Close'

Reported by:	Elaine Meng	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Volume Data	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-06-29)
Description
I'm not sure what happened.  I was using Fit to Segments and then I think its dialog disappeared.  I clicked the "Fit" button on the Segment Map tool to try to bring back the Fit to Segments dialog and then got this error message.

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.  
  

> open 5020 format ccp4 fromDatabase emdb

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 280, in _items_change  
prev_value = self.value  
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 "add 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.  
  
Opened emd_5020.map, grid size 100,100,100, pixel 4.1, shown at level 1.83,
step 1, values float32  

> open 1gc1

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  
  
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 280, in _items_change  
prev_value = self.value  
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 "add 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.  
  
  

> select clear

> select /C:108

8 atoms, 7 bonds, 1 model selected  

> ui mousemode rightMode "translate selected models"

> rainbow chains

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 280, in _items_change  
prev_value = self.value  
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.  
  
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 280, in _items_change  
prev_value = self.value  
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.  
  
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/map/fit/fitgui.py", line 371, in _fit  
fatoms = self._fit_atoms()  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 247, in _fit_atoms  
m = self._object_menu.value  
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'  
  
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.  
  

> toolshed show "Fit in Map"

Fit molecule 1gc1 (#2) to map 5020 (#1) using 7877 atoms  
average map value = 3.637, steps = 128  
shifted from previous position = 25.4  
rotated from previous position = 56.3 degrees  
atoms outside contour = 1061, contour level = 1.8319  
  
Position of 1gc1 (#2) relative to 5020 (#1) coordinates:  
Matrix rotation and translation  
0.87229791 0.05148246 0.48625705 178.81088248  
0.33087117 0.67005491 -0.66449280 281.44277948  
-0.36002865 0.74052412 0.56745343 179.16112985  
Axis 0.84444743 0.50863713 0.16791903  
Axis point 0.00000000 -51.15114820 200.75883753  
Rotation angle (degrees) 56.29595750  
Shift along axis 324.23320239  
  

> select clear

> close #2

> open 1gc1

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 #2

> open 1gc1

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 #1

> open emdb:5020

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

> close #2

> open 1gc1

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 clear

> select /C:103

8 atoms, 7 bonds, 1 model selected  

> rainbow chains

Fit molecule 1gc1 (#2) to map 5020 (#1) using 7877 atoms  
average map value = 2.861, steps = 120  
shifted from previous position = 22.6  
rotated from previous position = 43.7 degrees  
atoms outside contour = 3087, contour level = 1.8319  
  
Position of 1gc1 (#2) relative to 5020 (#1) coordinates:  
Matrix rotation and translation  
0.77917448 -0.48013754 -0.40293308 223.09833250  
0.30822887 0.85323977 -0.42068618 214.93977272  
0.54578576 0.20359233 0.81281490 142.54500251  
Axis 0.45155693 -0.68623309 0.57024599  
Axis point -40.80482075 0.00000000 537.35344697  
Rotation angle (degrees) 43.72923127  
Shift along axis 34.52853018  
  
Fit molecule 1gc1 (#2) to map 5020 (#1) using 7877 atoms  
average map value = 2.906, steps = 152  
shifted from previous position = 21.7  
rotated from previous position = 24.1 degrees  
atoms outside contour = 3518, contour level = 1.8319  
  
Position of 1gc1 (#2) relative to 5020 (#1) coordinates:  
Matrix rotation and translation  
0.74342134 -0.66779050 -0.03715603 203.64374968  
0.58919710 0.68019171 -0.43610322 203.24546166  
0.31649881 0.30231621 0.89912925 154.79403229  
Axis 0.49224103 -0.23575141 0.83792604  
Axis point -268.99668332 274.12604395 0.00000000  
Rotation angle (degrees) 48.59547156  
Shift along axis 182.03235332  
  
Fit molecule 1gc1 (#2) to map 5020 (#1) using 7877 atoms  
average map value = 2.906, steps = 104  
shifted from previous position = 43  
rotated from previous position = 0.0807 degrees  
atoms outside contour = 3519, contour level = 1.8319  
  
Position of 1gc1 (#2) relative to 5020 (#1) coordinates:  
Matrix rotation and translation  
0.74313867 -0.66805166 -0.03810384 203.78681225  
0.58945250 0.68052954 -0.43523015 203.21230359  
0.31668701 0.30097595 0.89951254 154.75669878  
Axis 0.49089214 -0.23656968 0.83848655  
Axis point -268.72547494 274.83604690 0.00000000  
Rotation angle (degrees) 48.57872285  
Shift along axis 181.72488611  
  
Fit molecule 1gc1 (#2) to map 5020 (#1) using 7877 atoms  
average map value = 2.861, steps = 140  
shifted from previous position = 47.5  
rotated from previous position = 24.1 degrees  
atoms outside contour = 3086, contour level = 1.8319  
  
Position of 1gc1 (#2) relative to 5020 (#1) coordinates:  
Matrix rotation and translation  
0.77910318 -0.48007933 -0.40314025 223.10761035  
0.30829232 0.85335188 -0.42041219 214.91292395  
0.54585170 0.20325943 0.81285394 142.53769244  
Axis 0.45114519 -0.68647209 0.57028422  
Axis point -40.94692269 0.00000000 537.35420540  
Rotation angle (degrees) 43.72592171  
Shift along axis 34.40919893  
  

