Opened 7 years ago

Closed 7 years ago

#1443 closed defect (fixed)

Clipper: cannot import name 'ArrayGridData'

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-11-06)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.8 (2018-11-06)  
How to cite UCSF ChimeraX  

> toolshed show Shell

QLineEdit::setSelection: Invalid start position (-1)  

Unknown command: install ChimeraX-
ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl  

QLineEdit::setSelection: Invalid start position (-1)  

QLineEdit::setSelection: Invalid start position (-1)  

> toolshed show ISOLDE

before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #1  
---  
Chain | Description  
A | predicted microcompartment protein  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 126, in invoke  
return self._func(self._name, data)  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1020, in _update_model_list  
self._change_selected_model(model=current_model, force=True)  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 2311, in _change_selected_model  
get_symmetry_handler(m, create=True)  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 145, in get_symmetry_handler  
return Symmetry_Manager(structure)  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 396, in __init__  
radius = spotlight_radius, live = spotlight_mode, debug=debug)  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 798, in __init__  
self.live_scrolling = live  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 228, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 965, in live_scrolling  
self._update_box()  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 1021, in _update_box  
from .crystal import find_box_params  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/crystal.py", line 25, in <module>  
from chimerax.map.data import ArrayGridData  
ImportError: cannot import name 'ArrayGridData'  
  
Error processing trigger "add models": cannot import name 'ArrayGridData':  
ImportError: cannot import name 'ArrayGridData'  
  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/crystal.py", line 25, in  
from chimerax.map.data import ArrayGridData  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 3219, in load_demo_data  
sym_handler = symmetry.get_symmetry_handler(before_struct, create=True)  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 145, in get_symmetry_handler  
return Symmetry_Manager(structure)  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 396, in __init__  
radius = spotlight_radius, live = spotlight_mode, debug=debug)  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 798, in __init__  
self.live_scrolling = live  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 228, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 965, in live_scrolling  
self._update_box()  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 1021, in _update_box  
from .crystal import find_box_params  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/crystal.py", line 25, in <module>  
from chimerax.map.data import ArrayGridData  
ImportError: cannot import name 'ArrayGridData'  
  
ImportError: cannot import name 'ArrayGridData'  
  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/crystal.py", line 25, in  
from chimerax.map.data import ArrayGridData  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 126, in invoke  
return self._func(self._name, data)  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 1171, in _model_changed_cb  
self._update_sym_coords()  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 1176, in _update_sym_coords  
res = atom_and_bond_sym_transforms_from_sym_atoms(*focal_set[0:3])  
TypeError: 'NoneType' object is not subscriptable  
  
Error processing trigger "changes": 'NoneType' object is not subscriptable:  
TypeError: 'NoneType' object is not subscriptable  
  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 1176, in _update_sym_coords  
res = atom_and_bond_sym_transforms_from_sym_atoms(*focal_set[0:3])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 126, in invoke  
return self._func(self._name, data)  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 1171, in _model_changed_cb  
self._update_sym_coords()  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 1176, in _update_sym_coords  
res = atom_and_bond_sym_transforms_from_sym_atoms(*focal_set[0:3])  
TypeError: 'NoneType' object is not subscriptable  
  
Error processing trigger "changes": 'NoneType' object is not subscriptable:  
TypeError: 'NoneType' object is not subscriptable  
  
File "/Users/rgk680/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/symmetry.py", line 1176, in _update_sym_coords  
res = atom_and_bond_sym_transforms_from_sym_atoms(*focal_set[0:3])  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.2.17
OpenGL renderer: Intel(R) Iris(TM) Graphics 650
OpenGL vendor: Intel Inc.

Change History (3)

comment:1 by Tristan Croll, 7 years ago

Platform: → all
Project: → ChimeraX

This is due to a change in the ChimeraX API that happened last week. If you update to the most recent daily build this error should go away.

comment:2 by Eric Pettersen, 7 years ago

Cc: Tom Goddard added
Component: Unassigned → Third Party
Owner: set to Tristan Croll
Status: new → assigned
Summary: ChimeraX bug report submission → Clipper: cannot import name 'ArrayGridData'

comment:3 by Eric Pettersen, 7 years ago

Resolution: → fixed
Status: assigned → closed
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