Opened 3 years ago

Closed 3 years ago

#8513 closed defect (duplicate)

self.structure is None

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

Description 

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-12-10)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-Registration' custom initialization failed  
warning | Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 432, in initialize  
api._api_caller.initialize(api, session, self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1624, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/__init__.py", line 41, in initialize  
nag(session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 28, in nag  
if not check_registration(logger=session.logger):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 49, in check_registration  
return _check_expiration(param, logger)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 140, in _check_expiration  
logger.warning("Registration file %r has expired" % reg_file)  
NameError: name 'reg_file' is not defined  
  
UCSF ChimeraX version: 0.91 (2019-12-10)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/yizhang_n/Documents/Facility/Projects/WuXD/volume-for-
> mask-J115-box384.mrc

Opened volume-for-mask-J115-box384.mrc, grid size 384,384,384, pixel 1.06,
shown at level 2.44e-05, step 2, values float32  

> volume #1 step 1

Updating list of available bundles failed: name 'reg_file' is not defined  

> toolshed show Toolbar

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> set bgColor white

> volume #1 level 0.1144

> volume #1 color #b2b2b2fe

> volume #1 color #b2b2b2fa

> volume #1 color #b2b2b2ee

> volume #1 color #b2b2b2de

> volume #1 color #b2b2b2d7

> volume #1 color #b2b2b2d3

> volume #1 color #b2b2b2c8

> volume #1 color #b2b2b2c2

> volume #1 color #b2b2b2ba

> volume #1 color #b2b2b2b7

> volume #1 color #b2b2b2b6

> volume #1 color #b2b2b2b5

> volume #1 color #b2b2b2b2

> volume #1 color #b2b2b2af

> volume #1 color #b2b2b2ab

> volume #1 color #b2b2b2a9

> volume #1 color #b2b2b2a8

> volume #1 color #b2b2b2a6

> volume #1 color #b2b2b2a1

> volume #1 color #b2b2b29c

> volume #1 color #b2b2b295

> volume #1 color #b2b2b291

> volume #1 color #b2b2b28f

> volume #1 color #b2b2b28b

> volume #1 color #b2b2b288

> volume #1 color #b2b2b287

> volume #1 color #b2b2b286

> volume #1 color #b2b2b285

> volume #1 color #b2b2b284

> volume #1 color #b2b2b283

> volume #1 color #b2b2b282

> volume #1 color #b2b2b281

> volume #1 color #b2b2b280

> open
> /Users/yizhang_n/Documents/Facility/Projects/WuXD/AF-Q9DBS2-F1-model_v4.pdb

AF-Q9DBS2-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for tumor protein P63-regulated gene 1-like
protein (Q9DBS2) [more info...]  
  
Chain information for AF-Q9DBS2-F1-model_v4.pdb #2  
---  
Chain | Description  
A | tumor protein P63-regulated gene 1-like protein  
  
AF-Q9DBS2-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for tumor protein P63-regulated gene 1-like
protein (Q9DBS2) [more info...]  
  
Chain information for AF-Q9DBS2-F1-model_v4.pdb  
---  
Chain | Description  
2.1/A | tumor protein P63-regulated gene 1-like protein  
  

> ui mousemode rightMode translate

> ui mousemode rightMode translate

> select #1

2 models selected  

> ~select #1

Nothing selected  

> select #2.1

2099 atoms, 2146 bonds, 5 models selected  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode rotate

> ui mousemode rightMode translate

> close #2.1

> toolshed show "Side View"

Traceback (most recent call last):  
File
"/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/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1385, in _box_moved_cb  
self._update_box()  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/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/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1385, in _box_moved_cb  
self._update_box()  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/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/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1385, in _box_moved_cb  
self._update_box()  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/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/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1385, in _box_moved_cb  
self._update_box()  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/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/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1385, in _box_moved_cb  
self._update_box()  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/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/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1385, in _box_moved_cb  
self._update_box()  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/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/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1385, in _box_moved_cb  
self._update_box()  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/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/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1385, in _box_moved_cb  
self._update_box()  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1398, in _update_box  
atoms = self.structure.atoms  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.31
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → self.structure is None

comment:2 by Eric Pettersen, 3 years ago

Resolution: → duplicate
Status: assigned → closed

From 0.91!

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