> ui mousemode rightMode "rotate selected models"

Fit molecule 1gc1 (#2) to map 5020 (#1) using 7877 atoms  
average map value = 2.824, steps = 240  
shifted from previous position = 22.5  
rotated from previous position = 50.2 degrees  
atoms outside contour = 3333, contour level = 1.8319  
  
Position of 1gc1 (#2) relative to 5020 (#1) coordinates:  
Matrix rotation and translation  
-0.41782425 0.72390600 -0.54898360 235.51614530  
0.37045496 -0.41599327 -0.83048945 251.96079458  
-0.82956978 -0.55037233 -0.09436249 262.79154095  
Axis 0.52737713 0.52826023 -0.66544308  
Axis point 243.06640036 210.77741815 0.00000000  
Rotation angle (degrees) 164.59883527  
Shift along axis 82.43388464  
  

> ui mousemode rightMode "translate selected models"

Fit molecule 1gc1 (#2) to map 5020 (#1) using 7877 atoms  
average map value = 2.089, steps = 96  
shifted from previous position = 27.8  
rotated from previous position = 43.8 degrees  
atoms outside contour = 3587, contour level = 1.8319  
  
Position of 1gc1 (#2) relative to 5020 (#1) coordinates:  
Matrix rotation and translation  
-0.54184248 0.75288861 -0.37358462 257.57245970  
0.73484733 0.20863726 -0.64534478 190.30008114  
-0.40792906 -0.62420288 -0.66630672 264.07387018  
Axis 0.47852343 0.77734829 -0.40834418  
Axis point 72.56365786 0.00000000 180.74488875  
Rotation angle (degrees) 178.73418906  
Shift along axis 163.35087147  
  
Segmenting 5020, density threshold 1.831886  
Showing 5020.seg - 0 regions, 0 surfaces  
Showing 4 region surfaces  
26 watershed regions, grouped to 4 regions  

> hide #!3 models

> show #!3 models

Showing 4 region surfaces  

> hide #!3 models

> show #!3 models

> molmap /h,l 8

> help https://cryoem.slac.stanford.edu/ncmi/resources/software/segger

No help found for
'https://cryoem.slac.stanford.edu/ncmi/resources/software/segger'  
Simulating map res 12.000, grid 4.000  

> molmap #2 12.000000 sigmaFactor 0.187 gridSpacing 4.000000 replace false

Please select a region to fit to  

> windowsize 500 500

Please select a region to fit to  
Top score: 0.90246, z-score: 24.42482 (avg: 0.8101, stdev: 0.0038)  
Visi scores...  
\- in map: 5020  
\- mol: 1gc1  
\- map: 1gc1 map 8  
\- Overlap: 1569.413731, Cross-correlation: 0.655820  
\- making tree, 7877 atoms  
\- checking clashes, 7877 atoms  
\- clashes: 0/7877 = 1.000 clash-free  
Visi scores...  
\- in map: 5020  
\- mol: 1gc1  
\- map: 1gc1 map 8  
\- Overlap: 1569.413731, Cross-correlation: 0.655820  
\- making tree, 7877 atoms  
\- checking clashes, 7877 atoms  
\- clashes: 0/7877 = 1.000 clash-free  

> open 2gbp

2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  
  
Chain information for 2gbp #6  
---  
Chain | Description  
A | D-galactose/D-glucose binding protein  
  
Non-standard residues in 2gbp #6  
---  
BGC — β-D-glucose  
CA — calcium ion  
  
  
Top score: 0.81028, z-score: 3.60037 (avg: 0.7652, stdev: 0.0125)  
Top score: 0.90239, z-score: 25.74219 (avg: 0.8103, stdev: 0.0036)  
Visi scores...  
\- in map: 5020  
\- mol: 1gc1  
\- map: 1gc1 map 8  
\- mol: 2gbp  
\- Overlap: 1569.413731, Cross-correlation: 0.655820  
\- making tree, 10452 atoms  
\- checking clashes, 10452 atoms  
\- clashes: 0/10452 = 1.000 clash-free  

> view

> select clear

> select #6/A:195

14 atoms, 15 bonds, 1 model selected  
Simulating map res 12.000, grid 4.000  

> molmap #6 12.000000 sigmaFactor 0.187 gridSpacing 4.000000 replace false

Please select a region to fit to  
Please select a region to fit to  
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/segger/segment_dialog.py", line 1550, in FitDialog  
fit_dialog.close_fit_segments_dialog( self.session );  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/fit_dialog.py", line 4957, in
close_fit_segments_dialog  
d.Close()  
AttributeError: 'FitSegmentsDialog' object has no attribute 'Close'  
  
AttributeError: 'FitSegmentsDialog' object has no attribute 'Close'  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/fit_dialog.py", line 4957, in
close_fit_segments_dialog  
d.Close()  
  
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

Change History (2)

comment:1 by Eric Pettersen, 6 years ago

Component:	Unassigned → Volume Data
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → 'FitSegmentsDialog' object has no attribute 'Close'

comment:2 by Tom Goddard, 6 years ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed.

Fit button was trying to close the previous fit dialog and create a new one. Not sure why. Changed so that it keeps the Fit to Segments dialog even if it is closed with the panel close button.

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