Opened 4 years ago

Closed 4 years ago

#4950 closed defect (duplicate)

KeyError in map menu

Reported by: ria2@… Owned by: pett
Priority: normal Milestone:
Component: General Controls Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.19.0-17-amd64-x86_64-with-debian-10.5
ChimeraX Version: 0.91 (2019-09-21)
Description
Trying to save map after erase outside sphere

Log:
Startup Messages  
---  
warning | could not retrieve bundle list from toolshed  
notes | available bundle cache has not been initialized yet  
Updating list of available bundles failed: Internal Server Error  
  
UCSF ChimeraX version: 0.91 (2019-09-21)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
/storage/ria2/Zika/2021-02-19_Zika7/relion_processing/Refine3D/job039/run_class001.mrc

Opened run_class001.mrc, grid size 400,400,400, pixel 2.2, shown at level
0.0181, step 2, values float32  

> close session

> open /storage/ria2/CPV/CPV-oligo15/LocalRec/run_class001_job247.mrc

Opened run_class001_job247.mrc, grid size 420,420,420, pixel 1.1, shown at
level 0.0456, step 2, values float32  

> open /storage/ria2/CPV/CPV-oligo15/LocalRec/CPV-outershell_job247.mrc

Opened CPV-outershell_job247.mrc, grid size 420,420,420, pixel 1.1, shown at
level 0.0456, step 2, values float32  

> toolshed show "Map Coordinates"

> hide #!1 models

> ui mousemode rightMode clip

> hide #!2 models

> open /storage/ria2/CPV/CPV-oligo15/phenix-
refinement/RealSpaceRefine_25/VP2-DNA-hex_chID_real_space_refined_025.pdb

Chain information for VP2-DNA-hex_chID_real_space_refined_025.pdb #3  
---  
Chain | Description  
A D G J M P | No description available  
B E H K N Q | No description available  
C F I L O R | No description available  
  

> hide #!3 models

> show #!3 models

> hide #!1 models

> hide #!3 models

> show #!3 models

> show #!1 models

> ui mousemode rightMode clip

> ui mousemode rightMode clip

> ui mousemode rightMode clip

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> show cartoons

> hide atoms

> close #3

> open /storage/ria2/CPV/CPV-oligo15/phenix-refinement/VP2-mon-Gly29-rbuild-
DNA.pdb

Summary of feedback from opening /storage/ria2/CPV/CPV-oligo15/phenix-
refinement/VP2-mon-Gly29-rbuild-DNA.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2  
  
Ignored bad PDB record found on line 21  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 22  
BOND : 0.008 0.078 4477  
  
Ignored bad PDB record found on line 23  
ANGLE : 0.863 10.174 6127  
  
Ignored bad PDB record found on line 24  
CHIRALITY : 0.059 0.259 659  
  
16 messages similar to the above omitted  
  
Chain information for VP2-mon-Gly29-rbuild-DNA.pdb #3  
---  
Chain | Description  
1 | No description available  
N | No description available  
  

> close #3

> open /storage/ria2/CPV/CPV-oligo15/phenix-refinement/chains_VP2-icos-
Gly29-DNA.pdb

Summary of feedback from opening /storage/ria2/CPV/CPV-oligo15/phenix-
refinement/chains_VP2-icos-Gly29-DNA.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
271100 messages similar to the above omitted  
  
Chain information for chains_VP2-icos-Gly29-DNA.pdb #3  
---  
Chain | Description  
a d g j m p s v | No description available  
a c d f g i j l m o p r s u v x y z | No description available  
b c e f h i k l n o q r t u w x y z | No description available  
b e h k n q t w | No description available  
  

> hide atoms

> show cartoons

> show cartoons

> ui mousemode rightMode clip

> hide #!1 models

Expected a keyword  

Expected a keyword  

> select nucleic

12720 atoms, 14040 bonds, 1 model selected  

> ~ribbon ~sel

> ui mousemode rightMode "map eraser"

> display sel

> show #!1 models

> open /storage/ria2/CPV/CPV-oligo15/phenix-refinement/run_class001-job190.mrc

Opened run_class001-job190.mrc, grid size 420,420,420, pixel 1.1, shown at
level 0.0431, step 2, values float32  

> hide #!1 models

> volume erase #5 center 231,231,231 radius 101.87 outside true

> ui mousemode rightMode clip

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> save /storage/ria2/CPV/CPV-
oligo15/processing_relion31/run_class001_map190-DNAcore.mrc models #6

Traceback (most recent call last):  
File "/opt/chimerax/daily/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 871, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "/opt/chimerax/daily/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in file_save_cb  
self.save_dialog.display(self, session)  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 114, in display  
fmt.update(session, self)  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/map/savemap.py", line 67, in update  
self._map_menu.value = m  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 273, in value  
or (val is not None and self.value == val):  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 250, in value  
self._sleep_check()  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 81, in _sleep_check  
self._items_change()  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 291, in _items_change  
prev_value = self.value  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 259, in value  
return self.item_map[text]  
KeyError: 'run_class001-job190.mrc copy #6'  
  
KeyError: 'run_class001-job190.mrc copy #6'  
  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 259, in value  
return self.item_map[text]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/chimerax/daily/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 871, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "/opt/chimerax/daily/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in file_save_cb  
self.save_dialog.display(self, session)  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 114, in display  
fmt.update(session, self)  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/map/savemap.py", line 67, in update  
self._map_menu.value = m  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 273, in value  
or (val is not None and self.value == val):  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 259, in value  
return self.item_map[text]  
KeyError: 'run_class001-job190.mrc copy #6'  
  
KeyError: 'run_class001-job190.mrc copy #6'  
  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 259, in value  
return self.item_map[text]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/chimerax/daily/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 871, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "/opt/chimerax/daily/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in file_save_cb  
self.save_dialog.display(self, session)  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 114, in display  
fmt.update(session, self)  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/map/savemap.py", line 67, in update  
self._map_menu.value = m  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 273, in value  
or (val is not None and self.value == val):  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 259, in value  
return self.item_map[text]  
KeyError: 'run_class001-job190.mrc copy #6'  
  
KeyError: 'run_class001-job190.mrc copy #6'  
  
File "/opt/chimerax/daily/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 259, in value  
return self.item_map[text]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 440.31
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by pett, 4 years ago

Component: Unassigned → General Controls
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → KeyError in map menu

comment:2 by pett, 4 years ago

Resolution: → duplicate
Status: accepted → closed

Hi Ibrahim,

I'm fairly certain that this is fixed in the latest release of ChimeraX. So you should get that and besides, it also has a whole bunch of improvements and new features!

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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